Influence of Histone Tails and H4 Tail Acetylations on Nucleosome–Nucleosome Interactions

Liu, Ying; Lu, Chenning; Yang, Yuxiang; Fan, Yanping; Yang, Renliang; Liu, Chuan Fa; Korolev, Nikolay; Nordenskiöld, Lars

doi:10.1016/j.jmb.2011.10.031

Cited by 65 publications

(77 citation statements)

References 66 publications

(153 reference statements)

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“…Although there is substantial evidence for a direct role of H4K16ac in reducing levels of chromatin compaction mediated by nucleosome-nucleosome interactions in vitro (Dorigo et al 2004;Shogren-Knaak et al 2006;Robinson et al 2008;Allahverdi et al 2011;Liu et al 2011), we did not detect any visible changes in higher-order chromatin compaction in vivo at loci (Nanog and Sox2), where large domains of H4K16ac are lost upon ESC differentiation (Fig. 3).…”

Section: Discussioncontrasting

confidence: 53%

“…However, we cannot rule out a role for H4K16ac in decompaction of chromatin at a smaller local nucleosomal level that is not amenable to analysis by FISH. Since H4K16 has been shown to be important in mediating interactions between adjacent nucleosomes (Allahverdi et al 2011;Liu et al 2011), we suggest that the levels of chromatin compaction that can be assayed by FISH may instead be due to interactions between chromatin fibers. Our data suggest that the grossly aberrant chromatin compaction apparent in Kat8-deficient embryos and ESCs (Thomas et al 2008;Li et al 2012) may be an indirect effect of pancellular loss of this important factor, rather than a direct consequence of the loss of H4K16ac on chromatin compaction.…”

Section: Discussionmentioning

confidence: 93%

“…In vitro, acetylation of H4K16 has been shown to result in a loss of nucleosome-nucleosome interactions and a disruption of chromatin compaction in vitro (Dorigo et al 2004;Shogren-Knaak et al 2006;Robinson et al 2008;Liu et al 2011). The gross chromatin compaction defects reported in Kat8-deficient murine ESCs (Li et al 2012) would be consistent with H4K16ac leading to chromatin decompaction in vivo.…”

Section: H4k16 Acetylation Does Not Impact Upon Large-scale Chromatinmentioning

confidence: 95%

“…H4K16 is particularly interesting from this point of view: It is the only acetylatable residue in the basic patch of the H4 N-terminal tail (Dorigo et al 2003), and by contacting the acidic patch of H2A/H2B in adjacent nucleosomes it can direct the formation of a compact higher-order chromatin structure in vitro (Dorigo et al 2004;Shogren-Knaak et al 2006;Robinson et al 2008). Conversely, by blocking the binding of the e-amino group of K16 to a site on H2B in an adjacent nucleosome, acetylation of H4K16 weakens the nucleosome-nucleosome stacking and the self-association of nucleosome core particles (Allahverdi et al 2011;Liu et al 2011). Consistent with these in vitro data, deacetylation of H4K16 is important in heterochromatin formation in budding yeast (Millar et al 2004).…”

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confidence: 99%

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H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

et al. 2013

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Compared with histone H3, acetylation of H4 tails has not been well studied, especially in mammalian cells. Yet, H4K16 acetylation is of particular interest because of its ability to decompact nucleosomes in vitro and its involvement in dosage compensation in flies. Here we show that, surprisingly, loss of H4K16 acetylation does not alter higher-order chromatin compaction in vivo in mouse embryonic stem cells (ESCs). As well as peaks of acetylated H4K16 and KAT8 histone acetyltransferase at the transcription start sites of expressed genes, we report that acetylation of H4K16 is a new marker of active enhancers in ESCs and that some enhancers are marked by H3K4me1, KAT8, and H4K16ac, but not by acetylated H3K27 or EP300, suggesting that they are novel EP300 independent regulatory elements. Our data suggest a broad role for different histone acetylation marks and for different histone acetyltransferases in long-range gene regulation.

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Section: Discussioncontrasting

confidence: 53%

Section: Discussionmentioning

confidence: 93%

Section: H4k16 Acetylation Does Not Impact Upon Large-scale Chromatinmentioning

confidence: 95%

mentioning

confidence: 99%

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H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

et al. 2013

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“…Generally, acetylation of histone H3, and H4 leads to open chromatin configuration, and active transcription which facilitates binding of transcription factors. [18] However deacetylation is related to inactivation of transcription, and generally correlates with methylation. Generally, histone acetylation is seen in regions of active transcription, hypoacetylated histones are localized in euchromatic, and heterochromatic regions.…”

Section: Sperm Histone Modificationmentioning

confidence: 99%

The role of epigenetics in spermatogenesis

Güneş

Kulac

2014

Turkish Journal of Urology

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Male germ cells have a unique morphology and function to facilitate fertilization. Sperm deoxyribonucleic acid (DNA) is highly condensed to protect the paternal genome during transfer from male to oocyte. Sperm cells undergo extensive epigenetic modifications during differentiation to become a mature spermatozoon. Epigenetic modifications, including DNA methylation, histone modifications, and chromatin remodeling are substantial regulators of spermatogenesis. DNA hypermethylation is associated with gene silencing. Meanwhile, hypomethylation is associated with gene expression. In sperm cells, promoters of developmental genes are highly hypomethylated. Proper DNA methylation is essential for embryo development. Histone modifications are chemical modifications that change the DNA-binding capacity of histones and the accessibility of regulatory factors to the DNA, thereby altering gene expression. Phosphorylation, methylation, acetylation, and ubiquitination are primary modifications of lysine and serine residues on histone tails. In addition to somatic histones, testis-specific histone variants are expressed, including histone H2B in mature sperm. The replacement of histones with protamines is a crucial step in spermatogenesis. Histone hyperacetylation induces a loose chromatin structure and facilitates topoisomerase-induced DNA strand breaks. As a result, histones are replaced with transition proteins. Next, the transition proteins are replaced with protamines that induce compaction of sperm DNA. This review provides an overview of epigenetic changes during spermatogenesis.

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Molecular dynamics simulations demonstrate the regulation of DNA‐DNA attraction by H4 histone tail acetylations and mutations

Korolev

Lyubartsev

et al. 2014

Biopolymers

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The positively charged N-terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription, recombination, and repair. The detailed mechanism of the interaction of histone tails with DNA remains elusive. To model the unspecific interaction of histone tails with DNA, all-atom molecular dynamics (MD) simulations were carried out for systems of four DNA 22-mers in the presence of 20 or 16 short fragments of the H4 histone tail (variations of the 16-23 a. a. KRHRKVLR sequence, as well as the unmodified fragment a. a.13-20, GGAKRHRK). This setup with high DNA concentration, explicit presence of DNA-DNA contacts, presence of unstructured cationic peptides (histone tails) and K(+) mimics the conditions of eukaryotic chromatin. A detailed account of the DNA interactions with the histone tail fragments, K(+) and water is presented. Furthermore, DNA structure and dynamics and its interplay with the histone tail fragments binding are analysed. The charged side chains of the lysines and arginines play major roles in the tail-mediated DNA-DNA attraction by forming bridges and by coordinating to the phosphate groups and to the electronegative sites in the minor groove. Binding of all species to DNA is dynamic. The structure of the unmodified fully-charged H4 16-23 a.a. fragment KRHRKVLR is dominated by a stretched conformation. The H4 tail a. a. fragment GGAKRHRK as well as the H4 Lys16 acetylated fragment are highly flexible. The present work allows capturing typical features of the histone tail-counterion-DNA structure, interaction and dynamics.

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Influence of Histone Tails and H4 Tail Acetylations on Nucleosome–Nucleosome Interactions

Cited by 65 publications

References 66 publications

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

The role of epigenetics in spermatogenesis

Molecular dynamics simulations demonstrate the regulation of DNA‐DNA attraction by H4 histone tail acetylations and mutations

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