Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Chromatin Assembly and Disassembly: The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Immunoprecipitation: The aggregation of soluble ANTIGENS with ANTIBODIES, alone or with antibody binding factors such as ANTI-ANTIBODIES or STAPHYLOCOCCAL PROTEIN A, into complexes large enough to fall out of solution.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Microchip Analytical Procedures: The preparation and analysis of samples on miniaturized devices.Molecular Biology: A discipline concerned with studying biological phenomena in terms of the chemical and physical interactions of molecules.Micropore Filters: A membrane or barrier with micrometer sized pores used for separation purification processes.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.Micrococcal Nuclease: An enzyme that catalyzes the endonucleolytic cleavage to 3'-phosphomononucleotide and 3'-phospholigonucleotide end-products. It can cause hydrolysis of double- or single-stranded DNA or RNA. (From Enzyme Nomenclature, 1992) EC 3.1.31.1.DNA-Formamidopyrimidine Glycosylase: A DNA repair enzyme that is an N-glycosyl hydrolase with specificity for DNA-containing ring-opened N(7)-methylguanine residues.Comet Assay: A genotoxicological technique for measuring DNA damage in an individual cell using single-cell gel electrophoresis. Cell DNA fragments assume a "comet with tail" formation on electrophoresis and are detected with an image analysis system. Alkaline assay conditions facilitate sensitive detection of single-strand damage.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Nucleosomes: The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4.Telomere Shortening: The loss of some TELOMERE sequence during DNA REPLICATION of the first several base pairs of a linear DNA molecule; or from DNA DAMAGE. Cells have various mechanisms to restore length (TELOMERE HOMEOSTASIS.) Telomere shortening is involved in the progression of CELL AGING.Telomere: A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. Its length is believed to be a few hundred base pairs.PubMed: A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.Periodicals as Topic: A publication issued at stated, more or less regular, intervals.BooksPublishing: "The business or profession of the commercial production and issuance of literature" (Webster's 3d). It includes the publisher, publication processes, editing and editors. Production may be by conventional printing methods or by electronic publishing.MEDLINE: The premier bibliographic database of the NATIONAL LIBRARY OF MEDICINE. MEDLINE® (MEDLARS Online) is the primary subset of PUBMED and can be searched on NLM's Web site in PubMed or the NLM Gateway. MEDLINE references are indexed with MEDICAL SUBJECT HEADINGS (MeSH).Islets of Langerhans: Irregular microscopic structures consisting of cords of endocrine cells that are scattered throughout the PANCREAS among the exocrine acini. Each islet is surrounded by connective tissue fibers and penetrated by a network of capillaries. There are four major cell types. The most abundant beta cells (50-80%) secrete INSULIN. Alpha cells (5-20%) secrete GLUCAGON. PP cells (10-35%) secrete PANCREATIC POLYPEPTIDE. Delta cells (~5%) secrete SOMATOSTATIN.Serial Publications: Publications in any medium issued in successive parts bearing numerical or chronological designations and intended to be continued indefinitely. (ALA Glossary of Library and Information Science, 1983, p203)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.

Specific targeting and constitutive association of histone deacetylase complexes during transcriptional repression. (1/5197)

Specific recruitment of corepressor complexes containing histone deacetylases (HDAC) by transcription factors is believed to play an essential role in transcriptional repression. Recent studies indicate that repression by unliganded nuclear hormone receptors and by the Mad family of repressors requires distinct HDAC-containing corepressor complexes. In this work, we show that unliganded TR specifically recruits only the closely related N-CoR and SMRT-HDAC3 complexes, whereas the Mad1 recruits only the Sin3-HDAC1/2 complex. Significantly, both the Sin3 and Mi-2/NURD complexes also exhibit constitutive association with chromatin and contribute to chromatin deacetylation in a nontargeted fashion. These results suggest that HDAC complexes can contribute to gene repression by two distinct mechanisms as follows: (1) specific targeting by repressors and (2) constitutive association with chromatin.  (+info)

Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes. (2/5197)

A cell's ability to generate different responses to different levels of stimulus is an important component of an adaptive environmental response. Transcriptional responses are frequently controlled by transcription factors regulated by phosphorylation. We demonstrate that differential phosphorylation of the budding yeast transcription factor Pho4 contributes to differential gene expression. When yeast cells are grown in high-phosphate growth medium, Pho4 is phosphorylated on four critical residues by the cyclin-CDK complex Pho80-Pho85 and is inactivated. When yeast cells are starved for phosphate, Pho4 is dephosphorylated and fully active. In intermediate-phosphate conditions, a form of Pho4 preferentially phosphorylated on one of the four sites accumulates and activates transcription of a subset of phosphate-responsive genes. This Pho4 phosphoform binds differentially to phosphate-responsive promoters and helps to trigger differential gene expression. Our results demonstrate that three transcriptional outputs can be generated by a pathway whose regulation is controlled by one kinase, Pho80-Pho85, and one transcription factor, Pho4. Differential phosphorylation of Pho4 by Pho80-Pho85 produces phosphorylated forms of Pho4 that differ in their ability to activate transcription, contributing to multiple outputs.  (+info)

Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. (3/5197)

Heritable, but reversible, changes in transposable element activity were first observed in maize by Barbara McClintock in the 1950s. More recently, transposon silencing has been associated with DNA methylation, histone H3 lysine-9 methylation (H3mK9), and RNA interference (RNAi). Using a genetic approach, we have investigated the role of these modifications in the epigenetic regulation and inheritance of six Arabidopsis transposons. Silencing of most of the transposons is relieved in DNA methyltransferase (met1), chromatin remodeling ATPase (ddm1), and histone modification (sil1) mutants. In contrast, only a small subset of the transposons require the H3mK9 methyltransferase KRYPTONITE, the RNAi gene ARGONAUTE1, and the CXG methyltransferase CHROMOMETHYLASE3. In crosses to wild-type plants, epigenetic inheritance of active transposons varied from mutant to mutant, indicating these genes differ in their ability to silence transposons. According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposon silencing. Furthermore, different transposons tend to be susceptible to different forms of epigenetic regulation.  (+info)

Role of Saccharomyces single-stranded DNA-binding protein RPA in the strand invasion step of double-strand break repair. (4/5197)

The single-stranded DNA (ssDNA)-binding protein replication protein A (RPA) is essential for both DNA replication and recombination. Chromatin immunoprecipitation techniques were used to visualize the kinetics and extent of RPA binding following induction of a double-strand break (DSB) and during its repair by homologous recombination in yeast. RPA assembles at the HO endonuclease-cut MAT locus simultaneously with the appearance of the DSB, and binding spreads away from the DSB as 5' to 3' exonuclease activity creates more ssDNA. RPA binding precedes binding of the Rad51 recombination protein. The extent of RPA binding is greater when Rad51 is absent, supporting the idea that Rad51 displaces RPA from ssDNA. RPA plays an important role during RAD51-mediated strand invasion of the MAT ssDNA into the donor sequence HML. The replication-proficient but recombination-defective rfa1-t11 (K45E) mutation in the large subunit of RPA is normal in facilitating Rad51 filament formation on ssDNA, but is unable to achieve synapsis between MAT and HML. Thus, RPA appears to play a role in strand invasion as well as in facilitating Rad51 binding to ssDNA, possibly by stabilizing the displaced ssDNA.  (+info)

ATF6 modulates SREBP2-mediated lipogenesis. (5/5197)

Activating transcription factor 6 (ATF6) and sterol regulatory element-binding proteins (SREBPs) are activated by proteolytic cleavage. The ensuing nuclear translocation of their N-termini (i.e., ATF6(N) and SREBP(N)) activates the respective target genes involved in unfolded protein response and lipogenesis. Here, we report that glucose deprivation activated ATF6 but suppressed the SREBP2-regulated transcription. Overexpression of ATF6(N) had similar inhibitory effects on SREBP2-targeted genes. The blockade of ATF6 cleavage by BiP/grp78 reversed this inhibitory effect. GST pull-down and immunoprecipitation assays revealed that ATF6(N) bound to SREBP2(N). Deletion analysis of the various functional domains of ATF6 indicated that the interaction was through its leucine-zipper domain. Chromatin immunoprecipitation assays revealed that ATF6(N) formed a complex with the SRE-bound SREBP2(N). The attenuated transcriptional activity of SREBP2 was due, in part, to the recruitment of HDAC1 to the ATF6-SREBP2 complex. As a functional consequence, the lipogenic effect of SREBP2(N) in liver cells was suppressed by ATF6(N). Our results provide a novel mechanism by which ATF6 antagonizes SREBP2 to regulate the homeostasis of lipid and glucose.  (+info)

Formation, maintenance and consequences of the imprint at the mating-type locus in fission yeast. (6/5197)

Mating-type switching in the fission yeast Schizosaccharomyces pombe is initiated by a strand-specific imprint located at the mating-type (mat1) locus. We show that the imprint corresponds to a single-strand DNA break (SSB), which is site- but not sequence-specific. We identified three novel cis-acting elements, involved in the formation and stability of the SSB. One of these elements is essential for a replication fork pause next to mat1 and interacts in vivo with the Swi1 protein. Another element is essential for maintaining the SSB during cell cycle progression. These results suggest that the DNA break appears during the S-phase and is actively protected against repair. Consequently, during the following round of replication, a polar double-strand break is formed. We show that when the replication fork encounters the SSB, the leading-strand DNA polymerase is able to synthesize DNA to the edge of the SSB, creating a blunt-ended recombination intermediate.  (+info)

MDR1 promoter hypermethylation in MCF-7 human breast cancer cells: changes in chromatin structure induced by treatment with 5-Aza-cytidine. (7/5197)

Resistance to the cytotoxic actions of antineoplastic drugs, whether intrinsic or acquired, remains a barrier to the establishment of curative chemotherapy regimens for advanced breast cancer. Over-expression of P-glycoprotein (P-gp), encoded by the MDR1 gene and known to mediate resistance to many antineoplastic drugs, may contribute to poor breast cancer treatment outcome. Nonetheless, the precise molecular mechanisms responsible for high or low level P-gp expression in breast cancer cells have not been established. We assessed the role of DNA hypermethylation near the MDR1 transcriptional regulatory region in MDR1 expression in MCF-7 breast cancer cells, which fail to express MDR1 mRNA, and MCF-7/ADR cells, known to express high MDR1 mRNA levels. When compared to MCF-7/ADR cells, MCF-7 cells manifested markedly diminished MDR1 transcription rates by nuclear run-off assay, but equivalent MDR1 promoter trans-activation activity in transient transfection experiments, indicating that cis factors were most likely responsible for the differences in MDR1 transcription between MCF-7/ADR cells and MCF-7 cells. Bisulfite genomic sequencing analyses revealed substantially less extensive MDR1 promoter methylation in MCF-7/ADR cells than in MCF-7 cells, suggesting that CpG dinucleotide methylation might contribute to the observed MDR1 transcription differences. Chromatin immunoprecipitation analyses indicated an inactive MDR1 chromatin conformation in MCF-7 cells, with a paucity of acetylated histones and the presence of 5-mC-binding proteins MeCP2 and MBD2, and an active MDR1 chromatin conformation in MCF-7/ADR cells, with an abundance of acetylated histones and the presence of the transcriptional trans-activator YB-1. Stable MCF-7 sublines which had been treated with the DNA methyltransferase inhibitor 5-azacytidine, exhibited a reduction in MDR1 promoter methylation and a complex MDR1 chromatin configuration, characterized by the simultaneous presence of transcriptional activators and repressors. In this state, MDR1 expression was markedly sensitive to treatment with the histone deacetylase inhibitor trichostatin A.  (+info)

Spatial organization and dynamics of the association of Rec102 and Rec104 with meiotic chromosomes. (8/5197)

Meiotic double-strand breaks (DSBs) are formed by Spo11 in conjunction with at least nine other proteins whose roles are not well understood. We find that two of these proteins, Rec102 and Rec104, interact physically, are mutually dependent for proper subcellular localization, and share a requirement for Spo11 and Ski8 for their recruitment to meiotic chromosomes, suggesting that they work together as a functional unit. Rec102 associated extensively with chromatin loops during leptotene and zygotene and showed preferential binding in the vicinity at least of most DSB sites, consistent with a direct role in DSB formation. However, Rec102 was associated with both DSB-hot and DSB-cold regions, ruling out a simple model in which sites of DSB formation are dictated by where Rec102/104 complexes load. Both proteins persisted on chromatin until pachytene before abruptly disappearing, indicating that they remain on chromosomes well after DSB formation. These studies reveal unexpected behaviors for Rec102 and Rec104, and point to distinct roles and subcomplexes among the DSB proteins.  (+info)

*Chromatin immunoprecipitation

... at the US National Library of Medicine Medical Subject Headings (MeSH) EpigenomeNOE.com Chromatin ... Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the ... on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications Chromatin Immunoprecipitation (ChIP) of Protein ... These reports are considered the pioneering studies in the field of chromatin immunoprecipitation. XChIP was further modified ...

*Chromosome conformation capture

In 1984, John T. Lis innovated the Chromatin immunoprecipitation technique. In 1993, the Nuclear Ligation Assay was published, ... Chromatin Immunoprecipitation Assays. Methods in Molecular Biology. Humana Press, Totowa, NJ. pp. 171-188. doi:10.1007/978-1- ... Walther Flemming coined the term chromatin . In 1883, August Weismann connected chromatin with heredity. In 1884, Albrecht ... In 1973/1974, chromatin fiber was discovered. In 1975, Chambon coined the term nucleosomes. In 1982, Chromosome territories ...

*Biotinylation

"Use of protein biotinylation in vivo for chromatin immunoprecipitation". Analytical Biochemistry. 325 (1): 68-76. doi:10.1016/j ... approach to study chromatin in proximity to a protein of interest". Genome Research. 23 (2): 331-40. doi:10.1101/gr.134874.111 ...

*Tiling array

Chromatin immunoprecipitation allows binding sites of proteins to be identified. A genome-wide variation of this is known as ... Proteins that bind to chromatin are cross-linked in vivo, usually via fixation with formaldehyde. The chromatin is then ... Methyl-DNA immunoprecipitation followed by tiling array allows DNA methylation mapping and measurement across the genome. DNA ... segments of open chromatin that are more readily cleaved by DNaseI. DNaseI cleaving produces larger fragments of around 1.2kb ...

*Cellular differentiation

This can be determined using a chromatin immunoprecipitation (ChIP) assay. DNA-nucleosome interactions are characterized by two ... 2013). "Genome-wide chromatin state transitions associated with developmental and environmental cues". Cell. 152 (3): 642-654. ... It is thought that they achieve this through alterations in chromatin structure, such as histone modification and DNA ... To a large extent, differences in transcription factor binding are determined by the chromatin accessibility of their binding ...

*SUZ12

Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ (October 2001). "Use of chromatin immunoprecipitation to clone novel E2F ... SUZ12, as part of Polycomb Repressive Complex 2 (PRC2), may be involved with chromatin silencing in conjunction with HOTAIR ... "Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs". Cell. 129 (7): 1311-23. doi ...

*BECN1

Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ (Oct 2001). "Use of chromatin immunoprecipitation to clone novel E2F ...

*ChIP-exo

Chromatin immunoprecipitation (ChIP) techniques have been in use since 1984 to detect protein-DNA interactions. There have been ... Chromatin immunoprecipitation Chip-sequencing ChIP-on-chip Protein-DNA interaction Gilmour, DS; JT Lis (1983). "Detecting ... ChIP-exo is a chromatin immunoprecipitation based method for mapping the locations at which a protein of interest ( ... Cells are then collected, broken open, and the chromatin sheared and solubilized by sonication. An antibody is then used to ...

*Pseudo-response regulator

Chromatin immunoprecipitation demonstrates that LUX binds to the PRR9 promoter to repress it. Additionally, ELF3 has been shown ...

*Mammalian promoter database

"Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis". ...

*E2F3

"Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis". ...

*CBX5 (gene)

"Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis". ... interaction between chromatin assembly factor 1 and HP1 proteins". Molecular Cell. 4 (4): 529-40. doi:10.1016/S1097-2765(00) ... as well as interacting with a variety of chromatin-associated, non-histone proteins. HP1α is 191 amino acids in length ... while the C-terminal CSD homodimerizes and interacts with a variety of other chromatin-associated, non-histone related proteins ...

*ChIP-on-chip

... (also known as ChIP-chip) is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray ... Chip-Sequencing is a recently developed technology that still uses chromatin immunoprecipitation to crosslink the proteins of ... Aparicio, O; Geisberg, JV; Struhl, K (2004). "Chromatin immunoprecipitation for determining the association of proteins with ... and application of genome-wide chromatin immunoprecipitation experiments, Genomics 83 (2004) 349-360. Royce TE, Rozowsky JS, ...

*GAS2L1

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ...

*HIST2H4A

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ... 2003). "Acetylation-dependent chromatin reorganization by BRDT, a testis-specific bromodomain-containing protein". Mol. Cell. ... 2001). "Enhancement of the p300 HAT activity by HIV-1 Tat on chromatin DNA". Virology. 289 (2): 312-26. doi:10.1006/viro. ... 2004). "Identification of chromatin-related protein interactions using protein microarrays". Proteomics. 3 (11): 2101-7. doi: ...

*HIST1H2BJ

2002). "Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray ... The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher ... 2001). "Enhancement of the p300 HAT activity by HIV-1 Tat on chromatin DNA". Virology. 289 (2): 312-326. doi:10.1006/viro. ... El Kharroubi A, Piras G, Zensen R, Martin MA (1998). "Transcriptional activation of the integrated chromatin-associated human ...

*ChIP-sequencing

ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of ... 2007). "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing". ... Biotechnology portal ChIP-on-chip ChIP-PET ChIP-PCR Sono-Seq, identical to ChIP-Seq but skipping the immunoprecipitation step. ... Specific DNA sites in direct physical interaction with transcription factors and other proteins can be isolated by chromatin ...

*ABI Solid Sequencing

Chromatin immunoprecipitation (ChIP) is a method for determining transcription factor binding sites and DNA-protein ... Methylation immunoprecipitation (MeDIP) can also be performed and also on arrays. The ability to learn more about methylation ...

*Regulome

Chromatin immunoprecipitation of transcription factors can be used to map transcription factor binding sites in the genome. ...

*SALL4

Through chromatin immunoprecipitation (ChIP) followed by next-generation sequencing or microarray, some SALL4 targets have been ... Since most of these interactions were identified by mass-spec or co-immunoprecipitation, whether they are direct are unknown. ...

*Zymo Research

Included in the company's epigenetics portfolio are kits for nucleosomal DNA purification, chromatin immunoprecipitation, and ...

*FOXO1

It was detected that human FOXO1 is linked with the cyclin D1 promoter using chromatin immunoprecipitation assays (ChIP assays ...

*Protein-DNA interaction

Chromatin immunoprecipitation is used to identify the sequence of the DNA fragments which bind to a known transcription factor ...

*H3K27me3

The histone mark H3K27me3 can be detected in a variety of ways: 1. Chromatin Immunoprecipitation Sequencing (ChIP-sequencing) ... The complexes formed by the looping of the DNA are known as Chromatin. The basic structural unit of chromatin is the Nucleosome ... Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of ... This lead to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone ...

*DLX1

... a direct Dlx homeodomain target in the developing mouse forebrain and retina by optimization of chromatin immunoprecipitation ...

*Epigenomics

Histone modification was first detected on a genome wide level through the coupling of chromatin immunoprecipitation (ChIP) ... Chromatin packaging of DNA varies depending on the cell cycle stage and by local DNA region. The degree to which chromatin is ... However instead of isolating a DNA-binding transcription factor or enhancer protein through chromatin immunoprecipitation, the ... By remodeling chromatin structure and changing the density of DNA packaging, gene expression can thus be modulated. Chromatin ...
The purpose of this study was to generate a transcriptional profile specific for mutant p53 in triple-negative breast cancer (TNBC), representing potential novel therapeutic targets. The highly heterogeneous TNBC tumor subgroup is established as having a poor clinical outcome. There are currently no targeted therapies for women with TNBC; consequently, there is an unmet clinical need to identify targetable pathways. Approximately 75% of these tumors are known to harbour a mutation in Tp53 (mutp53). Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for mutp53 and ETS-1 (a known mutp53 interactor) was carried out using the D0-1 (sc-126) and sc-20 antibodies respectively, in the MDA-MB-468 TNBC cell line. The aim of these ChIP-seq experiments was to identify sites bound by endogenous R273H mutp53 and ETS-1 and to confirm that target genes were co-regulated. We identified 282 novel mutp53 specific genomic binding sites and 37 mutant p53 and ETS1 shared binding sites. In-house data analysis and ...
The Hippo pathway is an important regulator of cell growth and stem cell activity. When Hippo signaling is inactive, the transcriptional coactivator YAP and its paralogue TAZ translocate to the nucleus, where they bind TEAD transcription factors and regulate genes that result in increased organ size and tumorigenesis. Despite the importance of this pathway in cancer, the factors recruited by YAP/TAZ and TEADs and the binding sites of YAP/TAZ on chromatin remain largely unknown. Galli and colleagues used chromatin immunoprecipitation sequencing (ChIP-seq) in liver cancer cells to analyze the genome-wide occupancy of YAP, TEAD1, TEAD4, and TAZ, which revealed that YAP and TAZ have redundant occupancy patterns at a small subset of TEAD-bound distal regulatory enhancer elements. The YAP-bound enhancers were highly active with a higher density of activating histone marks than the average enhancer and high expression of the associated target genes. Twenty-five percent of the YAP-bound enhancers were ...
The Hippo pathway is an important regulator of cell growth and stem cell activity. When Hippo signaling is inactive, the transcriptional coactivator YAP and its paralogue TAZ translocate to the nucleus, where they bind TEAD transcription factors and regulate genes that result in increased organ size and tumorigenesis. Despite the importance of this pathway in cancer, the factors recruited by YAP/TAZ and TEADs and the binding sites of YAP/TAZ on chromatin remain largely unknown. Galli and colleagues used chromatin immunoprecipitation sequencing (ChIP-seq) in liver cancer cells to analyze the genome-wide occupancy of YAP, TEAD1, TEAD4, and TAZ, which revealed that YAP and TAZ have redundant occupancy patterns at a small subset of TEAD-bound distal regulatory enhancer elements. The YAP-bound enhancers were highly active with a higher density of activating histone marks than the average enhancer and high expression of the associated target genes. Twenty-five percent of the YAP-bound enhancers were ...
I am a research technician for the ENCyclopedia Of DNA Elements (ENCODE) Project. The goal of the project is to identify all functional elements in the human genome through high-throughput sequencing. This project uses Bacterial Artificial Chromosomes (BAC) Recombineering to tag transcription factors with GFP in order to perform Chromatin Immunoprecipitation Sequencing (ChIP-Seq). Once the BAC is transfected into K562 cells, I maintain the stable cell lines. After I extract the chromatin from the cells, I sonicate the chromatin then perform ChIP. Finally, the purified DNA generated from ChIP is sequenced using next generation sequencing.. ...
Chromatin immunoprecipitation sequencing(ChIP-seq) rwas performed with the Diagenode recombinant antibody directed against H3K9me3 on sheared chromatin from 4 million K562 cells.
何謂ChIP-Seq? ChIP–seq ( Chromatin immunoprecipitation sequencing )是指染色質免疫沉澱後,所獲得的DNA片段進行高通量
L.Y.Wang, M. Snyder, M. Gerstein In order to understand the molecular mechanisms of gene regulation, a robust method is required to discriminate transcription factor binding sites from non-binding sites on a genomic scale. Experimental methods such as ChIP-chip experiments (microarray-based readout of chromatin immuno-precipitation assays), though gaining great success, remain time-consuming, expensive, and noisy. Traditional computational methods for binding site identification, such as consensus sequences, profile methods, and HMMs, are known to generate high false positive rates when applied genome-wide. They are based on training only with positive data, the small numbers of known binding sites. Thus, we are motivated to propose a new computational method to discover transcription-factor binding sites that synthesizes the noisy data from ChIP-chip experiments with known positive binding-site patterns. Our method (which we call BoCaTFBS) uses a boosted cascade of classifiers, where each ...
I have chip-seq data on histone modifications. Ive been scouring literature and blogs on Chip-seq analysis involving normalizing to input and normalizing across samples using spiked-in samples. There doesnt seem to be a cohesive differential binding analysis approach that can incorporate input normalization along with spike-in normalization. It seems most of the diff. binding approaches involves using RNA-seq methods (EdgeR, DESeq2) on read counts over genomic windows. I can substitute normalization factors used in these RNA-seq packages with spike-in normalization factors, but how do I account for input? Is blacklisting sites that are not different from input really the best way? Transforming the counts over input via log2fc or subtraction is not statistically sound (other bioinformaticians seems to agree).. Ive looked at the input signal for my data and have found signal patterns in areas consistent with some of my histone markers. This makes me think that I should really normalize my IP to ...
ChIP-chip and ChIP-seq data analysis workflow. ChIP-chip data (fold enrichment of immunoprecipitated material over genomic DNA) and/or ChIP-seq data are mapped to a reference genome. Control bound and unbound regions are visually inspected and validated by comparison to standard ChIP and qPCR. Genomic regions where signal is significantly greater than expected by chance (user-defined threshold) are identified as bound. Bound regions are then compared to a database of genomic elements of interest (e.g. promoters) to identify bound elements. Note that absence of detected binding from a genomic region may result from absence of complementary probes upon the array (ChIP-chip), masking of repetitive regions (ChIP-chip and ChIP-seq), or unmappable regions (ChIP-seq). ... Pol II distribution detected by ChIP, ChIP-chip, and ChIP-seq. Drosophila S2 cells were crosslinked, sonicated, and total Pol II (Rpb3) was immunoprecipitated. Pol II ChIP signal at the Tl promoter region was quantified with qPCR ...
Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the Encyclopedia of DNA Elements (ENCODE) Project. To this end, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the standard methodology. Mapping such protein-DNA interactions in vivo using ChIP-seq presents multiple challenges not only in sample preparation and sequencing but also for computational analysis. Here, we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis. At each step in our guidelines we discuss some of the software
Chromatin immunoprecipitation (ChIP) allows enrichment of genomic regions which are associated with specific transcription factors, histone modifications, and indeed any other epitopes which are present on chromatin. The original ChIP methods used site-specific PCR and Southern blotting to confirm which regions of the genome were enriched, on a candidate basis. The combination of ChIP with genomic tiling arrays (ChIP-chip) allowed a more unbiased approach to map ChIP-enriched sites. However, limitations of microarray probe design and probe number have a detrimental impact on the coverage, resolution, sensitivity, and cost of whole-genome tiling microarray sets for higher eukaryotes with large genomes. The combination of ChIP with high-throughput sequencing technology has allowed more comprehensive surveys of genome occupancy, greater resolution, and lower cost for whole genome coverage. Herein, we provide a comparison of high-throughput sequencing platforms and a survey of ChIP-seq analysis tools,
We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-γ (IFN-γ)-stimulated and unstimulated human HeLa S3 cells, and compared the methods performance to ChIP-PCR and to ChIP-chip for four chromosomes. By ChIP-seq, using 15.1 and 12.9 million uniquely mapped sequence reads, and an estimated false discovery rate of less than 0.001, we identified 41,582 and 11,004 putative STAT1-binding regions in stimulated and unstimulated cells, respectively. Of the 34 loci known to contain STAT1 interferon-responsive binding sites, ChIP-seq found 24 (71%). ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%.
Genome-wide assessment of protein-DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify hyper ChIPable regions as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses,
Before interpreting the biological results from ChIP-chip or ChIP-seq data using the Cistrome platform, researchers can upload raw data from their microarray or sequencing facilities and then preprocess those data using Cistrome peak-calling tools. Alternatively, researchers can also upload intermediate results from their own analysis tools. As illustrated in Figure 1, the peak calling step generates two types of intermediate files: peak location files (in BED format), indicating the predicted transcription factor binding sites or histone modification sites, and signal profile files (in WIGGLE format) of binding or histone modification across the genome.. Several methods can be used to import data into Cistrome. The Upload File function can import a file from the users computer or from an HTTP or FTP file server in the same manner as in Galaxy. In most cases, sequencing facilities will manage the low level base calling and read mapping processes. The least processed Cistrome data formats that ...
Background Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identifies genome-wide TF binding sites for one particular context-the cells used in the experiment. But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding? Results We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. We also find, however, that genotype differences between the cell types can explain differences in binding. Moreover, ChIP-seq signal intensity and peak ...
We propose to apply the emerging technology of Chromatin Immunoprecipitation on microarrays (ChIP chip) to identify the direct targets of transcription factors (TFs) known to be involved in breast and colon cancers. During the R21 phase of the project, we plan to identify these targets using a newly developed set of oligonucleotide microarrays that contain 15 million 50mer probes that tile through the non-repetitive sequence of the human genome at 100 bp resolution. We will validate that our ChIP chip protocols work with this new tiling array set. We will also develop and refine two new protocols, microarray reuse and 4-color hybridizations, that will allow economical use of this tiling array set so that it will be a more practical tool for research labs. In the R33 phase of this project, we will use this tiling array set to identify the direct targets of 9 TFs known to be involved in breast and colon cancers. Once we have collected the direct targets of these TFs, we will develop custom arrays ...
Amplification problem in DNA isolated after ChIP experiment, - posted in Genetics and Genomics: I am trying to work out a ChIP experiment. After my ChIP experiment, the DNA I am getting in INPUT is showing problem with amplification. In an RT PCR experiment when I am taking 1ul of this INPUT DNA, It shows a CT value of 36. While on increasing the volume of INPUT dna to 4ul in RT PCR, it does not even get amplified in 40 cycles. I am using diagenode Ipure kit for DNA isol...
His main focus is Genetics and Epigenetics profiling of MDS patients. He is an expert in DNA methylation analysis, Chromatin Immuno-precipitation, Next generation sequencing, Pyrosequencing and other molecular biology techniques. Mohsen is involved in high through put mutation analysis of MDS patients using targeted sequencing by Haloplexä technology.. ...
T-PIC :: DESCRIPTION T-PIC (Tree shape Peak Identification for ChIP-Seq) is a free software for determining DNA/protein binding sites from a ChIP-Seq experiment. ::DEVELOPER Valerie Hower :: SCREENSHOTS N
The ChIP-Seq Web Server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. Users can analyse their own data by uploading mapped sequence tags in various formats, including BED and BAM. The server also provides access to hundreds of publicly available data sets such as ChIP-seq data, RNA-seq data (i.e. CAGE), DNA-methylation data, sequence annotations (promoters, polyA-sites, etc.), and sequence-derived features (CpG, phastCons scores ...
I would like to perform a ChIP-seq on primary cells (FACS sorted). However, I can get only a limited number of cells per mouse (~3000/mouse). So Id end up with 20,000 cells, is that enough for ChIP-seq? How about reproducibility? I read the paper from the Myers lab, they used 50ng DNA and amplified it. 20,000 cells should give me ~200ng DNA, that might work. Has anyone experience with small cell numbers for ChIP-seq? Is there a protocol or article describing ChIP-seq on small number of sorted cells ...
Chromatrap®, a business unit of Porvair Sciences, has published a new application note that describes how Chromatrap® ChIP-seq assays now enable unbiased, genome-wide understanding of protein-DNA regulatory networks.  Genome-wide mapping of protein-DNA interactions is essential for a complete understanding of gene regulation. A detailed map of epigenetic marks and transcription factor binding is necessary for deducing the regulatory networks that underpin gene expression in a variety of biological systems. The most widely used tool for examining these interactions is ChIP followed by massively parallel sequencing (ChIP-seq). The new application note reports on how...
In ligation-based kits, a pre-PCR clean-up step is required to remove adapter dimers. The DNA SMART ChIP-Seq Kit does not use ligation, and high-quality ChIP-seq libraries can be obtained without size selection. However, specific applications, such as identification of transcription factor binding sites, may benefit from stringent size selection. We have found that pre-PCR size selection reduces the complexity of the final library, with increased PCR duplicates (see our tech note for more information). Our single-tube workflow allows for size selection and clean-up following the PCR step, and our protocol provides guidance for more or less stringent size selection. We have found that the basic protocol (Option 1) removes larger PCR fragments (that do not cluster well) without compromising library complexity.. ...
The calling card method provides an accurate and reproducible way to detect transcription factor binding that is orthogonal to ChIP and may be useful for analysis of the many TFs that appear to be recalcitrant to ChIP analysis (perhaps due to poor antibody quality).. While many calling card clusters show high concordance with ChIP-seq peaks, there are a number of peaks discordant between the two methods. Other orthogonal methods for measuring genomic data can generate disparate results at certain loci; for example, DNA methylation assayed by bisulfite-based sequencing methods and by immunoprecipitation enrichment methods yield similar, but not identical, results, particularly in terms of quantification (Harris et al. 2010). Of principal concern is the constraint on piggyBac to insert almost exclusively at the sequence TTAA, which can prevent the TF-PBase from recording its visit to regions devoid of that tetranucleotide. We observed ∼1% PB insertions at non-TTAA sites, raising the prospect of ...
chipchipnorm 1.0.1 :: DESCRIPTION chipchipnorm (ChIP-chip normalization) is a R package that can be incorporated into the normalization workflow for chip-chip data, chromatin immunoprecipitation (ChIP) with microarra
Lab on Chips Market (Product - Instruments, Reagents & Consumables, Software & Services; Application - Genomics & Proteomics, Diagnostics, Drug Discovery; End User -Biotechnology & Pharmaceutical Companies, Hospitals, Diagnostics Centers, Academic & Resea
This project will focus on two pan-animal signaling pathways, Wnt and TGF-beta, which are involved in a variety of developmemtal processes, such as symmetry breaking during embryonic development, axial patterning and regeneration. The techniques to be used include investigation of protein localization, protein-protein interactions and Chip-Seq (chromatin immunoprecipitation and sequencing). Project open to PhD students and Postdocs.
Immunoprecipitation and Western blot analysis. a. Immunoprecipitation: lung extract from E15.5 wild-type embryos was used for immunoprecipitation using Smad2 an
TY - JOUR. T1 - Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells. AU - Yukawa, Masashi. AU - Akiyama, Tomohiko. AU - Franke, Vedran. AU - Mise, Nathan. AU - Isagawa, Takayuki. AU - Suzuki, Yutaka. AU - Suzuki, Masataka G.. AU - Vlahovicek, Kristian. AU - Abe, Kuniya. AU - Aburatani, Hiroyuki. AU - Aoki, Fugaku. PY - 2014/3/21. Y1 - 2014/3/21. N2 - Genome-wide distribution of the majority of H2A and H3 variants (H2A, H2AX, H2AZ, macroH2A, H3.1, H3.2 and H3.3) was simultaneously investigated in mouse embryonic stem cells by chromatin immunoprecipitation sequencing. Around the transcription start site, histone variant distribution differed between genes possessing promoters of high and low CpG density, regardless of their expression levels. In the intergenic regions, regulatory elements were enriched in H2A.Z and H3.3, whereas repeat elements were abundant in H2A and macroH2A, and H3.1, respectively. Analysis of H2A and H3 variant ...
BayesPeak - Bayesian Analysis of ChIP-seq Data, This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.. ChIPpeakAnno - Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges.. Chipseq - A package for analyzing chipseq data. Tools for helping process short read data for chipseq experiments. ChIPseqR - ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.. ChIPsim - A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.. DESeq - Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count ...
With the microarray technology rapidly advanced, tiling arrays have quickly become one of the most powerful tools in genome-wide investigations. High density tiling arrays [1] can be used to address many biological problems such as transcriptome mapping, protein-DNA interaction mapping (ChIP-chip) and array CGH among others [2]. ChIP-chip [3], the focus of the paper, is a technique that combines chromatin immunoprecipitation (ChIP) with microarray technology (chip). It allows efficient, scalable and comprehensive identification of binding sites and profiles of DNA-binding proteins [4]. High density ChIP-chip tiling arrays not only help us map the binding sites of a protein in the genome, but also allow us to better understand the binding events of the protein by clearly displaying the binding occupancy profiles. Several methods have been proposed to analyze the ChIP-chip data; for example, Joint Binding De-convolution (JBD) [5] uses a probabilistic graphical model to improve spatial resolution ...
Single nucleotide polymorphisms (SNPs) have been associated with many aspects of human development and disease, and many non-coding SNPs associated with disease risk are presumed to affect gene regulation. We have previously shown that SNPs within transcription factor binding sites can affect transcription factor binding in an allele-specific and heritable manner. However, such analysis has relied on prior whole-genome genotypes provided by large external projects such as HapMap and the 1000 Genomes Project. This requirement limits the study of allele-specific effects of SNPs in primary patient samples from diseases of interest, where complete genotypes are not readily available. In this study, we show that we are able to identify SNPs de novo and accurately from ChIP-seq data generated in the ENCODE Project. Our de novo identified SNPs from ChIP-seq data are highly concordant with published genotypes. Independent experimental verification of more than 100 sites estimates our false discovery rate at
EZ-Magna ChIP™ HiSens Chromatin Immunoprecipitation Kit Single day chromatin immunoprecipitation (ChIP) kit containing all necessary reagents to enable ChIP from low input amounts of chromatin obtained from either cells or tissues using magnetic A/G beads. Control primers included. - Find MSDS or SDS, a COA, data sheets and more information.
Chromatin immunoprecipitation followed by genome-wide chip hybridization (ChIP-chip), provides a tool for identifying transcription factor (TF) binding sites in the upstream regulatory regions of genes that are differentially expressed in alternative phenotypes or under different environmental conditions (Sun et al. 2010; Qin et al. 2011; Vernes et al. 2011; Yu et al. 2011; Cho et al. 2012; Kwon et al. 2012; Federowicz et al. 2014). By combining ChIP-chip hybridization analyses with mutational analyses and genome-wide transcription profiling, transcriptional networks regulating phenotypic transitions and the expression of alternative phenotypes can be developed (Sun et al. 2010; Qin et al. 2011; Vernes et al. 2011; Wang et al. 2011; Cho et al. 2012; Kwon et al. 2012; Federowicz et al. 2014). However, while ChIP-chip analyses provide the locations of binding sites, they do not assess functionality (Anderson et al. 1989; Li et al. 2008; Cooke et al. 2009; Ucar et al. 2009; Qin et al. 2011; Carey ...
Peak calling is a fundamental step in the analysis of data generated by ChIP-seq or similar techniques to acquire epigenetics information. Current peak callers are often hard to parameterise and may therefore be difficult to use for non-bioinformaticians. In this paper, we present the ChIP-seq analysis tool available in CLC Genomics Workbench and CLC Genomics Server (version 7.5 and up), a user-friendly peak-caller designed to be not specific to a particular *-seq protocol. We illustrate the advantages of a shape-based approach and describe the algorithmic principles underlying the implementation. Thanks to the generality of the idea and the fact the algorithm is able to learn the peak shape from the data, the implementation requires only minimal user input, while still being applicable to a range of *-seq protocols. Using independently validated benchmark datasets, we compare our implementation to other state-of-the-art algorithms explicitly designed to analyse ChIP-seq data and provide an evaluation
Background TF-TFBS-TFT triplets -Transcription factors(TF) regulate transcription factor target(TFT) through binding to transcription factor DNA binding sites(TFBS).
This function reads in transcription factor information given the selected transcription factor target gene database. The information is downloaded via the AnnotationHub package and merged, if necessary.
Chromatrap® offers a one-of-a-kind solid state patented technology, which is characterized by unmatched sensitivity. This makes it possible for users to perform Chromatin immunoprecipitation (ChIP) assays using only 1000 cells per immunoprecipitation.
Chromatin Immunoprecipitation determines the in vivo chromatin binding sites of a transcription factor or other protein of interest. ...
www.millipore.com/epigenetics Cat # Agarose ChIP Kits 17-295 17-371 17-245 17-229 Tools for Chromatin Immunoprecipitation ...
Labomics offers research tools for life science: Genome Editing tools - TALEN CRISPR ,RNA, microRNA, DNA & protein analysis, magnetic beads separation, immuno-precipitation, virus isolation, shRNA clones collection, microRNA clones collection, cDNA ready for expression clones collection, More than 95000 highly characterized antibodies (Lifespan, Everest, BioHit, LabOmics).
BIC/miR-155 expression is not necessarily regulated by FoxP3.(A) Schematic overview of the ChIP-Seq analysis workflow. Genomic loci of all significantly and rep
Hojo, H. et al. Sp7/Osterix Is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification. Dev. Cell 37, 1-16 (2016).. This study used ChIP-seq and RNA-seq to analyze the role of the transcription factor Sp7/Osterix during bone formation in mice. The authors generated a transgenic mouse line in which a biotin motif and three FLAG epitopes were attached to the C-terminus of the Sp7 protein to enable the binding sites of Sp7 could be identified by ChIP. ThruPLEX DNA-seq kit was used to generate ChIP-seq libraries to identify osteoblast enhancers. The authors concluded that the appearance of Sp7 within the Sp family was likely to have played a key role in the emergence of bone-forming osteoblasts during vertebrate evolution.. Read now » ...
Discover our guide covering some of the latest and most advanced ChIP-based techniques. Including ChIP-loop, ChIA-PET, ChIP-exo and ChIP-BS-seq.
The Lens serves almost all the patents and scholarly work in the world as a free, open and secure digital public good, with user privacy a paramount focus.
... ,This kit allows for quick and reproducible immunoprecipitation (IP) by using a 96 well filter plate. The system is more reproducible than regular IPs, which are problematic with regards to washing the protein A/G agarose without disrupting the agarose bed. The binding of the antibody/antigen comple,biological,biology supply,biology supplies,biology product
The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3 ...
Packet-based on-chip interconnection networks, or Network-on-Chips (NoCs) are progressively replacing global on-chip interconnections in ...
Immunoprecipitation vs conventional WB - posted in Protein and Proteomics: Hi, folks. Sorry in advance for my naive question, its because Ive been reading some articles lately with a lot of IP. So here it is: what are the differences between IP and standard WB, regarding results? What are the differences between you precipitating the desired protein with protein G or A and then, detecting it on a SDS gel, and detecting it just with the 1st AB and 2nd AB, as it is in a convention...
Imagine instead of using your loose change on chips and a soda in the office breakroom vending machine, you could get egg-and-croissant sandwiches, or garden salads and fresh apricots.
高い抗原親和性、特異性と安定した品質を兼ね備えたアブカムのウサギ・モノクローナル抗体 RabMAb® ab32074 交差種: Ms,Rat,Hu 適用: WB,IP,IHC-P,Flow Cyt,ChIP/Chip,ICC/IF
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diazoethane definition: Noun (uncountable) 1. (organic chemistry) The diazo compound, CH3-CH=N+=N-Aldrichimica Acta Volume 30 No 4 (pdf) from Sigma-AldrichDiazomethane reacts rapidly with Smiths diene to produce pyrazoline (R = H) by exclusive reaction...
The TRIM37 (also known as MUL) gene is located in the 17q23 chromosomal region, which is amplified in up to approximately 40% of breast cancers. TRIM37 contains a RING finger domain, a hallmark of E3 ubiquitin ligases, but its protein substrate(s) is unknown. Here we report that TRIM37 mono-ubiquitinates histone H2A, a chromatin modification associated with transcriptional repression. We find that in human breast cancer cell lines containing amplified 17q23, TRIM37 is upregulated and, reciprocally, the major H2A ubiquitin ligase RNF2 (also known as RING1B) is downregulated. Genome-wide chromatin immunoprecipitation (ChIP)-chip experiments in 17q23-amplified breast cancer cells identified many genes, including multiple tumour suppressors, whose promoters were bound by TRIM37 and enriched for ubiquitinated H2A. However, unlike RNF2, which is a subunit of polycomb repressive complex 1 (PRC1), we find that TRIM37 associates with polycomb repressive complex 2 (PRC2). TRIM37, PRC2 and PRC1 are co-bound to
We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identifying the perturbed TRs.
The Signal Seeker Ubiquitination enrichment Kit can purify ubiquitnated or Ubiquitylated, antibody, mono-ubiquitin, polyubiquitin, ubiquitin chains, sumoylation, proteosome, mono-ubiquitination, signal transduction, signal pathway and affinity beads.
Cbf1p is a basic-helix-loop-helix-zipper protein of Saccharomyces cerevisiae required for the function of centromeres and MET gene promoters, where it binds DNA via the consensus core motif CACRTG (R = A or G). At MET genes Cbf1p appears to function in both activator recruitment and chromatin-remodeling. Cbf1p has been implicated in the regulation of other genes, and CACRTG motifs are common in potential gene regulatory DNA. A recent genome-wide location analysis showed that the majority of intergenic CACGTG palindromes are bound by Cbf1p. Here we tested whether all potential Cbf1p binding motifs in the yeast genome are likely to be bound by Cbf1p using chromatin immunoprecipitation. We also tested which of the motifs are actually functional by assaying for Cbf1p-dependent chromatin remodeling. We show that Cbf1p binding and activity is restricted to palindromic CACGTG motifs in promoter-proximal regions. Cbf1p does not function through CACGTG motifs that occur in promoter-distal locations within coding
In this post I have a look at the ENCODE RNA polymerase II ChIP-seq data and overlay the ChIP-seq peaks onto RefSeq transcription start sites.
COLD SPRING HARBOR, N.Y. (Tues., Sept. 1, 2009) - Chromatin Immunoprecipitation (ChIP) is an invaluable method for studying the interactions between proteins and DNA on a genome-wide scale. ChIP can be used to determine whether a transcription factor interacts with a candidate target gene, and is used to monitor the presence of histones with posttranslational modifications at specific genomic locations. The results are often extremely useful for investigating the functions of specific transcription factors or histone modifications. In the September issue of Cold Spring Harbor Protocols (www.cshprotocols.org/TOCs/toc9_09.dtl), Michael Carey (portal.ctrl.ucla.edu/biological-chemistry/institution/personnel?personnel_id=45403), Craig Peterson (www.umassmed.edu/pmm/faculty/peterson.cfm), and Stephen Smale (dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=45693) present Chromatin Immunoprecipitation (ChIP), an optimized protocol for use in mammalian cells. The article is freely ...
ChIP-Chip stands for Chromatin Immunoprecipitation and chip in the sense of DNA microarray. It is a technique to determine the genome-wide binding sites of a DNA-binding protein. While the basic principle is the same for all species, there are some differences in handling cells. This protocol is developed and tested for E. coli. It should work the same way for other bacteria but that remains to be proven. Published protocols also exist for other bacterial species, including Bacillus subtilis, Caulobacter crescentus and Mycobacterium tuberculosis. Because E. coli can be grown to high cell densities relative to eukaryotes, it is possible to generate sufficient DNA to label without using a PCR-based method [1]. This method uses strand displacement primer extension with Klenow DNA polymerase and amplifies the DNA ~10-fold, while simultaneously incorporating dye-coupled nucleotide. Other ChIP-Chip protocols can be found here: ...
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We used chromatin immunoprecipitation (ChIP) to determine whether E4bp4 promotes the transcription of Eomes and Id2 directly by binding in vivo to the regulatory regions of their genes. To do this, we took advantage of the new mouse NK-like cell line MNK-1, which allowed us to use a known E4bp4-binding site in the regulatory region of the mouse Per2 gene, Per2B, as a positive control (Ohno et al., 2007). MNK-1 cells were transduced with FLAG-E4bp4, and protein-chromatin complexes were immunoprecipitated using either IgG, anti-FLAG, or one of two polyclonal antibodies to E4bp4.. We searched regulatory regions within 2 kb 5′ and 3′ of the Eomes and Id2 genes and identified six putative E4bp4-binding sites (Fig. 5 B and Table S2). We examined their enrichment in chromatin immunoprecipitated with anti-FLAG or anti-E4bp4 compared with that immunoprecipitated with IgG. To rule out the possibility of spurious enrichment, we used primers that amplify a region in a gene desert on chromosome 11 as a ...
Only the PBM motif is a classic HLH motif. Three different ChIP-chip-derived motifs are all diverse, but all score highly on ChIP-chip data! Are they motifs of other TFs? Check. 602: GCN4; 1095, TEC1; 1096: resembles 602, but is a closer match to CUP9/TOS8. Also hits GCN4. According to the literature (PMID: 9032238) the core binding site for the Rtg1p-Rtg3p heterodimer is 5-GGTCAC-3; the only motif that resembles this is 1446. Vague resemblance to 602 and 1096. I am going to retain 1446, which represents the literature site; PBM motif 870, which resembles an E-box, and ChIP-chip motif 1445, which scores highest on ChIP-chip data. But give all low confidence ...
BACKGROUND: The CCTC-binding factor (CTCF) protein is involved in genome organization, including mediating three-dimensional chromatin interactions. Human patient lymphocytes with mutations in a single copy of the CTCF gene have reduced expression of enhancer-associated genes involved in response to stimuli. We hypothesize that CTCF interactions stabilize enhancer-promoter chromatin interaction domains, facilitating increased expression of genes in response to stimuli. Here we systematically investigate this model using computational analyses. RESULTS: We use CTCF ChIA-PET data from the ENCODE project to show that CTCF-associated chromatin loops have a tendency to enclose regions of enhancer-regulated stimulus responsive genes, insulating them from neighboring regions of constitutively expressed housekeeping genes. To facilitate cell type-specific CTCF loop identification, we develop an algorithm to predict CTCF loops from ChIP-seq data alone by exploiting the CTCF motif directionality in loop ...
Chromatin immunoprecipitation (ChIP) provides a means of enriching DNA associated with transcription factors, histone modifications, and indeed any other proteins for which suitably characterized antibodies are available. Over the years, sequence detection has progressed from quantitative real-time PCR and Southern blotting to microarrays (ChIP-chip) and now high-throughput sequencing (ChIP-seq). This progression has vastly increased the sequence coverage and data volumes generated. This in turn has enabled informaticians to predict the identity of multi-protein complexes on DNA based on the overrepresentation of sequence motifs in DNA enriched by ChIP with a single antibody against a single protein. In the course of the development of high-throughput sequencing, little has changed in the ChIP methodology until recently. In the last three years, a number of modifications have been made to the ChIP protocol with the goal of enhancing the sensitivity of the method and further reducing the levels of
Add Micrococcal Nuclease to each sample to digest the DNA. Mix by inverting the tube several times and incubate at 37°C for 20 minutes. Mix by inversion every 3-5 minutes. The amount and incubation time of Micrococcal Nuclease required to digest the genomic DNA to an optimal 150 900 bp length may need to be determined empirically for individual cell types ...
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Health,...4 of 7 patients with incurable disease fared better doctor says ...FRIDAY Sept. 21 (HealthDay News) -- DNA microarray chip analyses of t...Dr. Eric P. Lester president of Oncology Care Associates in St. Josep...To determine which drugs might offer them the most benefit Lester use...,Gene,Chip,Data,Can,Boost,Cancer,Outcomes,medicine,medical news today,latest medical news,medical newsletters,current medical news,latest medicine news
Ralf Eggeling, Teemu Roos, Petri Myllymäki, and Ivo Grosse authored a paper Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data that was accepted for publication in BMC Bioinformatics.. Eggeling recently defended his PhD thesis at the Halle-Wittenberg University in Germany, supervised by Grosse. Ralf then joined HIIT as a postdoctoral researcher.. ...
Xin Chen, Lingqiong Guo, Zhaocheng Fan, Tao Jiang: W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data. Bioinformatics 24(9): 1121-1128 (2008 ...
The Tomcat and Apache Certificates will expire two years after the installation of an iPrint Appliance server. When those certificates expire, errors will be presented to the administrator when attempting to manage iPrint within iManager and the /psmstatus. Also, end user secure printer authenticates will fail. The below script will partially automate the steps required … +read more. ...
TY - JOUR. T1 - Characterization of Nucleophosmin (B23) as a Myc Target by Scanning Chromatin Immunoprecipitation. AU - Zeller, Karen I.. AU - Haggerty, Timothy J.. AU - Barrett, John F.. AU - Guo, Qingbin. AU - Wonsey, Diane R.. AU - Dang, Chi V.. PY - 2001/12/21. Y1 - 2001/12/21. N2 - The genetic program through which a specific transcription factor regulates a biological response is fundamental to our understanding how instructions in the genome are implemented. The emergence of DNA microarray technology for gene expression analysis has generated vast numbers of target genes resulting from specific transcription factor activity. We use the oncogenic transcription factor c-Myc as proof-of-principle that human genome sequence analysis and scanning of a specific gene by chromatin immunoprecipitation can be coupled to identify target transcription factor binding sequences. We focused on nucleophosmin, also known as B23, which was identified as a candidate Myc-responsive gene from a subtractive ...
Purpose: Tumor protein 53-induced nuclear protein 1 (Tp53inp1) acts as a tumor suppressor by inducing cell death. Tp53inp1 mRNA is a predicted target of miR-221. Whether targeting Tp53inp1 plays a role in miR-221-mediated cardioprotection has not been investigated. We hypothesized that miRNA-221 directly targets Tp53inp1 to reduce ischemia/reperfusion (I/R)-induced autophagy.. Method: Myoblast H9c2 cells underwent 16 hours 0.2% O2 hypoxia followed by 2 hours re-oxygenation (H-R, simulating I/R). H9c2 were transfected with miRNA-221 mimic (25 nmol) and scrambled mimic control (miR-221 and MC). Cell count/viability, WST assay, cell injury-induced LDH release, and GFP-LC3 labeled autophagosome formation were measured. Cells were collected for RT-qPCR and western blot (WB) analyses. pCMV-Myc-Tp53inp1 and pcDNA3.1-Flag-p62 plasmids were cloned and transfected into H9c2 for recovery and immuno-precipitation (IP) studies. The effects of miRNA-221 inhibitor in H9c2 were also assessed.. Results: miR-221 ...
Scientific expertise:. Molecular biology ; genomics ; In vitro diagnostic ; marker identification ; genetics ; crop improvement ; plant-microbe interactions ; phytopathology ; Tilling platform creation and management ; primer/probe design ; microorganisms detection test set-up.. - Technical knowledge:. PCR, qPCR and RT-qPCR, isothermal amplification, DNA and RNA extraction, Cloning, sequencing, AFLP, Southern, northern, microbiology, plant cell lines culture, plant transformation (Agrobacterium, biolistic), microscopy, directed mutagenesis, transgenesis (tobacco, poplar, Arabidopsis), DNA micro-arrays, double-hybrid, proteomics (extraction, in vitro-ubiquitination, phosphorylation, western, immuno-precipitation), Tilling, genotyping, bioinformatical sequences analysis, bioinformatical tools (VNTI, ApE, CLUSTALW), lyophilisation.. - Project management: Scientific and technological monitoring ; feasibility studies ; project design and writing ; cost determination ; risk analysis; planning; ...
Thank you very much for your suggestion. It is easy to registrate on gene-regulation.com. But when I browse the TRANSFAC database, it links to http://www.biobase-international.com/. For a free trial, it must finish a registration form. It is hard to pass this registration form. It is like this http://www.biobase-international.com/pages/index.php?id=456. In JARSPAR I can not find the factors which I interested no profiles in JASPAR satisfies search criteria 2008/5/29 lichunjiang ,lichunjiang at sibs.ac.cn,: , , , Really? I registrated for gene-regulation.com a couple of years ago, it is , quite easy.�It does not make sense that you can not register. Or you , should just write to the service to fix the problem. , , Actually, , it is free to use a reduced version. For the full professional version, , you need to pay. , , Besides Transfac, I recommend another , database: JARSPAR available at http://jaspar.genereg.net/.�It is , totally free to use. , Hope this help. , Good luck! , , , ,, It seems ...
Chromatin structures are regulated by various mechanisms including histone modification and chromatin remodeling, which involve the binding of transcription factors. By using tools such as chromatin immunoprecipitation , it...
The NEXTFLEX-96 ChIP-seq barcodes are 96, sequence validated, single-index adapters for low input library prep enabling high throughput Illumina sequencing.
I investigate molecular mechanisms that are at the basis of Hox transcription factor specificity by implementing chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) in Drosophila.
The ChromaFlash High-Sensitivity ChIP Kit is a complete set of optimized reagents to carry out a successful chromatin immunoprecipitation procedure in a high throughput format starting from mammalian cells or tissues.The...
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Chromatrap® offers an optimised unique buffer chemistry that provides the leading solution for the isolation of high quality and high yield chromatin.
Welcome to Virology’s second Essential Collection, on Chromatin and Viruses. This Collection expands on a recent review article...
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Anti-FOXA1 antibody - ChIP Grade (ab23738) has been cited in 63 publications. References for Human, Mouse, Zfsh in ChIP, ChIP/Chip, CHIPseq, EMSA, ICC/IF, IHC…
Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme ...
ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence or absence of each chromatin mark. The resulting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biological characterization of each state. ChromHMM also produces files with genome-wide maps of chromatin state annotations that can be directly visualized in a genome browser. ...
TY - JOUR. T1 - Activation of pp60(src) is critical for stretch-induced orienting response in fibroblasts. AU - Sai, Xiaorui. AU - Naruse, Keiji. AU - Sokabe, Masahiro. PY - 1999. Y1 - 1999. N2 - When subjected to uni-axial cyclic stretch (120% in length, 1 Hz), fibroblasts (3Y1) aligned perpendicular to the stretch axis in a couple of hours. Concomitantly with this orienting response, protein tyrosine phosphorylation of cellular proteins (molecular masses of approximately 70 kDa and 120-130 kDa) increased and peaked at 30 minutes. Immuno-precipitation experiments revealed that paxillin, pp125(FAK), and pp30(CAS) were included in the 70 kDa, and 120-130 kDa bands, respectively. Treatment of the cells with herbimycin A, a tyrosine kinase inhibitor, suppressed the stretch induced tyrosine phosphorylation and the orienting response suggesting that certain tyrosine kinases are activated by stretch. We focused on pp60(src), the most abundant tyrosine kinase in fibroblasts. The kinase activity of ...
PAX8 is a lineage-restricted transcription factor expressed in a large proportion of epithelial ovarian cancers (EOCs). PAX8 is commonly upregulated in EOCs relative to precursor tissues, suggesting it functions as an oncogene. However, the biological role of PAX8 during cancer initiation and development is poorly understood, and the genome-wide transcriptional targets have yet to be comprehensively catalogued. Using stable models of PAX8 knockdown in HEYA8 and IGROV1 EOC cell lines we show that PAX8 knockdown reduces cell proliferation in vitro and tumor growth in vivo. To understand how PAX8 regulates neoplastic phenotypes in cancer cells we performed RNA expression profiling by microarray in HEYA8 and IGROV1 before and after PAX8 knockdown. We also performed chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) for PAX8 and a marker of active chromatin (H3K27ac) in both cell lines. De novo motif discovery in the ChIP-seq profiles identified a PAX-like binding motif ...
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has become standard technologies for genome wide identification of DNA-binding protein target sites. After read mappings and peak callings, the peak should be annotated to answer the biological questions. Annotation also create the possibility of integrating expression profile data to predict gene expression regulation. ChIPseeker1 was developed for annotating nearest genes and genomic features to peaks.. ChIP peak data set comparison is also very important. We can use it as an index to estimate how well biological replications are. Even more important is applying to infer cooperative regulation. If two ChIP seq data, obtained by two different binding proteins, overlap significantly, these two proteins may form a complex or have interaction in regulation chromosome remodelling or gene expression. ChIPseeker1 support statistical testing of significant overlap among ChIP seq data sets, and incorporate open access ...
The interplay of active and repressive histone modifications is assumed to have a key role in the regulation of gene expression. In contrast to this generally accepted view, we show that the transcription of genes temporally regulated during fly and worm development occurs in the absence of canonically active histone modifications. Conversely, strong chromatin marking is related to transcriptional and post-transcriptional stability, an association that we also observe in mammals. Our results support a model in which chromatin marking is associated with the stable production of RNA, whereas unmarked chromatin would permit rapid gene activation and deactivation during development. In the latter case, regulation by transcription factors would have a comparatively more important regulatory role than chromatin marks.. ...
Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15;295(5558):1306-11. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct;16(10):1299-309. Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22. ...
ChIRP is a novel and rapid technique to map genomic binding sites of long noncoding RNAs (lncRNAs). The method takes advantage of the...
Marinov, Georgi K, Wang, Jie, Handler, Dominik, Wold, Barbara J, Weng, Zhiping, Hannon, Gregory J, Aravin, Alexei A, Zamore, Phillip D, Brennecke, Julius, Toth, Katalin Fejes (March 2015) Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwis Genomic Targets Still Not Identified. Developmental Cell, 32 (6). pp. 765-771. ISSN 1534-5807 ...
Quality control of chromatin immunoprecipitation libraries (ChIP-seq) by quantitative polymerase chain reaction (qPCR). This function calculates Enrichment value with respect to reference for each histone modification (specific to Vii7 software ,http://www.thermofisher.com/ca/en/home/life-science/pcr/real-time-pcr/real-time-pcr-instruments/viia-7-real-time-pcr-system/viia-7-software.html,). This function is applicable to full panel of histone modifications described by International Human Epigenomic Consortium (IHEC).. ...
Covalent modifications of histones and histone variants have great influence on chromatin structure, which is involved in the transcriptional regulation of gene expression. Chromatin immunoprecipitation (ChIP) is a powerful tool for studying in vivo DNA-histone interactions. Strawberry is a model for Rosaceae and non-climacteric fruits, in which histone modifications have been implicated to affect fruit development and ripening. However, a validated ChIP method has not been reported in strawberry, probably due to its high levels of polysaccharides which affect the quality of prepared chromatin and the efficiency of immunoprecipitation. We describe a native chromatin immunoprecipitation (N-ChIP) protocol suitable for strawberry by optimizing the parameters for nuclei isolation, chromatin extraction, DNA fragmentation and validation analysis using quantitative real-time PCR (qRT-PCR). The qRT-PCR results show that both the active mark H3K36me3 and the silent mark H3K9me2 are efficiently immunoprecipitated
DNA is wrapped around a histone octamer to form the basic unit of chromatin structure. During embryogenesis, dynamic changes of chromatin structure and chromatin modification occur after fertilization; subsequently, the epigenetic information is inherited through many rounds of the cell cycle. Thus, chromatin is essential for the determination of cell identity. Two strategies are used to modulate a chromatin environment: the covalent modification of histone tails and energy-dependent chromatin remodeling. The acetylation, methylation or phosphorylation of histone tails can have profound effects on chromatin structure and transcription (Jenuwein and Allis, 2001). Chromatin remodeling reactions are catalyzed by large protein complexes that use the energy of ATP hydrolysis to alter the structure or positioning of nucleosomes (Becker and Hörz, 2002; Clapier and Cairns, 2009). In addition to these events, histone variants play important roles in modulating chromatin structure (Henikoff and Ahmad, ...
Arterial baroreflex sensitivity is attenuated in chronic heart failure (CHF) state, which is associated with cardiac arrhythmias and sudden cardiac death in patients with CHF. Our previous study showed that CHF-induced sodium channel dysfunction in the baroreceptor neurons was involved in the blunted baroreflex sensitivity in CHF rats. Mitochondria-derived superoxide overproduction decreased expression and activation of the sodium channels in the baroreceptor neurons from CHF rats. However, the molecular mechanisms responsible for the sodium channel dysfunction in the baroreceptor neurons from CHF rats remain unknown. We tested the involvement of nuclear factor κB (NFκB) in the sodium channel dysfunction and evaluated the effects of in vivo transfection of manganese superoxide dismutase gene and NFκB shRNA on the baroreflex function in CHF rats. CHF was developed at 6 to 8 weeks after left coronary artery ligation in adult rats. Western blot and chromatin immunoprecipitation data showed that ...
TY - JOUR. T1 - CAME. T2 - Identification of chromatin accessibility from nucleosome occupancy and methylome sequencing. AU - Piao, Yongjun. AU - Lee, Seong Keon. AU - Lee, Eun Joon. AU - Robertson, Keith D. AU - Shi, Huidong. AU - Ryu, Keun Ho. AU - Choi, Jeong Hyeon. PY - 2017/4/15. Y1 - 2017/4/15. N2 - Motivation: Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, Methyltransferase Accessibility Protocol for individual templates-Bisulfite Genome Sequencing (MAPit-BGS) and nucleosome occupancy and methylome sequencing (NOMe-seq) have been developed for simultaneously profiling chromatin accessibility and DNA methylation on single molecules. Therefore, there is a great demand in developing computational methods to identify chromatin ...
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This ...

Chromatin immunoprecipitation from 1000 cellsChromatin immunoprecipitation from 1000 cells

This makes it possible for users to perform Chromatin immunoprecipitation (ChIP) assays using only 1000 cells per ... Chromatin immunoprecipitation. The Chromatrap® ChIP-seq Protein A kit (Cat no 500189) was used for ChIP in accordance with the ... Efficient Extraction and Immunoprecipitation of Chromatin from Complex Formalin Fixed Paraffin Embedded Tissue. ... Slurries were prepared for immunoprecipitation using 100 µl chromatin stock from each extraction, depending on the number of ...
more infohttps://www.news-medical.net/whitepaper/20170223/Chromatin-immunoprecipitation-from-1000-cells.aspx

Native chromatin immunoprecipitation protocol | AbcamNative chromatin immunoprecipitation protocol | Abcam

Find out how to perform native chromatin immunoprecipitation with this detailed step-by-step protocol. ... Immunoprecipitation. *100-200 μg unfixed chromatin + 100-200 μl affinity purified antibody (50-100 μg Ig) and the final volume ... After reading this ChIP protocol, review more ChIP assay /chromatin immunoprecipitation resources and products, or go straight ... flexible Chromatin Extraction Kit ab117152 which is used to extract native, cross-linked, sheared or unsheared chromatin ...
more infohttps://www.abcam.com/protocols/native-chromatin-immunoprecipitation-protocol

Chromatin Immunoprecipitation Sequencing (ChIP Seq) News, ResearchChromatin Immunoprecipitation Sequencing (ChIP Seq) News, Research

Chromatin Immunoprecipitation Sequencing (ChIP Seq) News and Research. RSS ChIP-seq, or chromatin immunoprecipitation and ...
more infohttps://www.news-medical.net/?tag=/Chromatin-Immunoprecipitation-Sequencing-

ChIP (chromatin immunoprecipitation) protocol | AbcamChIP (chromatin immunoprecipitation) protocol | Abcam

Immunoprecipitation. *Use the chromatin prepared from Step 2.2. Approximately 25 μg of DNA per IP is recommended. Dilute each ... After reading this ChIP protocol, review more ChIP assay / chromatin immunoprecipitation resources and products, or go straight ... This chromatin preparation will be used for the immunoprecipitation (IP) in Step 4. ... flexible Chromatin Extraction Kit ab117152 which is used to extract native, cross-linked, sheared or unsheared chromatin ...
more infohttps://www.abcam.com/Protocols/cross-linking-chromatin-immunoprecipitation-x-chip-protocol

Chromatin ImmunoprecipitationChromatin Immunoprecipitation

... can be used to study protein DNA complexes. Visit this page to learn more about how to optimize ... Sheared chromatin may be saved at -80°C prior to performing the immunoprecipitation. If you are saving the chromatin, we would ... Immunoprecipitation. Immunoprecipitation of chromatin-bound protein can be performed with Protein A, G, or A/G magnetic or ... Fixation and Chromatin Isolation. A successful ChIP experiment is dependent on high quality chromatin. Chromatin quality can be ...
more infohttps://biolegend.com/fr-ch/chip

Chromatin ImmunoprecipitationChromatin Immunoprecipitation

... can be used to study protein DNA complexes. Visit this page to learn more about how to optimize ... Sheared chromatin may be saved at -80°C prior to performing the immunoprecipitation. If you are saving the chromatin, we would ... Immunoprecipitation. Immunoprecipitation of chromatin-bound protein can be performed with Protein A, G, or A/G magnetic or ... Fixation and Chromatin Isolation. A successful ChIP experiment is dependent on high quality chromatin. Chromatin quality can be ...
more infohttps://biolegend.com/de-at/chip

Chromatin ImmunoprecipitationChromatin Immunoprecipitation

... can be used to study protein DNA complexes. Visit this page to learn more about how to optimize ... Sheared chromatin may be saved at -80°C prior to performing the immunoprecipitation. If you are saving the chromatin, we would ... Immunoprecipitation. Immunoprecipitation of chromatin-bound protein can be performed with Protein A, G, or A/G magnetic or ... Fixation and Chromatin Isolation. A successful ChIP experiment is dependent on high quality chromatin. Chromatin quality can be ...
more infohttps://www.biolegend.com/en-us/chip

Chromatin Immunoprecipitation | Cell Signaling TechnologyChromatin Immunoprecipitation | Cell Signaling Technology

Chromatin immunoprecipitation (ChIP) is a powerful research technique used to identify and analyze protein-DNA interactions ... Whatever your preferred method of chromatin preparation we have a ChIP kit suited to your needs. ...
more infohttps://www.cellsignal.com/contents/resources-applications/chromatin-immunoprecipitation/apps-chromatin-immunoprecipitation

Phys.org - chromatin immunoprecipitationPhys.org - chromatin immunoprecipitation

Phys.org internet news portal provides the latest news on science including: Physics, Space Science, Earth Science, Health and Medicine
more infohttps://phys.org/tags/chromatin%20immunoprecipitation/sort/popular/1d/

Phys.org - chromatin immunoprecipitationPhys.org - chromatin immunoprecipitation

Phys.org internet news portal provides the latest news on science including: Physics, Space Science, Earth Science, Health and Medicine
more infohttps://phys.org/tags/chromatin%20immunoprecipitation/sort/liverank/1d/

chromatin immunoprecipitation Protocols and Video...'chromatin immunoprecipitation' Protocols and Video...

Chromatin Immunoprecipitation, Chromatin Immunoprecipitation (ChIP) using Drosophila tissue, Chromatin Immunoprecipitation ... Chromatin Immunoprecipitation from Human Embryonic Stem Cells, Generation of High Quality Chromatin Immunoprecipitation DNA ... Efficient Chromatin Immunoprecipitation using Limiting Amounts of Biomass, Chromatin Immunoprecipitation (ChIP) Protocol for ... Chromatin Immunoprecipitation from Dorsal Root Ganglia Tissue following Axonal Injury, Chromatin Immunoprecipitation Assay ...
more infohttps://www.jove.com/keyword/chromatin+immunoprecipitation

Tools for Chromatin Immunoprecipitation | Immunoprecipitation | Molecular BiologyTools for Chromatin Immunoprecipitation | Immunoprecipitation | Molecular Biology

G Chromatin Immunoprecipitation Kit Magna ChIP™ A/G Chromatin Immunoprecipitation Kit EZ-Magna ChIP™ A/G Chromatin ... A Chromatin Immunoprecipitation Kit Magna ChIP™ G Chromatin Immunoprecipitation Kit EZ-Magna ChIP™ A Chromatin ... Universal Chromatin Immunoprecipitation DNA Microarray Quad Kit Magna ChIP-Seq Chromatin Immunoprecipitation and Next ... Chromatin Immunoprecipitation Human Promoter 244K Microarray Kit Magna ChIP2™ Chromatin Immunoprecipitation Mouse Promoter 244K ...
more infohttps://www.scribd.com/document/115827388/Tools-for-Chromatin-Immunoprecipitation

Imprint® Chromatin Immunoprecipitation Kit - ChIP Kit | Sigma-AldrichImprint® Chromatin Immunoprecipitation Kit - ChIP Kit | Sigma-Aldrich

A complete solution for Chromatin Immunoprecipitation including columns and reagents for DNA purification. ... The Imprint Chromatin Immunoprecipitation Kit combines speed and convenience with performance. ... View the Chromatin IP (ChIP) Troubleshooting Questions. View the poster Rapid and easy method for Chromatin IP (ChIP) analysis ... Successful chromatin immunoprecipitation requires an effective, specific, and high quality antibody. Not all antibodies work in ...
more infohttps://www.sigmaaldrich.com/life-science/epigenetics/chip.html

Chromatin Immunoprecipitation - OpenWetWareChromatin Immunoprecipitation - OpenWetWare

Chromatin Immunoprecipitation determines the in vivo chromatin binding sites of a transcription factor or other protein of ... Retrieved from "https://openwetware.org/mediawiki/index.php?title=Chromatin_Immunoprecipitation&oldid=287188" ...
more infohttps://openwetware.org/wiki/Chromatin_Immunoprecipitation

Chromatin Immunoprecipitation | Springer for Research & DevelopmentChromatin Immunoprecipitation | Springer for Research & Development

This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP- ... Chromatin Immunoprecipitation from Mouse Embryonic Tissue or Adherent Cells in Culture, Followed by Next-Generation Sequencing ... Chromatin Immunoprecipitation Assay in the Hyperthermoacidophilic Crenarchaeon, Sulfolobus acidocaldarius Kun Wang, Ann- ... ChIP-re-ChIP: Co-occupancy Analysis by Sequential Chromatin Immunoprecipitation Timothy V. Beischlag, Gratien G. Prefontaine, ...
more infohttps://rd.springer.com/book/10.1007/978-1-4939-7380-4

Chromatin Immunoprecipitation (ChIP) on Unfixed Chromatin | Sigma-AldrichChromatin Immunoprecipitation (ChIP) on Unfixed Chromatin | Sigma-Aldrich

... these covalent modifications on the core histones are thought to play essential roles in chromatin organization and gene ... Chromatin Immunoprecipitation (ChIP) Protocol. In cells and tissues, the histone proteins that constitute the nucleosomes can ... View the protocol Chromatin Immunoprecipitation (ChIP) on Unfixed Chromatin from Cells and Tissues to Analyze Histone ... For other applications, chromatin immunoprecipitation should be performed on cross-linked chromatin. ...
more infohttps://www.sigmaaldrich.com/life-science/molecular-biology/learning-center/protocols/chip.html

Chromatin Immunoprecipitation (ChIP) | Thermo Fisher Scientific - CNChromatin Immunoprecipitation (ChIP) | Thermo Fisher Scientific - CN

The chromatin immunoprecipitation (ChIP) assay is a powerful method for analyzing epigenetic modifications and genomic DNA ... 2. Optimization of chromatin shearing Shearing the chromatin allows the chromatin to be soluble and dictates the resolution of ... Chromatin immunoprecipitation (ChIP) is a technique used in epigenetic research that takes a snapshot of protein-DNA ... Mechanical chromatin shearing. Sonication is commonly used for chromatin shearing as it produces random fragments. Since ...
more infohttps://www.thermofisher.com/cn/zh/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html

Protocol - Chromatin Immunoprecipitation ChIP Assay ProtocolProtocol - Chromatin Immunoprecipitation ChIP Assay Protocol

Chromatin Immunoprecipitation Assay. *Mix the Chromatin Sample, Protease Inhibitor Cocktail (PIC), optimal quantity of ... Chromatin Immunoprecipitation (ChIP) Assay Protocol. Reagents. *Basic cell culture media: respective to the cell line used and ... Make sure the DNA fragments from the chromatin samples are not too small. Do not sonicate or digest chromatin to a fragment ... Chromatin Sample Preparation. *Culture between 1-15 million cells. Collect cells by spinning down at 500xg at 4°C for 5 minutes ...
more infohttps://www.biolegend.com/nl-nl/protocols/chromatin-immunoprecipitation-chip-assay-protocol

Chromatin Immunoprecipitation Sequencing (ChIP-Seq) | Thermo Fisher Scientific - ZAChromatin Immunoprecipitation Sequencing (ChIP-Seq) | Thermo Fisher Scientific - ZA

Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a ... Chromatin Immunoprecipitation Sequencing (ChIP-Seq) * Chromatin Immunoprecipitation Sequencing (ChIP-Seq) on the 5500xl Genetic ... Chromatin Immunoprecipitation Sequencing (ChIP-Seq) Sample Prep Products * Chromatin Immunoprecipitation Sequencing by Ion ... Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a ...
more infohttps://www.thermofisher.com/za/en/home/life-science/sequencing/epigenetic-sequencing/chromatin-immunoprecipitation.html

Measurement of protein-DNA interactions in vivo by chromatin immunoprecipitation.  - PubMed - NCBIMeasurement of protein-DNA interactions in vivo by chromatin immunoprecipitation. - PubMed - NCBI

Measurement of protein-DNA interactions in vivo by chromatin immunoprecipitation.. Im H1, Grass JA, Johnson KD, Boyer ME, Wu J ... The chromatin is sonicated to generate small fragments, and an immunoprecipitation is conducted with an antibody against the ... These seemingly complex issues can be directly addressed by a powerful methodology termed the chromatin immunoprecipitation ( ... Chromatin-domain scanning coupled with quantitative analysis is a powerful means of dissecting mechanisms by which signaling ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/15173613?dopt=Abstract

Chromatin immunoprecipitation - WikipediaChromatin immunoprecipitation - Wikipedia

Chromatin immunoprecipitation at the US National Library of Medicine Medical Subject Headings (MeSH) EpigenomeNOE.com Chromatin ... Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the ... on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications Chromatin Immunoprecipitation (ChIP) of Protein ... These reports are considered the pioneering studies in the field of chromatin immunoprecipitation. XChIP was further modified ...
more infohttps://en.wikipedia.org/wiki/Chromatin_immunoprecipitation

Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples | ProtocolChromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples | Protocol

... we describe a chromatin immunoprecipitation (ChIP) and ChIP-seq library preparation protocol to generate global epigenomic... ... Chromatin Immunoprecipitation (ChIP) using Drosophila tissue…. Published 3/23/2012. Epigenetic Regulation of Cardiac ... Chromatin Immunoprecipitation (ChIP) Protocol for Low-abundance Embryonic Samples. Rizwan Rehimi1, Michaela Bartusel1, ... Chromatin Immunoprecipitation (ChIP) to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells… ...
more infohttps://www.jove.com/video/56186/chromatin-immunoprecipitation-chip-protocol-for-low-abundance

Analysis of Histone Modifications in Rodent Pancreatic Islets by Native Chromatin Immunoprecipitation.  - PubMed - NCBIAnalysis of Histone Modifications in Rodent Pancreatic Islets by Native Chromatin Immunoprecipitation. - PubMed - NCBI

Analysis of Histone Modifications in Rodent Pancreatic Islets by Native Chromatin Immunoprecipitation.. Sandovici I1,2, ... Histones represent the main protein components of the chromatin and undergo diverse covalent modifications that are very ... pancreatic islets from rodents and subsequently outline the methods used to immunoprecipitate and analyze the native chromatin ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/31586329

Genomewide Identification of Protein Binding Locations Using Chromatin Immunoprecipitation Coupled with Microarray |...Genomewide Identification of Protein Binding Locations Using Chromatin Immunoprecipitation Coupled with Microarray |...

ChIP-chip chromatin immunoprecipitation microarray RNA polymerase transcription factor transcription factor binding ... Ren B,d Dynlacht BD (2004) Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian ... Lee TI, Johnstone SE, Young RA (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat ... To better understand these interactions, researchers developed a method that couples chromatin immunoprecipitation with ...
more infohttps://link.springer.com/protocol/10.1007%2F978-1-59745-188-8_9

Difference between revisions of Chromatin Immunoprecipitation - OpenWetWareDifference between revisions of "Chromatin Immunoprecipitation" - OpenWetWare

Chromatin Immunoprecipitation determines the in vivo chromatin binding sites of a transcription factor or other protein of ... Retrieved from "https://openwetware.org/mediawiki/index.php?title=Chromatin_Immunoprecipitation&oldid=115673" ...
more infohttps://openwetware.org/wiki/?title=Chromatin_Immunoprecipitation&diff=115673&oldid=69675
  • It is essential that 5 mM Na butyrate is present in all solutions throughout chromatin isolation when using antibodies to acetylated histones to prevent deacetylation. (abcam.com)
  • Chromatin is isolated and antibodies to the antigen of interest are used to determine whether the target binds to a specific DNA sequence or to map the distribution across the genome (microarray or DNA sequencing). (abcam.com)
  • At BioLegend, we offer a wide-array of Go-ChIP-Grade™ antibodies and an enzymatic kit featuring a solid-state immunoprecipitation platform ideal for consistency between experiments. (biolegend.com)
  • Sigma's Imprint brand of antibodies are validated in ChIP application and lot tested each time for successful chromatin immunoprecipitation experiment. (sigmaaldrich.com)
  • This can be achieved by several methods including the use of knockout and knockdown cell lines, treatment of cells that alters target expression levels, relative expression of the target of interest (if it is differentially expressed), and immunoprecipitation-mass spectrometry (IP-MS). Invitrogen antibodies that have been verified for specificity by one of these techniques have an Advanced Verification badge on our website. (thermofisher.com)
  • The immunoprecipitated complexes (i.e., the bead-antibody-protein-target DNA sequence complex) are then collected and washed to remove non-specifically bound chromatin, the protein-DNA cross-link is reversed and proteins are removed by digestion with proteinase K. An epitope-tagged version of the protein of interest, or in vivo biotinylation can be used instead of antibodies to the native protein of interest. (wikipedia.org)
  • This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP-related methods in a variety of biological research areas. (springer.com)
  • Authoritative and practical, Chromatin Immunoprecipitation: Methods and Protocols features techniques, including bioinformatic analysis of ChIP data, will be of interest to a very broad research community in the fields of biochemistry, molecular biology, microbiology, and biomedicine. (springer.com)
  • Traditional immunoprecipitation (IP) uses agarose beads coated in protein A/G. Most of these IP protocols require more than three washing steps to eliminate background and non-specific binding. (genscript.com)
  • Enzymatic chromatin shearing does not require specialized equipment, is generally reproducible (although it requires optimization for cell type), and requires minimal hands-on time. (thermofisher.com)
  • 3. Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BO (2005) Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarray. (springer.com)
  • Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a particular protein of interest. (thermofisher.com)
  • Chromatin-domain scanning coupled with quantitative analysis is a powerful means of dissecting mechanisms by which signaling pathways target genes within a complex genome. (nih.gov)
  • To better understand these interactions, researchers developed a method that couples chromatin immunoprecipitation with microarrays (also known as ChIP-chip), which is capable of providing a whole-genome map of protein-DNA interactions. (springer.com)
  • The sonicated chromatin samples can be used to calculate the DNA concentration for subsequent IPs and measure DNA fragment size. (abcam.com)
  • In order to make ChIP efficient from lower cell numbers, some of the techniques include spiking of samples with chromatin from another source, or DNA amplification before downstream analysis. (news-medical.net)
  • Chromatin immunoprecipitation (ChIP) can be used as a tool to study protein:DNA complexes and identify protein-binding sites in the DNA. (biolegend.com)
  • Sometimes samples are small, cell types can be hard to come by or are difficult because they offer only a low chromatin yield. (news-medical.net)
  • The yield of chromatin (in µg) is given by: A 260 x dilution factor x volume x 50. (abcam.com)
  • Chromatin Immunoprecipitation (ChIP) can be technically challenging and yield results that are difficult to interpret. (activemotif.com)
  • Complete your experimental design with Active Motif's ChIP-IT ® Control Kits , qPCR Primer Sets and Ready-to-ChIP Chromatin to validate your results at every step. (activemotif.com)
  • Such interactions may result from biological functions, such as promoter-enhancer interactions, or from random polymer looping, where undirected physical motion of chromatin causes loci to collide. (wikipedia.org)
  • Orian, A. Chromatin profiling, DamID and the emerging landscape of gene expression. (nature.com)