AssaysChIPAntibodyMicroarrayNative chromatinProteinHistonesProteinsGenesMassively parallelAssayReagentsTranscriptional regulationHomologousPromotersTargetsGenome-wideDemonstratesBindsCellsFragmentationQPCRExperimentsGene transcriptionLeucine zipperReporterCombineRegulatoryEnhancerSiteSpecificArabidopsisMagnitudeExpressionAnalysisHumanGeneticStudies
Assays4
- Chromatin immunoprecipitation assays identified SOX2-binding sites on COL1A1 and COL1A2, indicating SOX2 as a transcription factor in collagen synthesis. (cdc.gov)
- Mechanistically, chromatin immunoprecipitation (ChIP) assays indicated that the transcription factor TCF4 directly binds to the promoter region of ERLR and promotes its transcription. (stanford.edu)
- We demonstrate by electromobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) that HNF1 binds to this element both in vitro and in vivo. (duke.edu)
- The combination of careful expression profiling, electromobility shift assays, reporter experiments, and chromatin immunoprecipitation demonstrates that, among 16 different KLF proteins tested, KLF11 is the most reliable activator of this site. (elsevierpure.com)
ChIP31
- Huh7 cells that overexpress USF1 were used with whole transcriptome profiling through RNA sequencing and chromatin immunoprecipitation (ChIP) sequencing methods to investigate the downstream targets of USF1. (spandidos-publications.com)
- Chromatin immunoprecipitation, or ChIP, is an antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets. (cellsignal.com)
- ChIP utilizes antibodies that selectively recognize and bind proteins, including histones, histone modifications, transcription factors, and cofactors, to provide information about chromatin states and gene transcription. (cellsignal.com)
- ChIP can be used to answer a multitude of scientific questions involving the interaction of proteins and chromatin. (cellsignal.com)
- The principle behind ChIP is relatively straightforward and relies on the use of an antibody to isolate, or precipitate, a certain protein, histone, transcription factor, or cofactor and its bound chromatin from a protein mixture that was extracted from cells or tissues. (cellsignal.com)
- In N-ChIP, no fixing agent is used to crosslink proteins to the chromatin. (cellsignal.com)
- In X-ChIP, chemical fixatives such as formaldehyde are used to crosslink the protein of interest to the DNA and fragmentation of chromatin is achieved through sonication or nuclease digestion. (cellsignal.com)
- X-ChIP also minimizes the chances of chromatin protein loss during extraction, allowing for the detection of transient protein interactions. (cellsignal.com)
- To date, the most widely used and powerful method to identify regions of the genome associated with specific proteins is the Chromatin Immunoprecipitation (ChIP) assay. (thermofisher.com)
- The ChIP assay has been widely used to study both histones and non-histone proteins, such as transcription factors, within the context of the cell. (thermofisher.com)
- This kit provides a faster and more reproducible solution for Chromatin Immunoprecipitation (ChIP) and includes all reagents needed to perform ChIP with an antibody of interest. (thermofisher.com)
- A key aspect for a successful ChIP is having antibodies that recognize the target protein in the context of chromatin. (thermofisher.com)
- Sheared chromatin from MCF7 cells was prepared from 1 million cells in 50 μl lysis buffer and diluted to indicated number of cells per ChIP according to the MAGnify™ ChIP protocol. (thermofisher.com)
- Sheared chromatin from 293Gt cells was prepared and 50,000 cells used for ChIP (MAGnify™ ChIP) and 1 million cells per ChIP used for the conventional ChIP protocol. (thermofisher.com)
- Transcription factor (TF) genes were modified endogenously to include epitope tags for identification of TF protein binding sites by Chromatin Immunoprecipitation (ChIP), followed by high throughput sequencing. (oregonstate.edu)
- Native Chromatin Immunoprecipitation (N-ChIP) is an alternative to traditional cross-linked (X-ChIP), which removes the need for fixing cells with formaldehyde prior to extraction. (technologynetworks.com)
- Native ChIP is the technique of choice for the study of histone modifiers and certain abundant transcription factors that are likely to be bound to DNA. (technologynetworks.com)
- In addition Chromatrap® N-ChIP technology increases the affinity of antibody binding to antigens on Native chromatin as peptides are more accessible. (technologynetworks.com)
- As a result the Chromatrap® N-ChIP kit sets a new standard for enriching transcription factors from Native Chromatin. (technologynetworks.com)
- Use of chromatin immunoprecipitation (ChIP) to detect transcription factor binding to highly homologous promoters in chromatin isolated from unstimulated and activated primary human B cells. (southernbiotech.com)
- Chromatin immunoprecipitation coupled with hybridization to a tiling array (ChIP-chip) is a cost-effective and routinely used method to identify protein-DNA interactions or chromatin/histone modifications. (biomedcentral.com)
- Chromatin immunoprecipitation coupled with hybridization to a tiling array (ChIP-chip) is a cost-effective and routinely used method for identifying target genes of transcription factors, for analyzing histone modifications or for studying the methylome on a genome-wide scale [ 1 ]. (biomedcentral.com)
- In a ChIP-chip experiment, a chromatin immunoprecipitation sample (IP) is compared against a reference sample of genomic DNA (Input). (biomedcentral.com)
- iDeal ChIP-seq kit for Transcription Factors to my shopping cart. (diagenode.com)
- To solve this issue, we used the Diagenode ChIPmentation solution composed of iDeal ChIP-seq Kit for Transcription Factor, TAG Kit for ChIPmentation, and 24 SI for ChIPmentation. (diagenode.com)
- Chromatin preparation and immunoprecipitation have been performed on hiPSCs (human induced Pluripotent Stem Cells) overexpressing Gata6 using the iDeal ChIP-seq kit for TFs (Cat. (diagenode.com)
- A) Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors and the Diagenode ChIP-seq-grade CTCF antibody. (diagenode.com)
- Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). The IP'd DNA was subsequently analysed on an Illumina ® Genome Analyzer. (diagenode.com)
- Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), initially introduced more than a decade ago, is widely used by the scientific community to detect protein/DNA binding and histone modifications across the genome. (biomedcentral.com)
- One widely used technology is chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). (biomedcentral.com)
- We performed chromatin immunoprecipitation sequencing (ChIP-seq) using a histone 3 lysine 9 acetylation (H3K9ac) mark in peripheral blood mononuclear cells from patients with atherosclerosis with T2D (n = 8) or without T2D (ND, n = 10). (lu.se)
Antibody4
- Key elements of a conventional protocol use an overnight immunoprecipitation step of antibody and chromatin, followed by enrichment with Protein A sepharose beads and extensive washes with buffers containing variable salt concentrations. (thermofisher.com)
- It uses discs of an inert, porous, polymer to which Protein A or Protein G has been covalently attached to maximize the capture efficiency of the target chromatin/antibody complex. (technologynetworks.com)
- Chromatin from 2,000,000 cells was used for the immunoprecipitation in combination with either anti-GATA6 antibody. (diagenode.com)
- In the experimental design, for example, the quality of the experiment is predetermined by antibody and immunoprecipitation specificity. (biomedcentral.com)
Microarray1
- In this study, we found that ERLR is upregulated in RPE cells stimulated with transforming growth factor (TGF)-β1 as detected by lncRNA microarray and RT-PCR. (stanford.edu)
Native chromatin2
- Instead, native chromatin is isolated from cell nuclei that are digested with a nuclease. (cellsignal.com)
- Chromatrap has announced a new patented protocol that is able to simply, quickly and efficiently enrich transcription factors from Native Chromatin. (technologynetworks.com)
Protein11
- Chromatin immunoprecipitation sequencing in T helper 17 (T(H)17) cells reveals that IRF4 targets sequences enriched for activating protein 1 (AP-1)-IRF composite elements (AICEs) that are co-bound by BATF, an AP-1 factor required for T(H)17, B, and dendritic cell differentiation. (nih.gov)
- In addition, loss of protein binding during the chromatin digestion and immunoprecipitation steps may bias the data or impede proper analyses. (cellsignal.com)
- Site-Directed Cleavage of DNA by Protein-Fe(II) EDTA Conjugates within Model Chromatin Complexes David R. Chafin and Jeffrey J. Hayes 11. (nhbs.com)
- Importantly, antibodies that recognize a protein of interest can be used to determine the relative association of that antigen in the context of chromatin at one or more loci in the genome. (thermofisher.com)
- Here, we develop a high-throughput indexed Chromatin ImmunoPrecipitation (iChIP) method coupled to massively parallel sequencing to systematically map protein-DNA interactions. (nih.gov)
- To test our hypothesis that histone H4R3 and H3R17 methylation regulates ferritin transcription, H4R3 and H3R17 protein arginine (R) methyltransferases 1 and 4 (PRMT1 and PRMT4) were investigated. (embl.de)
- The assembly of PRMT6 protein network allowed us to formulate functional hypotheses which led to the discovery of new molecular partners for the architectural transcription factor HMGA1a, a known substrate for PRMT6, and to provide evidences for a modulatory role of HMGA1a on the methyltransferase activity of PRMT6. (embl.de)
- Five friends of methylated chromatin target of protein-arginine-methyltransferase[prmt]-1 (chtop), a complex linking arginine methylation to desumoylation. (embl.de)
- Chromatin target of Prmt1 (Chtop) is a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation. (embl.de)
- Prior to immunoprecipitation, the DNA-protein complexes undergo fragmentation. (biomedcentral.com)
- Analysis of site mutants showed that the region targeted by the polymerase protein contained the signal transducer and activator of transcription (Stat) binding site. (edu.au)
Histones4
- Once the chromatin immunoprecipitation itself is complete, several downstream analyses can be conducted on the purified chromatin and the associated proteins, histones, transcription factors, and cofactors. (cellsignal.com)
- The mechanism of epigenetic regulation involves the CpG site methylation of promoter regions and the modification of DNA and histones by altering chromatin structure ( 9 - 11 ). (spandidos-publications.com)
- Transcription factors and other DNA-binding proteins have a weaker affinity than histones, which generally are tightly associated within the chromatin complex. (thermofisher.com)
- Arsenic exposure activated ferritin transcription via the ARE concomitant with increased methylation of histones H4Arg3 (H4R3) and H3Arg17 (H3R17). (embl.de)
Proteins2
- DNA meth-ylation represses transcription by interfering with transcription factor binding and indirectly by recruiting methyl-CpG-binding proteins and reducing chromatin remodeling activities ( 12 ). (spandidos-publications.com)
- To avoid dissociation of non-histone proteins from the chromatin binding site, it is necessary to incorporate a cross-linking step. (thermofisher.com)
Genes6
- Functionally, the TFs are organized in a hierarchy of different types: Cell differentiation factors bind most of the genes and remain largely unchanged during the stimulation. (nih.gov)
- We used RNA sequencing coupled with chromatin immunoprecipitation sequencing to analyze primed microglial inflammatory gene expression and modifications to histone H3 lysine 4 trimethylation (H3K4me3) at the promoters of primed genes. (frontiersin.org)
- We found that HDAC7 specifically interacted with the transcription factor MEF2C in pre-B cells and was recruited to MEF2 binding sites located at the promoters of genes critical for macrophage function. (eur.nl)
- Antioxidant genes such as ferritin are transcriptionally activated in oxidative stress via the antioxidant responsive element (ARE), to which nuclear factor-E2-related factor 2 (Nrf2) binds and activates transcription. (embl.de)
- Here we show through systematic epigenetic studies that the histone acetyltransferase p300/CBP-associated factor (PCAF) promotes acetylation of histone 3 Lys 9 at the promoters of established key regeneration-associated genes following a peripheral but not a central axonal injury. (nature.com)
- We found that p300/CBP-associated factor (PCAF)-dependent acetylation of histone 3 lysine 9 (H3K9ac), paralleled by a reduction in methylation of H3K9 (H3K9me2), occurred at the promoters of select genes only after PNS axonal injury. (nature.com)
Massively parallel1
- Here we combine chromatin immunoprecipitation with a massively parallel reporter assay to identify functional enhancers in human embryonic stem cells (hESCs) genome-wide in a quantitative unbiased manner. (biorxiv.org)
Assay3
- Ketamine treatment increased the binding of NF‑κB and permissive histone H3 lysine‑4 (H3K4)m3, but caused a decrease in the repressive histone H3K27m3 and H3K36m3 on the COX‑2 promoter ranging from ‑1,522 to ‑1,331 bp as determined by a chromatin immunoprecipitation assay. (spandidos-publications.com)
- Moreover, in the ketamine group, the level of Ten‑Eleven‑Translocation methylcytosine dioxygenase for demethylation as determined by reverse transcription‑quantitative PCR assay was increased in comparison with the control group, but that was not the case for the level of DNA methyltransferases for methylation. (spandidos-publications.com)
- To validate the approach, nine predicted targets of E2F1 in HeLa cells were tested using chromatin immunoprecipitation assay. (biomedcentral.com)
Reagents2
- Addressing topics such as chromatin immunoprecipitation, topological studies, photocrosslinking, FRET and imaging techniques, the volume fully updates and expands upon the successful previous editions.Written in the convenient and informative 'Methods in Molecular Biology' series format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. (nhbs.com)
- This complete solution contains all buffers and reagents for cell lysis, chromatin shearing, immunoprecipitation, and DNA purification. (diagenode.com)
Transcriptional regulation2
- The present study investigated the methylation of CpG sites in the cyclooxygenase (COX)‑2 promoter via nuclear factor (NF)‑κB transcriptional regulation and elucidated its effect on the COX‑2 transcriptional expression in a ketamine‑induced ulcerative cystitis (KIC) animal model. (spandidos-publications.com)
- A Swiss team takes a look at transcription factor dynamics and transcriptional regulation in various mouse tissue types over time to untangle circadian clock features. (genomeweb.com)
Homologous1
- Results: Our results indicated higher expression levels of the Pdr1 transcriptional factor, compared to its homologous Pdr3 after treatment with menadione. (srce.hr)
Promoters1
Targets5
- Upstream transcription factor 1 (USF1) is a canonical transcription factor (TF) and is associated with the pathogenesis of several cancers, but its biological functions and molecular targets in HCC remain unclear. (spandidos-publications.com)
- Reverse transcription‑quantitative PCR was then used to validate the downstream targets. (spandidos-publications.com)
- As a result, context-specific roles of transcription factors as well as their functional targets are readily explored. (biomedcentral.com)
- REGNET is a useful tool for exploring the ternary relationships among the transcription factors, their functional targets and the corresponding cell conditions. (biomedcentral.com)
- One main reason for the difficulty is the dynamic nature of the networks: Transcription factors (TFs) not only regulate different targets depending on the cell conditions, but their effects on these targets can also change. (biomedcentral.com)
Genome-wide1
- We apply iChIP to reconstruct the physical regulatory landscape of a mammalian cell, by building genome-wide binding maps for 29 transcription factors (TFs) and chromatin marks at four time points following stimulation of primary dendritic cells (DCs) with pathogen components. (nih.gov)
Demonstrates1
- Our data demonstrates that transcription factors vary substantially in their binding dynamics, genomic localization, number of binding events, and degree of interaction with other factors. (nih.gov)
Binds1
- For instance, a previous study by the authors validated that USF1 binds to the core promoter of APOBEC3G and increases its transcription level in hepatocytes ( 7 ). (spandidos-publications.com)
Cells3
- Calycosin dose- and time-dependently inhibited proliferation, migration, and invasion by T47D and MCF-7 breast cancer cells by downregulating basic leucine zipper ATF-like transcription factor expression. (news-medical.net)
- Stromal endothelial cells establish a bidirectional crosstalk with chronic lymphocytic leukemia cells through the TNF-related factors BAFF, APRIL, and CD40L. (southernbiotech.com)
- To gain insight into the molecular mechanisms mediating HDAC7 repression in pre-B cells, we undertook co-immunoprecipitation and chromatin immunoprecipitation experimental approaches. (eur.nl)
Fragmentation1
- However, due to the non-uniform nature of the chromatin structure (DNA), some regions are more densely packed (heterochromatin) than others and are thus more resistant to fragmentation. (biomedcentral.com)
QPCR1
- Additionally, the regulation of the DNA binding of the transcriptional activators after stimulation is quantified using chromatin immunoprecipitation, employing epitope-tagged factors and real-time qPCR. (srce.hr)
Experiments1
- Together with transcription factor binding site information, chromosome conformation capture sequencing, and/or DNase-seq experiments to explore chromatin accessibility, the transcriptomic data provided clues to the regulatory features such as chromatin folding that mediate tissue-specific circadian rhythms. (genomeweb.com)
Gene transcription1
- however, its role in antioxidant gene transcription remains elusive. (embl.de)
Leucine zipper1
- Upstream transcription factor (USF) 1 belongs to the basic helix-loop-helix leucine zipper family and serves as a cellular transcription factor (TF). (spandidos-publications.com)
Reporter1
- Transfection of promoter-reporter constructs demonstrated that the element displays classical tissue-specific enhancer properties and can independently recruit factors necessary for transcription initiation. (duke.edu)
Combine1
- Using a composite gene-set analysis method, we combine the information of transcription factor binding sites, Gene Ontology or pathway gene sets and gene expression fold-change profiles for a variety of cell conditions. (biomedcentral.com)
Regulatory6
- The proximal promoter region (upstream of the core-promoter region) contains the cis-regulatory elements of most of the transcription factors (TFs). (wikipedia.org)
- Interferon regulatory factor 4 (IRF4) and IRF8 regulate B, T, macrophage, and dendritic cell differentiation. (nih.gov)
- This genomic regulatory element and cognate factors appear to have evolved to integrate diverse immunomodulatory signals. (nih.gov)
- Here, we confirmed that SISTER OF TM3 (STM3), a homolog of Arabidopsis SOC1, is a major positive regulatory factor of tomato inflorescence architecture by map-based cloning. (nature.com)
- My research involves identifying gene regulatory elements across the genome to help us understand how chromatin structure dictates cell function and fate. (duke.edu)
- In occurs through the inhibition of DNA binding of cognate cis- hematopoiesis there exist several lineage branch points with regulatory motif while in the other case DNA binding is unaffected identified key transcription factors and external signals [3-5]. (lu.se)
Enhancer4
- Researchers from the University of Texas Southwestern Medical Center, Baylor College of Medicine, and elsewhere explore enhancer patterns and related expression activity in breast cancer cell lines, using a combination of RNA sequencing, global run-on sequencing, and chromatin immunoprecipitation sequencing. (genomeweb.com)
- With the help of a computational pipeline that brings together enhancer transcription magnitude, transcription factor expression, and telltale binding and chromatin motifs, the team profiled more than a dozen breast cancer cell lines from five molecular subtypes, uncovering enhancers and related transcription factors active within specific breast cancer subtypes. (genomeweb.com)
- Enhancer function requires transcription factor (TF) binding and correlates with histone modifications. (biorxiv.org)
- Lymphoid enhancer-binding factor 1 (LEF1), a member of the T-cell factor (TCF)/LEF1 family of high mobility transcription factors, is predominantly involved in the Wnt/β-catenin signaling pathway [ 12 ]. (biomedcentral.com)
Site4
- Determination of a Transcription Factor-Binding Site by Nuclease Protection Footprinting onto Southwestern Blots Athanasios G. Papavassiliou 15. (nhbs.com)
- In vitro DNase I footprinting analysis identified a protected region that corresponds to a conserved, predicted binding site for hepatocyte nuclear factor 1 (HNF1). (duke.edu)
- Thus, these data demonstrate an important role for KLF11 in the regulation of INS transcription via the novel c.-331 KLF site. (elsevierpure.com)
- Out of all the peaks, 753 domains near the transcription start site (TSS) were unique to T2D. (lu.se)
Specific4
- To date, the central role of specific transcription factors in positively regulating these distinct differentiation processes to acquire a B cell-specific genetic program is well established. (eur.nl)
- These findings uncover a nonredundant and stage-specific influence of T-box transcription factors in the antiviral NK cell response. (aai.org)
- We propose an approach for mining context-specific transcription networks from a large collection of gene expression fold-change profiles and composite gene-set information. (biomedcentral.com)
- We then collected all the significant patterns and constructed a database of context-specific transcription networks for human ( REGNET ). (biomedcentral.com)
Arabidopsis1
- We demonstrate improved performance of MultiChIPmixHMM compared to ChIPmix for the target identification of the chromatin mark H3K27me3 of the model plant Arabidopsis thaliana . (biomedcentral.com)
Magnitude1
- Together these factors determine the magnitude and timing of stimulus induced gene expression. (nih.gov)
Expression1
- Dynamic binding of transcription factors to DNA elements specifies gene expression and cell fate, in both normal physiology and disease. (nih.gov)
Analysis1
- Chromatin immunoprecipitation analysis showed that the IFN-induced DNA-binding activity of Stat1 was affected. (edu.au)
Human3
- We have generated fitCons scores for three human cell types based on public data from EN-CODE. (biorxiv.org)
- Krüppel-like transcription factors (KLFs) have elicited significant attention because of their regulation of essential biochemical pathways and, more recently, because of their fundamental role in the mechanisms of human diseases. (elsevierpure.com)
- The transcription factor 7-like 2 (TCF7L2) rs7903146, together with several human leukocyte antigen (HLA) variants, were among the domains with the most dramatic changes of H3K9ac enrichments. (lu.se)
Genetic1
- Biochemical studies suggest that in one case this transcription factors to implement particular genetic programs. (lu.se)
Studies1
- Mechanistic studies revealed sex-determining region Y-box 2 (SOX2), a self-renewal associated transcription factor, as a key driver of FSC acquisition and fibrogenesis. (cdc.gov)