Chromatin. Medical search. Frequent questions

For additional information, see Chromatin variant, Histone modifications in chromatin regulation and RNA polymerase control by chromatin structure. (wikipedia.org)
Therefore, proper establishment, regulation, and maintenance of the telomere chromatin structure are required for cell homeostasis. (nih.gov)
Here, we review the current knowledge on telomeric chromatin dynamics during cell division and early development in mammals, and how its proper regulation safeguards genome stability. (nih.gov)
Beyond being the product of gene expression, RNA can also influence the regulation of chromatin. (portlandpress.com)
in some cases, there are clear examples of direct RNA-mediated chromatin regulation mechanisms stemming from these interactions, while others have yet to be determined. (portlandpress.com)
Recent studies have highlighted examples of chromatin regulation via RNA matchmaking, a term we use broadly here to describe intermolecular base-pairing interactions between one RNA molecule and an RNA or DNA match. (portlandpress.com)
In addition to dissecting these mechanistic aspects of gene regulation, we are interested in the roles and physiological consequences of the products of genes regulated by chromatin proteins. (universiteitleiden.nl)
Chromatin regulation by Brg1 underlies heart muscle development and disease. (ca.gov)
The AICC has grown into a network of several hundred scientists with a common focus of investigating epigenetics and chromatin regulation in development and disease. (tcd.ie)
Recent studies have also implicated ISWI in the regulation of higher-order chromatin structure, but its role in this process remains poorly understood. (ca.gov)
Together, our dynamic studies provide a rich resource for investigating chromatin regulation, and identify a significant role for the "activating" mark H3K4me3 in gene repression. (harvard.edu)
However, it is now clear that chromatin structure is an integral part of the process of gene regulation. (nih.gov)
ChIP has also been used to determine the temporal regulation underlying the occupation of the particular chromatin locus by multiple proteins. (sigmaaldrich.com)
The hyperactive Tn5 transposase in the ATAC-seq method has been widely used to determine the open DNA regions and understand the overall epigenomic regulation in the chromatins of eukaryotic cells . (bvsalud.org)

Chromatin immunoprecipitation, or ChIP, is an antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets. (cellsignal.com)
In addition, loss of protein binding during the chromatin digestion and immunoprecipitation steps may bias the data or impede proper analyses. (cellsignal.com)
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)
I have assayed chromatin structure on all these levels using Chromatin Immunoprecipitation and Sucrose Gradient Sedimentation Analysis of Chromatin Fibre structure, partnered with oligonucleotide microarrays and Fluorescent In-Situ Hybridisation. (bl.uk)
EZ-Zyme™ Chromatin Prep Kit Contains proprietary reagents optimized for the enzymatic shearing of chromatin from mammalian cells at higher resolution than sonication for use in chromatin immunoprecipitation (ChIP) assays. (sigmaaldrich.com)
Chromatin Immunoprecipitation (ChIP) is a widely utilized experimental technique to monitor the association of proteins with specific DNA sequences. (sigmaaldrich.com)
The EZ-Zyme kit contains reagents optimized for generating enzymatically processed chromatin from mammalian cells for use in chromatin immunoprecipitation. (sigmaaldrich.com)
Today's epigenetics researchers need to squeeze every last bit of detail from the chromatin immunoprecipitation (ChIP) experiments they run. (epigenie.com)

In general, there are three levels of chromatin organization: DNA wraps around histone proteins, forming nucleosomes and the so-called beads on a string structure (euchromatin). (wikipedia.org)
Epigenetic modification of the structural proteins in chromatin via methylation and acetylation also alters local chromatin structure and therefore gene expression. (wikipedia.org)
Histone proteins are the basic packers and arrangers of chromatin and can be modified by various post-translational modifications to alter chromatin packing (histone modification). (wikipedia.org)
An imbalance of charge within the polymer causes electrostatic repulsion between neighboring chromatin regions that promote interactions with positively charged proteins, molecules, and cations. (wikipedia.org)
Polycomb-group proteins play a role in regulating genes through modulation of chromatin structure. (wikipedia.org)
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)
In N-ChIP, no fixing agent is used to crosslink proteins to the chromatin. (cellsignal.com)
This folded structure including the associated architectural proteins is referred to as chromatin. (universiteitleiden.nl)
Remodeling of chromatin is also mediated by chemical modifications of the DNA, the architectural proteins that shape it or physicochemical cues. (universiteitleiden.nl)
Models suggest that in bacteria and archaea there are direct effects of physicochemical factors such as osmolarity, temperature and pH on the action of chromatin proteins, in addition to indirect effects by modulating the expression ratios of different types of chromatin proteins. (universiteitleiden.nl)
Also, my group is investigating the (architectural) interplay between different types of chromatin proteins in vitro (Laurens et al. (universiteitleiden.nl)
As transcription of many genes and operons responds to environmental changes and as these are often mediated by chromatin proteins, it is expected that 1) the architectural interplay of such proteins and/or 2) their direct response to physicochemical changes determines loop formation and dissolution leading to altered transcription levels. (universiteitleiden.nl)
Chromatin is composed of nucleosomes-structures consisting of DNA wound around histone proteins. (jove.com)
Histone variants can replace the major histone proteins, leading to chromatin remodeling. (jove.com)

During interphase, the chromatin is structurally loose to allow access to RNA and DNA polymerases that transcribe and replicate the DNA. (wikipedia.org)
The local structure of chromatin during interphase depends on the specific genes present in the DNA. (wikipedia.org)
Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. (yeastgenome.org)
The SMC complex cohesin organizes interphase chromatin into loops by a process known as "loop extrusion," through which cohesin progressively reels in DNA and extrudes it as a loop. (aps.org)
Chromatin is structured on a number of different levels, by the covalent modification of nucleosomes, the arrangement of nucleosomes into chromatin fibres and the arrangement of chromatin fibres into higher order structures within the interphase nucleus. (bl.uk)

The Chromatin and Epigenetics Program currently encompasses 34 faculty members, and participation of several laboratories from the National Institute of Environmental Health. (unc.edu)
The chromatin and epigenetics program at UNC provides undergraduate, graduate students and postdoctoral fellows with an exceptional training environment to conduct their research studies. (unc.edu)
Monthly chromatin group meetings involving all of the epigenetics community at UNC and NIEHS allow trainees the opportunity to hear cutting edge science and to receive feedback on their research. (unc.edu)
This collective group has formed the Carolina Chromatin Consortium (C3), which focuses on the organization of team science groups and tracking key seminars and events related to epigenetics. (unc.edu)
Graduate students in the Chromatin and Epigenetics program will be able to earn a certificate in Chromatin and Epigenetics that can be an additional element of their doctoral training. (unc.edu)
This certificate can be earned through participation in the many ongoing events focused on epigenetics at UNC, presenting at an international meeting, and by taking an advanced topics course in chromatin and epigenetics where students participate in the analysis of recent impactful papers in the field. (unc.edu)
Cambridge Bioscience offers a collection of tools for chromatin analysis from leaders in the field of epigenetics. (bioscience.co.uk)
The topic of my lecture is skin epigenetics or the story on how chromatin regulators orchestrate skin functions. (hstalks.com)
Epigenetics & chromatin 2021 0 0. (cdc.gov)

Chromatin is a complex of DNA and protein found in eukaryotic cells. (wikipedia.org)
The primary protein components of chromatin are histones. (wikipedia.org)
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 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)
Here we show that Brg1, a chromatin-remodelling protein, has a critical role in regulating cardiac growth, differentiation and gene expression. (ca.gov)
Set1-dependent repression of ribosomal genes occurs via distinct pathways for ribosomal protein genes and ribosomal biogenesis genes, which can be separated based on genetic requirements for repression and based on chromatin changes during gene repression. (harvard.edu)
The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. (duke.edu)
When performing ChIP, chromatin from cells and tissues needs to be fragmented so that it becomes soluble and resolution can be achieved in detecting protein-DNA interaction at specific loci. (sigmaaldrich.com)
For example, foaming and overheating associated with sonication can result in protein denaturation or incomplete chromatin fragmentation. (sigmaaldrich.com)
The protein produced from this gene helps control the activity (expression) of other genes through a process called chromatin remodeling. (medlineplus.gov)
Although it is unclear how mutations in the ADNP gene affect ADNP protein function, researchers suggest that the mutations result in abnormal chromatin remodeling. (medlineplus.gov)

Our findings provide new insights and generate testable hypotheses about the roles of caRNAs in shaping chromatin organization. (biorxiv.org)
We have proposed that this specific organization could result from the constraints of accommodating the replication and transcription initiation processes at chromatin level, and reducing head-on collisions between the two machineries. (ens-lyon.fr)
Our findings has provided a new model of gene organization in the human genome, which integrates transcription, replication, and chromatin structure as coordinated determinants of genome architecture. (ens-lyon.fr)

WhichTF is dominant in your open chromatin data? (biorxiv.org)
In order to disentangle the cis - and trans -regulatory roles of caRNAs, we compared models with nascent transcripts, trans -located caRNAs, open chromatin data, or DNA sequence alone. (biorxiv.org)

ISWI regulates higher-order chromatin structure and histone H1 assembly in vivo. (ca.gov)
The expression of a dominant-negative form of ISWI leads to dramatic alterations in higher-order chromatin structure, including the apparent decondensation of both mitotic and polytene chromosomes. (ca.gov)

Here, using genome-scale biochemical reconstitution with approximately 300 replication origins, we screened 17 purified chromatin factors from budding yeast and found that the ORC established nucleosome depletion over replication origins and flanking nucleosome arrays by orchestrating the chromatin remodellers INO80, ISW1a, ISW2 and Chd1. (nature.com)

Remodeling transforms the condensed chromatin to a relaxed form, inducing the gene expression necessary for pluripotency. (jove.com)
Our studies show that Brg1 maintains cardiomyocytes in an embryonic state, and demonstrate an epigenetic mechanism by which three classes of chromatin-modifying factors-Brg1, HDAC and PARP-cooperate to control developmental and pathological gene expression. (ca.gov)
Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. (harvard.edu)
However, in many single-gene studies it has become clear that chromatin regulators often do not affect steady-state transcription, but instead are required for normal transcriptional reprogramming by environmental cues. (harvard.edu)
Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression. (harvard.edu)
It is thought that the developmental program of gene expression at the locus is regulated by specific changes in chromatin structure (Williams et al. (bl.uk)
changes in the chromatin structure of a gene were considered to be the passive consequence of the binding of these factors. (nih.gov)

the characteristic shapes of chromosomes visible during this stage are the result of DNA being coiled into highly condensed chromatin. (wikipedia.org)
For example, spermatozoa and avian red blood cells have more tightly packed chromatin than most eukaryotic cells, and trypanosomatid protozoa do not condense their chromatin into visible chromosomes at all. (wikipedia.org)
The packaging of DNA onto nucleosomes, and the segregation of chromosomes into chromosome territories was well understood, but the development of chromatin conformation capture (3C) techniques has enabled the first thorough study of intermediate scales. (cam.ac.uk)

In addition to mutations in TP53 and KRAS, we identify genetic alterations in chromatin remodelling genes, ARID1A and ARID1B, in histone methyltransferase MLL3, in histone deacetylase modifier SPOP and in chromatin assembly factor BAZ1A, in nearly two thirds of cases. (nih.gov)
Therefore, to understand the interplay between SWR1-C and NuA4-C in flowering time, we studied in detail the Arabidopsis SWC4 and YAF9 genes using a combination of molecular genetics, chromatin biology and biochemical approaches. (europa.eu)
A University of Tokyo research group has revealed that novel chromatin domains repress the action of genes involved in fat storage by analyzing the epigenome, the information contained in chemical changes to the genome, in a type of immature cell (preadipocytes) that will later differentiate into mature fat cells (adipocytes). (u-tokyo.ac.jp)
In preadipocytes the researchers identified novel chromatin domains containing H3K4me3, which activates genes, and H3K9me3, which represses them, in tandem on approximately 200 genes. (u-tokyo.ac.jp)
Finally, they revealed that the novel chromatin domains repress genes involved in lipid accumulation in preadipocytes. (u-tokyo.ac.jp)
Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset of genes bound to or modified by the regulator in question. (harvard.edu)

E , Left) Computational 3D model of the genome in a diploid human fibroblast nucleus taking into account genome-wide chromosomal interactions and interactions between chromatin and the nuclear periphery. (frontiersin.org)
Whilst auxin affects canonical ARFs indirectly by facilitating degradation of Aux/IAA repressors, direct ETTIN-auxin interactions allow switching between repressive and de-repressive chromatin states in an instantly-reversible manner. (jic.ac.uk)
Furthermore, by jointly analyzing the substrates (histone mutants) and enzymes (chromatin modifier deletions) we identify specific interactions between histone modifications and their regulators. (harvard.edu)
Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA-DNA interactions to investigate the roles of chromatin-associated RNAs (caRNAs) on genome folding in HFFc6 cells. (biorxiv.org)
Furthermore, we identified non-coding RNAs (ncRNAs) known to regulate chromatin structures, such as MALAT1 and NEAT1, as well as several novel RNAs, RNY5, RPPH1, POLG-DT and THBS1-IT, that might modulate chromatin architecture through trans -interactions in HFFc6. (biorxiv.org)
Our modeling also suggests that transcripts from Alus and other repetitive elements may facilitate chromatin interactions through trans R-loop formation. (biorxiv.org)
Chromatin-remodeling ATPases modulate histones-DNA interactions within nucleosomes and regulate transcription. (whiterose.ac.uk)

Projects of the TRR 81 investigate the role of chromatin in the context of cellular differentiation and malignancies at the Philipps-University of Marburg, the Justus-Liebig-University of Giessen, the Erasmus Medical Centre in Rotterdam, the Max Planck Institute for Heart and Lung Research in Bad Nauheim, the Medical Faculty Mannheim of the Ruprecht-Karls-University Heidelberg, and the Georg-August-University Göttingen. (uni-marburg.de)

As these modifications occur, the electrostatic environment surrounding the chromatin will flux and the level of chromatin compaction will alter. (wikipedia.org)
By doing so I have examined the role each level of chromatin structure plays in regulating the human EDC and, characterised the relationships between the different levels across a large co-ordinately regulated locus in the human genome. (bl.uk)

There is limited understanding of chromatin structure and it is active area of research in molecular biology. (wikipedia.org)
Our program is centered on a highly collaborative and team science environment that has a dedicated goal of solving fundamental and challenging problems in chromatin biology - with an emphasis on developing novel approaches towards treating human disease. (unc.edu)
In K. Appasan, Epigenomics: from Chromatin Biology to Therapeutics . (bvsalud.org)

For example, histone acetylation results in loosening and increased accessibility of chromatin for replication and transcription. (wikipedia.org)
Our genome-wide chromatin profiling revealed that FLD, as well as its associating factor LUMINIDEPENDENS 9 , downregulates histone H3K4me1 in regions with convergent overlapping transcription. (nature.com)
Furthermore, the effect of FLD on transcription dynamics is antagonized by DNA topoisomerase I. Our study reveals chromatin-based mechanisms to cope with overlapping transcription, which may occur by modulating DNA topology. (nature.com)
Unlike methylation, acetylation weakens histones' interaction with DNA and loosens the chromatin to make it accessible to transcription factors. (jove.com)
Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. (jove.com)
Imitation SWI (ISWI) and other ATP-dependent chromatin-remodeling factors play key roles in transcription and other processes by altering the structure and positioning of nucleosomes. (ca.gov)
Dans une étroite relation avec l'expérimentation, les activités de l'équipe visent à l'analyse de la structuration du génome dans les cellules en connexion avec la transcription et la réplication. (ens-lyon.fr)

Table gives corral size 'rc'-The size of the region in which a given particle or the chromatin locus can translocate its centre of mass during an observation time of up to a few minutes, defined by a circle with radius rc, and the diffusion coefficient within the corral. (harvard.edu)

This singular modification changed the dynamics of the chromatin which shows that acetylation of H4 at K16 is vital for proper intra- and inter- functionality of chromatin structure. (wikipedia.org)
Görisch SM, Lichter P, Rippe K. Mobility of multi-subunit complexes in the nucleus: accessibility and dynamics of chromatin subcompartments.Histochem Cell Biol. (harvard.edu)
Görisch SM, Wachsmuth M, Ittrich C, Bacher CP, Rippe K, Lichter P. Nuclear body movement is determined by chromatin accessibility and dynamics. (harvard.edu)

The EZ-Zyme Chromatin Prep kit allows ChIP analysis at nucleosome resolution by performing complete or partial digestions with a proprietary enzymatic cocktail to obtain chromatin fragments of on average one to a few nucleosomes in length. (sigmaaldrich.com)

An integrated genomics analysis of epigenetic subtypes in human breast tumors links DNA methylation patterns to chromatin states in normal mammary cells. (lu.se)

The loss of ISWI function does not cause obvious defects in nucleosome assembly, but results in a significant reduction in the level of histone H1 associated with chromatin in vivo. (ca.gov)
Mechanistic analysis of the interplay between DNA replication, the cell cycle, and the epigenome has provided insights into replication-coupled chromatin assembly and post-replicative chromatin maintenance. (ku.dk)

These mutations impaired replication through chromatin in vitro and were lethal in vivo. (nature.com)
Fig. 4: Chromatin defects due to Orc1 mutations correlate with replication defects. (nature.com)

The consequences in terms of chromatin accessibility and compaction depend both on the modified amino acid and the type of modification. (wikipedia.org)
Lysine trimethylation can either lead to increased transcriptional activity (trimethylation of histone H3 lysine 4) or transcriptional repression and chromatin compaction (trimethylation of histone H3, lysine 9 or lysine 27). (wikipedia.org)
These findings suggest that ISWI plays a global role in chromatin compaction in vivo by promoting the association of the linker histone H1 with chromatin. (ca.gov)

Analyses of feature importance scores revealed the contribution of caRNAs at TAD boundaries, chromatin loops and nuclear sub-structures such as nuclear speckles and nucleoli to the models' predictions. (biorxiv.org)

A-type lamins also associate with chromatin in the nuclear interior, away from the peripheral nuclear lamina. (frontiersin.org)
The hot-spot lamin A R482W mutation causing familial partial lipodystrophy of Dunnigan-type (FPLD2), affects lamin A association with chromatin at the nuclear periphery and in the nuclear interior, and is associated with 3-dimensional (3D) rearrangements of chromatin. (frontiersin.org)
Association of A-type lamins with chromatin at the nuclear periphery and in the nuclear interior. (frontiersin.org)
(D) Nucleoplasmic lamin A interacts with chromatin in the nuclear interior. (frontiersin.org)
In nonmegaloblastic macrocytosis, the marrow is not megaloblastic, but in myelodysplasia and advanced liver disease there are megaloblastoid RBC precursors with dense nuclear chromatin that differ from the usual fine fibrillar pattern in megaloblastic anemias. (msdmanuals.com)

Another study tested the role of acetylation of histone 4 on lysine 16 on chromatin structure and found that homogeneous acetylation inhibited 30 nm chromatin formation and blocked adenosine triphosphate remodeling. (wikipedia.org)
Scientists experimentally induce chromatin remodeling to enhance the conversion of cells into pluripotent stem cells. (jove.com)
therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells. (jove.com)
Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis. (duke.edu)
Here it is shown that metastatic cells undergo specific chromatin remodeling in the liver. (duke.edu)
However, structural bases for enzyme mechanisms through chromatin remodeling are not known. (nii.ac.jp)
In this study, we have determined the crystal structure of one subunit in an ATP-dependent chromatin remodeling factor and suggested the overall shape combined with a lot of physicochemical, biochemical and molecular biological methods. (nii.ac.jp)

abstract = 'Propagation of the chromatin landscape across cell divisions is central to epigenetic cell memory. (ku.dk)

Here, we describe POP-seq (Prokaryotic chromatin Openness Profiling sequencing), an adaptation of the ATAC-seq method , to interrogate changes in the openness of prokaryotic nucleoids. (bvsalud.org)

The overall structure of the chromatin network further depends on the stage of the cell cycle. (wikipedia.org)
Berbenetz, N. M., Nislow, C. & Brown, G. W. Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure. (nature.com)
The length of telomeric repeats is dynamically regulated and can be affected by changes in the telomere chromatin structure. (nih.gov)
2002). To investigate this, I have characterised the chromatin structure of the EDC in cultured cell lines. (bl.uk)
Adding absolute positional restraints from images is shown to be useful in better determining chromatin structure in synthetic tests. (cam.ac.uk)
The structure of chromatin can be changed (remodeled) to alter how tightly DNA is packaged. (medlineplus.gov)

The aim of this project is to study the interplay between SWR1 and NuA4 chromatin remodelling complexes in the control of flowering time. (europa.eu)

When you're ready to make a deep connection with your chromatin, check out the High Sensitivity ChIP Kit available on the Abcam website. (epigenie.com)

Determination of the Chromatin Openness in Bacterial Genomes. (bvsalud.org)

Plasmodium parasites are always intracellular, and they demonstrate, if stained correctly, blue cytoplasm with a red chromatin dot. (cdc.gov)

Sonication is a common method for producing sheared chromatin. (sigmaaldrich.com)

We develop a theory that explains how cohesin accumulation patterns result from the probability of encounter with polymerase and cohesin lifetimes on chromatin. (aps.org)

Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. (jic.ac.uk)

Researchers from Trinity recently attended the first in-person conference of the All-Ireland Chromatin Consortium (AICC), which was established in 2021 to promote scientific exchange and collaborations between chromatin researchers on the island of Ireland, particularly in the aftermath of the COVID-19 pandemic and Brexit. (tcd.ie)

Peptide Epitalon activates chromatin at the old age. (nel.edu)

Epitalon has shown its ability to activate chromatin by modifying heterochromatin and heterochromatinized chromosome regions in the cells of older persons. (nel.edu)

Anatomy25

Organisms5

Chemicals and Drugs75

Analytical, Diagnostic and Therapeutic Techniques and Equipment17

Phenomena and Processes67

Information Science3

Regulation14

Immunoprecipitation8

Proteins15

Interphase5

Epigenetics9

Protein12

Organization3

Open chromatin data2

Higher order chromatin2

Purified chromatin factors1

Gene7

Chromosomes3

Genes6

Interactions7

Role of chromatin1

Level of chromatin2

Biology3

Transcription7

Locus1

Dynamics3

Nucleosomes1

Methylation1

Assembly2

Mutations2

Compaction3

Loops1

Nuclear5

Remodeling7

Abstract1

Prokaryotic1

Structure6

Complexes1

ChIP1

Genomes1

Cytoplasm1

Sonication1

Polymerase1

Interaction1

20211

Activates1

Heterochromatin1