Spatial Distribution of Di- and Tri-methyl Lysine 36 of Histone H3 at Active Genes

Bannister, Andrew J.; Schneider, Robert; Myers, Fiona A.; Thorne, Alan W.; Crane‐Robinson, Colyn; Kouzarides, Tony

doi:10.1074/jbc.m500796200

Cited by 387 publications

(315 citation statements)

References 21 publications

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“…So far, these studies have revealed that actively transcribed chromatin regions are enriched in H3/K4 mono-, di-, or trimethylation, H3/K36 trimethylation, and monomethylation of H3/K9, H3/ K27, and H4/K20. The distribution of these marks over the transcribed region of genes is not equal; trimethylation of H3/K4 is enriched at the 5Ј end of transcribed regions and can serve as an indicator for transcription start sites, whereas H3/K36 methylation is enriched at the 3Ј end and may be linked to processing of the transcripts (Bannister et al 2005). In contrast to this, trimethylation of H3/K9, H3/K27, and H3/K79 is linked with repression (Barski et al 2007).…”

Section: Chromatin Modificationsmentioning

confidence: 81%

Dynamics and interplay of nuclear architecture, genome organization, and gene expression

Schneider¹,

Grosschedl²

2007

Genes Dev.

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367

313

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The organization of the genome in the nucleus of a eukaryotic cell is fairly complex and dynamic. Various features of the nuclear architecture, including compartmentalization of molecular machines and the spatial arrangement of genomic sequences, help to carry out and regulate nuclear processes, such as DNA replication, DNA repair, gene transcription, RNA processing, and mRNA transport. Compartmentalized multiprotein complexes undergo extensive modifications or exchange of protein subunits, allowing for an exquisite dynamics of structural components and functional processes of the nucleus. The architecture of the interphase nucleus is linked to the spatial arrangement of genes and gene clusters, the structure of chromatin, and the accessibility of regulatory DNA elements. In this review, we discuss recent studies that have provided exciting insight into the interplay between nuclear architecture, genome organization, and gene expression.

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Section: Chromatin Modificationsmentioning

confidence: 81%

Dynamics and interplay of nuclear architecture, genome organization, and gene expression

Schneider¹,

Grosschedl²

2007

Genes Dev.

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367

313

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“…regions of active genes and peaked at the 3 0 end of genes, 40 and H3K79me3, a promoter mark, were all depleted in the aDMRs and aGENs (Fig. 3, Fig.…”

Section: Resultsmentioning

confidence: 99%

Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes

Dozmorov

2015

Epigenetics

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Although age-associated gene expression and methylation changes have been reported throughout the literature, the unifying epigenomic principles of aging remain poorly understood. Recent explosion in availability and resolution of functional/regulatory genome annotation data (epigenomic data), such as that provided by the ENCODE and Roadmap Epigenomics projects, provides an opportunity for the identification of epigenomic mechanisms potentially altered by age-associated differentially methylated regions (aDMRs) and regulatory signatures in the promoters of ageassociated genes (aGENs). In this study we found that aDMRs and aGENs identified in multiple independent studies share a common Polycomb Repressive Complex 2 signature marked by EZH2, SUZ12, CTCF binding sites, repressive H3K27me3, and activating H3K4me1 histone modification marks, and a "poised promoter" chromatin state. This signature is depleted in RNA Polymerase II-associated transcription factor binding sites, activating H3K79me2, H3K36me3, H3K27ac marks, and an "active promoter" chromatin state. The PRC2 signature was shown to be generally stable across cell types. When considering the directionality of methylation changes, we found the PRC2 signature to be associated with aDMRs hypermethylated with age, while hypomethylated aDMRs were associated with enhancers. In contrast, aGENs were associated with the PRC2 signature independently of the directionality of gene expression changes. In this study we demonstrate that the PRC2 signature is the common epigenomic context of genomic regions associated with hypermethylation and gene expression changes in aging.

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“…However, active genes themselves possess a high enrichment of H3K4me3, which marks the transcriptional start site (TSS) [86,90]. In addition, H3K36me3 is highly enriched throughout the entire transcribed region [91]. The mechanisms by which H3K4me1 is laid down at enhancers is unknown, but work in yeast has provided mechanistic detail into how the H3K4 and H3K36 methyltransferases are recruited to genes, which in turn helps to explain the distinct distribution patterns of these two modifications ( Figure 3).…”

Section: Euchromatinmentioning

confidence: 99%

Regulation of chromatin by histone modifications

2011

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Chromatin is not an inert structure, but rather an instructive DNA scaffold that can respond to external cues to regulate the many uses of DNA. A principle component of chromatin that plays a key role in this regulation is the modification of histones. There is an ever-growing list of these modifications and the complexity of their action is only just beginning to be understood. However, it is clear that histone modifications play fundamental roles in most biological processes that are involved in the manipulation and expression of DNA. Here, we describe the known histone modifications, define where they are found genomically and discuss some of their functional consequences, concentrating mostly on transcription where the majority of characterisation has taken place.

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Spatial Distribution of Di- and Tri-methyl Lysine 36 of Histone H3 at Active Genes

Cited by 387 publications

References 21 publications

Dynamics and interplay of nuclear architecture, genome organization, and gene expression

Dynamics and interplay of nuclear architecture, genome organization, and gene expression

Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes

Regulation of chromatin by histone modifications

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