Retain chromatin. Medical search. Frequent questions

Cytosine modifications directly affect the positioning of nucleosomes (the first level of chromatin organization into chromosome involving the DNA chain wound around a core of 8 histone proteins), and recruit chromatin-modifying complexes that modify histones. (i-sis.org.uk)
SMC3 is acetylated during S-phase to establish cohesiveness of chromatin-loaded cohesin, and in yeast, the class I histone deacetylase Hos1 deacetylates SMC3 during anaphase. (nih.gov)
Thus, unlike most genomic chromatin, histone synthesis and assembly are uncoupled from DNA replication at the kinetochore. (rupress.org)
A closely related debate around chromatin modifications is about causality: several histone PTMs correlate with specific transcriptional states, but in many cases they are not responsible for a transcriptional outcome but rather are a consequence of it [7] . (plos.org)
The histones and non-histone proteins of chromatin compact the DNA and govern its accessibility to enzymes during transcription, replication, repair and recombination. (biomedcentral.com)
These advances establish a third mechanism of chromatin reconfiguration, raising fundamental questions about the stability of nucleosomes in nonreplicative phases of the cell cycle and the cellular machinery responsible for incorporating histone variants into nucleosomes (Mizuguchi, 2004). (sdbonline.org)
Binding of sequence-specific transcription factors and associated chromatin-modifying enzymes can induce post-translational modification of histone tails and can facilitate nucleosome removal [ 3 - 5 ], which can turn functional sequences such as promoters and enhancers into active, nucleosome-depleted sites [ 2 ]. (biomedcentral.com)
Eukaryotic genomes are usually packed into nucleosomes, which comprise of 147 bp DNA wrapping around a histone octamer, forming the structural units of chromatin. (biomedcentral.com)

Native ChIP (NChIP) uses native chromatin sheared by micrococcal nuclease digestion. (wikipedia.org)
Generally, native chromatin is used as starting chromatin. (wikipedia.org)
Chromatrap has announced a new patented protocol that is able to simply, quickly and efficiently enrich transcription factors from Native Chromatin. (technologynetworks.com)
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)
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)
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (genomeweb.com)
These, however, are spaced 145 base-pairs apart and not 200 base-pairs apart as is found in native chromatin. (ox.ac.uk)

In eukaryotes, DNA is packed inside the cell nucleus in the form of chromatin, which consists of DNA, proteins such as histones, and RNA. (nature.com)
However, genes expressed early in development may preferentially retain histones. (i-sis.org.uk)
Post-translational modifications of histones represent an important mechanism modulating the accessibility of chromatin and contributing to the recruitment of other proteins to chromatin [ 2 ]. (biomedcentral.com)
These results describe a novel pathway for regulating transcription using variant histones to modulate chromatin structure (Santisteban, 2000). (sdbonline.org)
The DNA in all eukaryotic cells is packaged with histones to form chromatin. (biomedcentral.com)
The basic unit of chromatin in eukaryotes, the nucleosome, consists of 147 base pairs (bp) of DNA wrapped around an octamer of four core histones, comprising an H3-H4 tetramer and two H2A-H2B dimers. (biomedcentral.com)

Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. (wikipedia.org)
Briefly, the conventional method is as follows: DNA and associated proteins on chromatin in living cells or tissues are crosslinked (this step is omitted in Native ChIP). (wikipedia.org)
citation needed] Cross-linked ChIP is mainly suited for mapping the DNA target of transcription factors or other chromatin-associated proteins, and uses reversibly cross-linked chromatin as starting material. (wikipedia.org)
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)
It has been suggested, for example, that nuclear bodies, including those formed from RNA and RNA-binding proteins (RBPs), can displace transcriptionally inactive chromatin 18 . (nature.com)
As the active nuclear compartment contains high levels of RNA and RNA-binding proteins 1 , 5 , this provides a potential mechanism for the selective exclusion of inactive chromatin from the active compartment. (nature.com)
Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization. (ca.gov)
Molecular analysis suggested that Esc2p contributed to silencing in a manner similar to Sir1p and probably helped recruit or stabilize the other Sir proteins, while Htz1p present at HMR assembled a specialized chromatin structure necessary for silencing (Dhillon, 2000). (sdbonline.org)
These nucleoids contain all the nuclear RNA and DNA but few of the proteins characteristic of chromatin. (ox.ac.uk)

Chromatin Immunoprecipitation sequencing, also known as ChIP-seq, is an experimental technique used to identify transcription factor binding events throughout an entire genome. (wikipedia.org)
Immunoprecipitation-enrichment of chromatin fragments were defined and the bound DNA were purified using phenol:chloroform extractions. (nih.gov)
SMC3 with retained acetylation is loaded onto chromatin, and chromatin immunoprecipitation sequencing analysis demonstrates decreased occupancy of cohesin localization sites that results in a consistent pattern of altered transcription seen in CdLS cell lines with either NIPBL or HDAC8 mutations. (nih.gov)
RNA sequencing, shRNA knockdown, and chromatin Immunoprecipitation (ChIP) sequencing were performed to detect the target genes of ginsenoside Rg1-CNV that regulate angiogenesis. (cbinsights.com)

Here, we examined long-range chromatin interactions genome-wide in mouse embryonic stem cells (ESCs), iPSCs, and fibroblasts and uncovered a pluripotency-specific genome organization that is gradually reestablished during reprogramming. (ca.gov)
Our data confirm that long-range chromatin interactions are primarily associated with the spatial segregation of open and closed chromatin, defining overall chromosome conformation. (ca.gov)

In summary, the work descried in this thesis uncovers a model where replication-timing is regulated at the unit of chromatin structure called TADs, which are generally stable across cell-types, but the compartment that they reside in corresponds to the time of their replication. (fsu.edu)

NcRNAs such as those involved in RNA interference can be independently inherited, and can also direct chromatin modification and DNA methylation see [7, 8] RNA Inheritance of Acquired Characters , and Nucleic Acid Invaders from Food Confirmed , SiS 63). (i-sis.org.uk)
Hallmarks of naive pluripotency include driving Oct4 (also known as Pou5f1) transcription by its distal enhancer, retaining a pre-inactivation X chromosome state, global reduction in DNA methylation and in H3K27me3 repressive chromatin mark deposition on developmental regulatory gene promoters.Upon withdrawal of 2i/LIF, naïve mouse ES cells can drift towards a primed pluripotent state resembling that of the post-implantation epiblast. (nih.gov)
We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. (elifesciences.org)

Regulator of chromosome structure during mitosis required for condensin-depleted chromosomes to retain their compact architecture through anaphase. (antikoerper-online.de)
Loss of heterozygosity and mutation of the retained allele of a putative tumor suppressor gene SMARCB1 (INI1) located on chromosome 22q11.2 is the defining molecular characteristic of AT/RT. (medscape.com)
Finally, replication timing and its association with chromatin structure are highly conserved and are observed even at the single chromosome level. (fsu.edu)

We investigated the presence of transposable elements (TEs) in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses (PERVs) exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements. (biomedcentral.com)

The team also discovered that epithelial stem cells retain an epigenetic memory of their inflammatory encounters. (rockefeller.edu)
Uncoupling DNA replication from CENP-A synthesis suggests that regulated chromatin assembly or remodeling could play a role in epigenetic centromere propagation. (rupress.org)
Here we will describe our current knowledge of the biological processes and mechanisms that can be considered bona fide epigenetic phenomena in Plasmodium biology, and attempt to distinguish them from those unlikely to involve epigenetic flow of information, even if chromatin changes occur. (plos.org)
We will not judge the use of the term epigenetic in different situations, but will rather attempt to clarify the roles of chromatin-based modifications in the different processes. (plos.org)
It is presumed that Dri, like Osa, which is a member of the Trithorax Group of genes implicated in the modification of chromatin structures required for epigenetic regulation (Vazquez, 1999), is acting to establish stable chromatin structures. (sdbonline.org)

Specifically, shortening the Epl1 linker causes severe growth defects and reduced H4 acetylation levels over broad chromatin regions in fission yeast. (nature.com)
Loss of HDAC8 activity results in increased SMC3 acetylation and inefficient dissolution of the 'used' cohesin complex released from chromatin in both prophase and anaphase. (nih.gov)
Acetylation of H4-K16 neutralizes its basic charge and inhibits compaction of the chromatin. (biomedcentral.com)

By reconstituting the S. Cerevisiae replication machinery at the single complex level we are able to study critical transient intermediates formed during chromatin replication. (mpg.de)
Consistent with this, the binary nuclear compartments defined by chromatin spatial proximity maps, align precisely with the replication-timing program. (fsu.edu)
Genome-wide analysis of replication domains revealed that they are indeed stable structural units corresponding to Topologically-Associating Domains (TADs) defined by Hi-C. Next we showed that the interphase chromatin structure consisting of TADs and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program. (fsu.edu)
In G2 phase, the replication timing-program is lost while inter-phase chromatin structure acquired in early G1 was retained. (fsu.edu)
This shows that interphase chromatin structure is not sufficient to dictate RT and lead us to hypothesize that the chromatin structure set-up during early G1 may act as a scaffold to seed the assembly of some factor capable of setting replication initiation thresholds. (fsu.edu)
Interphase chromatin structure is established along with the establishment of RT and may act as scaffold for replication regulation factors like Rif1. (fsu.edu)

Nuclear chromatin retains basophilia - distinguishing them from yellow fever. (cdc.gov)
The type Aund* presents irregular nucleus, eccentric and decondensed chromatin, and nuages near the nuclear envelope and/or associated to mitochondria. (usp.br)
In some processes, chromatin modifications carry heritable regulatory information that is transmitted from mother to daughter cells, whereas in other cases, they are implicated in the execution of the information contained in the DNA sequence, or occur as a consequence of dynamic nuclear processes such as transcription. (plos.org)

It is now known that there are multiple levels of chromatin organization in the nucleus of cells, including chromosomal territories, compartments, domains, and looping structures that coordinate regulatory interactions. (arimagenomics.com)
One might expect that the position of centromeres and telomeres could influence the organization of chromatin and thereby regulate gene expression. (genengnews.com)
To their surprise, they found little difference in gene expression, indicating the robustness of chromatin organization regardless of the type of centromere distribution. (genengnews.com)
Thus, it is likely that CTCF plays a conserved role in chromatin domain organization. (biomedcentral.com)

Chromosomal centromeres attached to microtubules and pulled to opposite poles of the cell during mitosis are retained in the chromatin structure even when the cell is done dividing. (genengnews.com)
Experiments show CTCF partially remains associated with chromatin during mitosis. (biomedcentral.com)

Triton X-100-treated nuclei retain the majority of these binding sites. (rupress.org)
CRBP is also capable of delivering retinol specifically to isolated chromatin with no apparent loss of binding sites, as compared to whole nuclei. (rupress.org)
When HeLa cells are lysed in solutions containing a non-ionic detergent and 2 M-NaCl, structures are released that retain many of the morphological features of nuclei. (ox.ac.uk)

First, sequence: because the 3D genome is studied using next-generation sequencing, sequence information is retained and can be combined with chromatin conformation. (arimagenomics.com)
The work should be of interest to colleagues in the fields of evolutionary biology, chromatin biology and genome biology. (elifesciences.org)
Many processes in parasite biology involve changes at the chromatin level, including regulation of transcription along a complex life cycle, delimitation of functional elements in the genome, and antigenic variation. (plos.org)
However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs. (biomedcentral.com)
Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. (biomedcentral.com)
Our results revealed different functions of dCTCF during the cell cycle and suggested that dCTCF might contribute to the establishment of the three-dimensional architecture of the Drosophila genome by maintaining local chromatin compartments throughout the whole cell cycle. (biomedcentral.com)

The DNA-protein complexes (chromatin-protein) are then sheared into ~500 bp DNA fragments by sonication or nuclease digestion. (wikipedia.org)
Then the cross-linked chromatin is usually sheared by sonication, providing fragments of 300 - 1000 base pairs (bp) in length. (wikipedia.org)
Chromatin fragments of 400 - 500bp have proven to be suitable for ChIP assays as they cover two to three nucleosomes. (wikipedia.org)
Then the chromatin is sheared by micrococcal nuclease digestion, which cuts DNA at the length of the linker, leaving nucleosomes intact and providing DNA fragments of one nucleosome (200bp) to five nucleosomes (1000bp) in length. (wikipedia.org)

We used integrative three-dimensional (3D) spatial genomics to identify the chromatin interaction targets of 45 prostate cancer risk alleles, 31 of which were associated with the transcriptional regulation of target genes in 565 localized prostate tumors. (stanford.edu)
We demonstrate that LRH-1-mediated p21 regulation in HCT116 cells does not involve altered p53 protein or phosphorylation, and we show that LRH-1 inhibits p53 recruitment to the p21 promoter, likely through a mechanism involving chromatin remodelling. (dundee.ac.uk)

Enhancers promote transcription by providing a binding platform for transcription factors [ 12 ] that can act on (distal) target genes through three-dimensional chromatin looping [ 13 - 15 ]. (biomedcentral.com)

Geminin also inhibits the chromatin remodeling things Brahma and Brg1 to retain an undifferentiated state and acts being a transcription repressor or corepressor. (gabasignaling.com)

Avian erythrocytes differ from most vertebrates in retaining the nucleus at maturity. (cellimagelibrary.org)
In the Rabl configuration, the free ends of the chromatids-another region of condensed chromatin called telomeres-are clustered at the opposite end of the nucleus, with respect to the centromeres. (genengnews.com)
The type Aund presents spherical central nucleus, with slightly condensed chromatin and nuages . (usp.br)
Thus, CRBP delivers retinol to the interior of the nucleus, to specific binding sites which are primarily, if not solely, on the chromatin. (rupress.org)
We demonstrated that UPF1 can be localized to the nucleus and predominantly associated with the chromatin. (molcells.org)

Depletion of MERVL transcripts results in embryonic lethality with profound defects in development and is associated with dysregulation of MERVL including their adjacent transcripts, and retaining two-cell-like transcriptome and chromatin state (Fig. 6i). (evolutionnews.org)
Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. (genomeweb.com)

A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. (biomedcentral.com)
Thus, we propose that cytoplasmic UPF1-centric RNA surveillance mechanism could be extended further up to the chromatin-associated UPF1 and co-transcriptional RNA surveillance. (molcells.org)

Genomic DNA in eukaryotes is packaged into chromatin. (biomedcentral.com)
However, the chromatin landscape of pig genomic TEs has not been explored yet. (biomedcentral.com)

Consistently, among 13 drugs targeting chromatin modifiers, EHMT2 inhibitors were highly effective in reducing ERMS cell viability. (elifesciences.org)

Nucleolar nucleolin has a role in chromatin remodeling and gene transcription, and interestingly enough, Wnt pathway genes were differentially expressed in the RNA-seq data following iSN04 suppression. (shinshu-u.ac.jp)
identify translocation recombinants that retained Lr54/Yr37 and to characterize these using molecular markers (ii) Test for the presence of genes for photoperiod insensitivity (Ppd) and reduced height (Rht) believed to be associated with the translocation (iii) Develop a SCAR marker for the most useful recombinant that could be recovered. (sun.ac.za)
Recombinant #74 retained both Lr54 and Yr37 and the two genes therefore occur towards the centromere. (sun.ac.za)

Thus, euchromatin and heterochromatin each contains components that antagonize switching to the opposite chromatin state (Meneghini, 2003). (sdbonline.org)

CRBP again does not remain bound after transferring retinol to the chromatin binding sites. (rupress.org)

Mutation in the Drosophila retained/dead ringer ( retn ) gene leads to female behavioral defects and alters a limited set of neurons in the CNS. (sdbonline.org)

Our study suggests an important role for LRH-1 in the growth of CRC cells that retain wild-type p53. (dundee.ac.uk)

Her team investigates how stem cells establish unique chromatin landscapes and programs of gene expression, and how this shifts in response to changes in their local environment. (rockefeller.edu)

The novel naive pluripotent cells validated herein retain molecular characteristics and functional properties that are highly similar to mouse naive ES cells, and distinct from conventional primed human pluripotent cells. (nih.gov)

These findings define a previously unknown role for the adenosine triphosphate-dependent chromatin remodeling machinery (Mizuguchi, 2004). (sdbonline.org)
These findings suggest a novel role of UPF1 in transcription elongation-coupled RNA machinery in the chromatin, as well as in translation-coupled NMD in the cytoplasm. (molcells.org)

There are mainly two types of ChIP, primarily differing in the starting chromatin preparation. (wikipedia.org)

Unlike other approaches the Chromatrap® N-ChIP kit eliminates using agarose or magnetic beads resulting in more sample being retained during the extraction process. (technologynetworks.com)

Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions, as well as regulatory variants of loci associated with complex traits in pigs. (biomedcentral.com)

In the last few years, chromatin modifications have been extensively studied in the malaria parasite Plasmodium falciparum (for recent reviews, see [9] - [13] ). (plos.org)

It is possible that CTCF, through using different combinations of zinc fingers, interacting with different protein partners, and the last but not the least, employing various post-translational modifications, could mediate extensive intra- and inter-chromatin interactions [ 7 , 8 ]. (biomedcentral.com)

The de-coupling of chromatin structure and RT could then be due to the removal of this factor during S-phase. (fsu.edu)

Alternatively, chromatin-antibody complexes can be selectively retained and eluted by inert polymer discs. (wikipedia.org)

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)

Over the past decades, several chromatin accessibility profiling methods including DNase I hypersensitive site sequencing (DNase-seq), micrococcal nuclease sequencing (MNase-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) have been developed. (biomedcentral.com)

Mild formaldehyde crosslinking followed by nuclease digestion has been used to shear the chromatin. (wikipedia.org)

Embryonic stem cells (ESCs), on the other hand, have not committed to a particular cell fate and retain the ability to become one of the 200-odd types of specialized cell. (ca.gov)
Four chromatin marks H3K4me1, H3K4me3, H3K27ac and H3K27me3 were measured in 5 cell lines: C1, WIBR3, LIS2 and WIS2 (naïve and conventional/primed stem cells), and BGO1 (only naïve stem cells). (nih.gov)
Additionally, by the BrdU incorporation and retention technique, we found the possible candidates to spermatogonial stem cells, called "labeling-retaining cells", since these cells have retained BrdU over the entire study period (21 days), showing a long cell cycle, a stem cells characteristic. (usp.br)

Germ cell chromatin is vastly different from that of other cells. (i-sis.org.uk)
Chromosomes must be folded and compacted in an orderly fashion to fit inside cells but retain dynamic flexibility to allow for rapid information access. (mpg.de)
Adicionalmente, de acordo com a técnica de incorporação e retenção de BrdU foi possível analisar a existência de possíveis candidatas às espermatogônias-tronco, chamadas de labeling-retaining cells, visto que estas células retiveram BrdU ao longo de todo período avaliado, demonstrando um longo ciclo celular, característica esta de célula-tronco. (usp.br)

Chromosomes are structured such that domains with a similar chromatin signature cluster spatially, a phenomenon first appreciated by traditional microscopy studies. (biomedcentral.com)

The first uses reversibly cross-linked chromatin sheared by sonication called cross-linked ChIP (XChIP). (wikipedia.org)

We show that accumulation of RNA induces formation of transcription pockets which displace transcriptionally inactive chromatin. (nature.com)

Anatomy25

Organisms5

Chemicals and Drugs75

Analytical, Diagnostic and Therapeutic Techniques and Equipment17

Phenomena and Processes67

Information Science3

Histone8

Native chromatin8

Histones6

Proteins9

Immunoprecipitation4

Long-range chromatin2

Unit of chromatin1

Methylation3

Chromosome3

Open chromatin1

Epigenetic5

Acetylation3

Replication6

Nuclear3

Organization4

Mitosis2

Nuclei3

Genome6

Fragments4

Regulation2

Transcription factors1

Inhibits1

Nucleus5

Transcripts2

Mechanism2

Genomic2

Modifiers1

Genes3

Euchromatin1

Bound1

Drosophila1

Suggests1

Establish1

Molecular1

Machinery2

Primarily1

Magnetic beads1

Variants1

Extensively1

Interactions1

Structure1

Complexes1

Protein1

Accessibility1

Nuclease1

Stem cells3

Cells3

Chromosomes1

ChIP1

Inactive1