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About: Chromatin is a(n) research topic. Over the lifetime, 50794 publication(s) have been published within this topic receiving 2709057 citation(s). The topic is also known as: Chromatin & GO:0000785. more


Open accessJournal ArticleDOI: 10.1016/J.CELL.2007.02.005
Tony Kouzarides1Institutions (1)
23 Feb 2007-Cell
Abstract: The surface of nucleosomes is studded with a multiplicity of modifications. At least eight different classes have been characterized to date and many different sites have been identified for each class. Operationally, modifications function either by disrupting chromatin contacts or by affecting the recruitment of nonhistone proteins to chromatin. Their presence on histones can dictate the higher-order chromatin structure in which DNA is packaged and can orchestrate the ordered recruitment of enzyme complexes to manipulate DNA. In this way, histone modifications have the potential to influence many fundamental biological processes, some of which may be epigenetically inherited. more

Topics: Histone code (67%), Histone-modifying enzymes (66%), Chromatin remodeling (66%) more

9,366 Citations

Journal ArticleDOI: 10.1016/0003-2697(80)90165-7
C Labarca1, Kenneth Paigen1Institutions (1)
Abstract: A simple and rapid assay for quantitative determinations of DNA in crude homogenates is described. The method is based on the enhancement of fluorescence seen when bisbenzimidazole (Hoechst 33258) binds to DNA. Crude homogenates in which chromatin has been dissociated with high salt buffer can be assayed directly and reliably in a few minutes. The dissociation of chromatin is critical to accurate determinations of DNA in biological materials using this method. The assay can detect as little as 10 ng of DNA with rather unsophisticated instrumentation. more

Topics: Bisbenzimidazole (54%), Chromatin (52%)

4,880 Citations

Open accessJournal ArticleDOI: 10.1016/J.CELL.2006.02.041
21 Apr 2006-Cell
Abstract: The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that HCNE-rich regions may contain key regulatory controls involved in development. We explored this by examining histone methylation in mouse embryonic stem (ES) cells across 56 large HCNE-rich loci. We identified a specific modification pattern, termed "bivalent domains," consisting of large regions of H3 lysine 27 methylation harboring smaller regions of H3 lysine 4 methylation. Bivalent domains tend to coincide with TF genes expressed at low levels. We propose that bivalent domains silence developmental genes in ES cells while keeping them poised for activation. We also found striking correspondences between genome sequence and histone methylation in ES cells, which become notably weaker in differentiated cells. These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency. more

Topics: Bivalent chromatin (71%), DNA methylation (61%), Histone methylation (61%) more

4,800 Citations

Open accessJournal ArticleDOI: 10.1038/NATURE11082
Jesse R. Dixon1, Siddarth Selvaraj2, Siddarth Selvaraj1, Feng Yue1  +7 moreInstitutions (3)
17 May 2012-Nature
Abstract: The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct chromosome territories, and numerous models have been proposed for how chromosomes fold within chromosome territories. These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function. Recent advances in genomic technologies have led to rapid advances in the study of three-dimensional genome organization. In particular, Hi-C has been introduced as a method for identifying higher order chromatin interactions genome wide. Here we investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types at unprecedented resolution. We identify large, megabase-sized local chromatin interaction domains, which we term 'topological domains', as a pervasive structural feature of the genome organization. These domains correlate with regions of the genome that constrain the spread of heterochromatin. The domains are stable across different cell types and highly conserved across species, indicating that topological domains are an inherent property of mammalian genomes. Finally, we find that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome. more

Topics: Scaffold/matrix attachment region (61%), Genome evolution (61%), Chromatin Loop (59%) more

4,793 Citations

Open accessJournal ArticleDOI: 10.1074/JBC.273.10.5858
Emmy P. Rogakou1, Duane R. Pilch1, Ann Orr1, Vessela S. Ivanova1  +1 moreInstitutions (1)
Abstract: When mammalian cell cultures or mice are exposed to ionizing radiation in survivable or lethal amounts, novel mass components are found in the histone H2A region of two-dimensional gels Collectively referred to as γ, these components are formed in vivo by several procedures that introduce double-stranded breaks into DNA γ-Components, which appeared to be the only major novel components detected by mass or 32PO4incorporation on acetic acid-urea-Triton X-100-acetic acid-urea-cetyltrimethylammonium bromide or SDS-acetic acid-urea-cetyltrimethylammonium bromide gels after exposure of cells to ionizing radiation, are shown to be histone H2AX species that have been phosphorylated specifically at serine 139 γ-H2AX appears rapidly after exposure of cell cultures to ionizing radiation; half-maximal amounts are reached by 1 min and maximal amounts by 10 min At the maximum, approximately 1% of the H2AX becomes γ-phosphorylated per gray of ionizing radiation, a finding that indicates that 35 DNA double-stranded breaks, the number introduced by each gray into the 6 × 109 base pairs of a mammalian G1 genome, leads to the γ-phosphorylation of H2AX distributed over 1% of the chromatin Thus, about 003% of the chromatin appears to be involved per DNA double-stranded break This value, which corresponds to about 2 × 106 base pairs of DNA per double-stranded break, indicates that large amounts of chromatin are involved with each DNA double-stranded break Thus, γ-H2AX formation is a rapid and sensitive cellular response to the presence of DNA double-stranded breaks, a response that may provide insight into higher order chromatin structures more

Topics: Chromatin (61%), Histone H2A (60%), H2AFX (58%) more

4,773 Citations

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Topic's top 5 most impactful authors

Gary S. Stein

100 papers, 4.8K citations

Michael Bustin

98 papers, 7.2K citations

Steven Henikoff

94 papers, 11.3K citations

Gordon L. Hager

69 papers, 7.2K citations

C. David Allis

69 papers, 14.1K citations

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