Histone variants: dynamic punctuation in transcription

Weber, Christopher M.; Henikoff, Steven

doi:10.1101/gad.238873.114

Cited by 252 publications

(218 citation statements)

References 123 publications

(152 reference statements)

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“…36 Several studies also involve H2A.Z in the relaxation of chromatin, explained by instability of H2A.Z-containing nucleosomes. 37,38 Altogether, this provides a logic for H2A.Z detection in MNase LiDs. Additionally, although H2A.Z is positively involved in transcription, 30,[38][39][40] it also localizes to poised promoters bound by the Polycomb repressor 2 complex.…”

Section: Discussionmentioning

confidence: 99%

“…37,38 Altogether, this provides a logic for H2A.Z detection in MNase LiDs. Additionally, although H2A.Z is positively involved in transcription, 30,[38][39][40] it also localizes to poised promoters bound by the Polycomb repressor 2 complex. 41,42 This is in line with the enrichment of MNase LiDs in H3K27me3 and in the H3K27 methyltransferase EZH2, a component of this complex.…”

Section: Discussionmentioning

confidence: 99%

“…It is also possible that by preparing chromatin with MNase we have selected heterochromatin areas with a particular folding state permissive to remodeling or transcription factors loading. 38 It will be important to determine the impact of local (e.g., promoter level 12 ) and global (LiD level) LMNA association and dissociation events from the genome on chromatin remodeling processes.…”

Section: Discussionmentioning

confidence: 99%

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Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

Lund

Duband-Goulet

Oldenburg

et al. 2015

Nucleus

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The nuclear lamina has been shown to interact with the genome through lamina-associated domains (LADs). LADs have been identified by DamID, a proximity labeling assay, and more recently by chromatin immunoprecipitationsequencing (ChIP-seq) of A-and B-type lamins. LADs form megabase-size domains at the nuclear periphery, they are gene-poor and mostly heterochromatic. Here, we show that the mode of chromatin fragmentation for ChIP, namely bath sonication or digestion with micrococcal nuclease (MNase), leads to the discovery of common but also distinct sets of lamin-interacting domains, or LiDs. Using ChIP-seq, we show the existence of lamin A/C (LMNA) LiDs with distinct gene contents, histone composition enrichment and relationships to lamin B1-interacting domains. The extent of genome coverage of lamin A/C (LMNA) LiDs in sonicated or MNase-digested chromatin is similar (»730 megabases); however over half of these domains are uniquely detected in sonicated or MNase-digested chromatin. Sonicationspecific LMNA LiDs are gene-poor and devoid of a broad panel of histone modifications, while MNase-specific LMNA LiDs are of higher gene density and are enriched in H3K9me3, H3K27me3 and in histone variant H2A.Z. LMNB1 LiDs are gene-poor and show no or little enrichment in these marks. Comparison of published LMNB1 DamID LADs with LMNB1 and LMNA LiDs identified here by ChIP-seq further shows that LMNA can associate with 'open' chromatin domains displaying euchromatin characteristics, and which are not associated with LMNB1. The differential genomic and epigenetic properties of lamin-interacting domains reflect the existence of distinct LiD populations identifiable in different chromatin contexts, including nuclease-accessible regions presumably localized in the nuclear interior.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

Lund

Duband-Goulet

Oldenburg

et al. 2015

Nucleus

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“…New information in these fields might be also helpful for understanding quantitative genetics and phenotypic evolution [4][5][6][7][8][9][10]. Gene structures of replication-dependent histones (RDHs) and replication-independent histones (RIHs) were studied in a broad range of the species [11][12].…”

Section: Introductionmentioning

confidence: 99%

Epigenetics Evolution and Replacement Histones: Evolutionary Changes at Drosophila H4r

Yamamoto¹,

Watanabe²

2016

J Phylogen Evolution Biol

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Histone 4 replacement (H4r) can replace replication-dependent H4 in Drosophila. To study the evolution of epigenetic mechanisms, the H4 and H4r genes from 14 Drosophila species were compared with regard to gene arrangement, codon bias and flanking sequences. Although the amino acid sequences of H4 and H4r are identical or nearly identical, the gene structures are quite different. The H4r gene is a single copy gene located 3R88C9 in D. melanogaster between punt and CEP78K, as it is in 11 closely related Drosophila species, but not in the three distantly related species. The H4r gene, unlike the H4 gene, has two introns and generates polyadenylated transcripts. The codon usage bias at particular sites differed between H4r and H4. The H4r gene had more GC pairs at 3 rd codon position. Strongly conserved signal sequence was not found in the 5'-region or 3'-region of the H4r gene. These results suggested that the post transcriptional process such as modifying histone at or after translation will be important for replacing histones and remodeling the chromatin. The evolutionary changes that affect gene structure and codon usage might be a key step to develop epigenetic systems by replacement histones.

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“…Most of the early histone studies investigated the replication-dependent type in sea urchin, Xenopus and Drosophila, and therefore this type is called a 'canonical' histone. The other histone type, which is expressed independently of replication, was called a 'variant' or a 'replacement' because of some amino acid substitutions compared to the corresponding canonical histone [12]. The codon usage for the two histone types is reviewed here; however, many interesting results have also been reported regarding CEN-P and histone-like proteins [3,5,11,[13][14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

Epigenetics and Codon Usage of the Histone Genes in 12 Drosophila Species

Matsuo¹

2017

J Phylogenetics Evol Biol

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Histones are proteins that bind to DNA and form nucleosomes. There are several types of histones that differ in chromosome distribution and timing of their expression. In Drosophila, each canonical type histone is identical or highly similar in amino acid sequence to its corresponding replacement type histone; however, gene structure and codon usage differ between the two types of histones. Identification of the evolutionary changes responsible for the differences between these two histone types will lead to an understanding of the development of epigenetic regulation. Here, recent findings regarding codon usage for canonical and replacement types of histones are outlined for study of the evolution of these histone genes and their epigenetic regulation in Drosophila.

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Histone variants: dynamic punctuation in transcription

Cited by 252 publications

References 123 publications

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

Epigenetics Evolution and Replacement Histones: Evolutionary Changes at Drosophila H4r

Epigenetics and Codon Usage of the Histone Genes in 12 Drosophila Species

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