How Is Epigenetic Information on Chromatin Inherited After DNA Replication?

Nakatani, Yoshihiro; Tagami, Hideaki; Shestakova, Elena

doi:10.1007/3-540-37633-x_5

Cited by 16 publications

(13 citation statements)

References 20 publications

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“…In fact, the homotypic nucleosome composition in vivo was observed in the case of two H3-like replacement histones, H3.3 and CenpA, consistent with their suggested role in epigenetic maintenance (25,36,40). The prediction was also consistent with the crystallographic analysis of an in vitro-reconstituted nucleosome containing H2AZ, which led to the conclusion that H2AZ cannot coexist in the same nucleosome with regular H2A (39).…”

Section: Vol 26 2006 Analysis Of Human Histone H2az Deposition In Vsupporting

confidence: 57%

“…Given the evidence toward a role for the H3-like variant histones in epigenetic stability (25,36,40), the fact that we could not find similar evidence for an H2A class variant histone could reflect yet another essential difference between the H3/H4 and H2A/H2B-like histones. However, we cannot rule out the possibility that the direct recruitment model will be correct for other replacement H2A/H2B variants.…”

Section: Vol 26 2006 Analysis Of Human Histone H2az Deposition In Vmentioning

confidence: 62%

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Analysis of Human Histone H2AZ Deposition In Vivo Argues against Its Direct Role in Epigenetic Templating Mechanisms

Viens

Mechold

Brouillard

et al. 2006

Molecular and Cellular Biology

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Chromatin is considered to be a principal carrier of epigenetic information due to the ability of alternative chromatin states to persist through generations of cell divisions and to spread on DNA. Replacement histone variants are novel candidates for epigenetic marking of chromatin. We developed a novel approach to analyze the chromatin environment of nucleosomes containing a particular replacement histone. We applied it to human H2AZ, one of the most studied alternative histones. We find that neither H2AZ itself nor other features of the H2AZ-containing nucleosome spread to the neighboring nucleosomes in vivo, arguing against a role for H2AZ as a self-perpetuating epigenetic mark.Packaging into chromatin is a key distinguishing characteristic of the eukaryotic genome. Chromatin exists in different higher-order structures, which vary in terms of the degree of DNA condensation and methylation, the accessibility of the chromatin for regulatory proteins, and various histone posttranslational modifications (9). Different histone modifications were shown to be associated with different functional states. The extreme density and variety of modifications and their association with various functional states of chromatin have led to the "histone code" hypothesis (14, 38, 41), which postulates that the posttranslational modifications of core histones control association of chromatin with regulatory proteins, which regulate the structure and activity of chromatin.An important aspect of the histone code is its postulated epigenetic role. Currently, the term "epigenetic" is used to describe heritable or stable changes of phenotype that do not depend on changes in primary DNA sequence (34). Chromatin is considered a principal carrier of epigenetic information (9). However, unlike DNA replication, which relies on the complementary base-base recognition (44), the postulated epigenetic templating mechanisms depend on preferential recruitment of the enzymes that deposit particular epigenetic marks (DNA methylation, histone acetylation, or methylation) on chromatin to sites containing the same mark (13,14,28,42).The replacement histone variants add another dimension to the field of histone code studies (16,33,35,43). Unlike their canonical counterparts, the replacement histones are expressed in a replication-independent manner and employ specialized machineries for their deposition into chromatin (21, 24, 40). They can be associated with active or silenced chromatin and are involved in the regulation of gene expression and the organization of chromatin structure (16,17,22). Recent studies also suggest a role for replacement histones in epigenetic templating. One example is provided by neocentromeres in higher eukaryotes. Their formation and propagation do not require a particular DNA sequence (1, 5). CenpA, the specialized version of H3 histone, replaces H3 in the centromeric nucleosomes and likely serves as an epigenetic mark determining the maintenance of the centromere-specific nucleoprotein complex independent of DNA sequence...

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Section: Vol 26 2006 Analysis Of Human Histone H2az Deposition In Vsupporting

confidence: 57%

Section: Vol 26 2006 Analysis Of Human Histone H2az Deposition In Vmentioning

confidence: 62%

Analysis of Human Histone H2AZ Deposition In Vivo Argues against Its Direct Role in Epigenetic Templating Mechanisms

Viens

Mechold

Brouillard

et al. 2006

Molecular and Cellular Biology

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“…35). Transmission of histone modifications could involve Polycomb proteins (discussed below) and has been alternately hypothesized to follow a "semi-conservative" model (similar to DNA replication) 36 or a random pattern, in either case most likely relying on a "reader" molecule to recognize and spread the parental methylation to newly synthesized histones. 37 As we will illustrate with specific examples below, ncRNA species are involved in gene silencing and activation by influencing the mechanisms mentioned above.…”

Section: Defining Epigeneticsmentioning

confidence: 99%

Non-coding RNAs as direct and indirect modulators of epigenetic regulation

Peschansky¹,

2013

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Section: Introductionmentioning

confidence: 99%

“…Nuclear complex containing the histone chaperone CAF-1 and histone variant H3.1 that is involved in the replication-coupled (RC) histone deposition during S-phase of cell cycle and nuclear complex containing histone chaperone HIRA and histone variant H3.3 that participate in the replication-independent (RI) histone deposition during transcription were purified from HeLa cells. 2,3 Cytoplasmic histone predeposition complexes were not extensively characterized as nuclear ones.In this study histone H3.1 predeposition complexes were purified from both cytoplasm and nucleus of HeLa cells and compared using mass spectrometry analysis and immunoblotting. This analysis showed that ASF1A/B histone chaperone is a component of both cytoplasmic and nuclear complexes while large subunit of CAF1 chaperone, CAF1p150 is present only in nuclear complex.…”

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confidence: 99%

Characterization of Histone Predeposition Complexes from Different Cellular Compartments

Shestakova

Nakatani

2015

JIG

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Abbreviations: RC, replication coupled; RI, replication independent; TAP, tandem affinity purification; TSA, trichostatin A Introduction DNA replication involves the chromatin assembly on new DNA strands which involves the formation of new nucleosomes, the basic unit of chromatin. Nucleosome consists of the tetramer of H3/ H4 histones and two dimers of histones H2A/H2B surrounded by DNA segment. 1 Some histones composing nucleosome exist in one isoform such as histone H4, while other histones exist in several isoforms such as histone H3 (H3.1 and H3.3). Histone H3 is of special interest as different isoforms are involved in different key cellular processes: H3.1 isoform is involved in DNA replication maintaining the genome integrity and H3.3 isoform is involved in transcription which comprises the first step of gene expression. Several histone predeposition complexes were purified and characterized. Nuclear complex containing the histone chaperone CAF-1 and histone variant H3.1 that is involved in the replication-coupled (RC) histone deposition during S-phase of cell cycle and nuclear complex containing histone chaperone HIRA and histone variant H3.3 that participate in the replication-independent (RI) histone deposition during transcription were purified from HeLa cells. 2,3 Cytoplasmic histone predeposition complexes were not extensively characterized as nuclear ones.In this study histone H3.1 predeposition complexes were purified from both cytoplasm and nucleus of HeLa cells and compared using mass spectrometry analysis and immunoblotting. This analysis showed that ASF1A/B histone chaperone is a component of both cytoplasmic and nuclear complexes while large subunit of CAF1 chaperone, CAF1p150 is present only in nuclear complex. Importinbeta3 was identified as a part of cytoplasmic complex and not of nuclear one indicating that it dissociated when the complex entered the nucleus. Experiments with TSA, a histone deacetylase inhibitor, demonstrated that increased acetylation of histone H3.1 and possibly of other proteins allows the formation of H3/H4 tetramer in cytoplasm and nucleoplasm instead of dimers of H3/H4 histones identified in this and previous studies. This study provides new possibilities to develop medicaments directed against epigenetic targets and especially acetylated histones helping to treat cancer, one of the most harmful diseases of our days. Materials and methodscontaining complexes purification H3.1-containing complexes were purified essentially as described in. 4 Nuclear and cytoplasmic extracts were prepared from suspension growing HeLa cell line expressing H3.1 histone fused with C-terminal Flag-and HA-epitope tags (e-H3.1). Then, cytoplasmic and nuclear H3.1-containing complexes were purified from corresponding extracts by immuno precipitation on anti-Flag antibody-conjugated agarose beads, eluted with Flag peptide and were further affinity purified on anti-HA antibody-conjugated agarose beads followed by the elution with HA peptide. Mononucleosomes purificationNuclear pellets were hom...

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How Is Epigenetic Information on Chromatin Inherited After DNA Replication?

Cited by 16 publications

References 20 publications

Analysis of Human Histone H2AZ Deposition In Vivo Argues against Its Direct Role in Epigenetic Templating Mechanisms

Analysis of Human Histone H2AZ Deposition In Vivo Argues against Its Direct Role in Epigenetic Templating Mechanisms

Non-coding RNAs as direct and indirect modulators of epigenetic regulation

Characterization of Histone Predeposition Complexes from Different Cellular Compartments

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