Sequence-dependent histone variant positioning signatures

Le, Ngoc Tu; Ho, Tu Bao; Ho, Bich Hai

doi:10.1186/1471-2164-11-s4-s3

Cited by 6 publications

(6 citation statements)

References 59 publications

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“…In contrast, however, visual inspection reveals that both the intensity and frequency γH2AX foci reconstitution are markedly reduced or absent in cells after ∼72 h following damage (Figure 4A and B). Quantification of γH2AX and 53BP1 foci size over time shows the clear increase in foci size over time as previously reported (8,55,56) (Figure 4C). In contrast to 53BP1 and the in vivo phosphorylated H2AX, the size of reconstituted γH2AX foci that are detectable at late time points was markedly smaller (Figure 4A–C).…”

Section: Resultssupporting

confidence: 86%

“…As a corollary to this line of reasoning, chromatin conformations that limit the meeting of the termini in space would disfavor repair. Although speculative, the residence of persisting DNA breaks in regions of heterochromatin (77) and the increased size of γH2AX foci at later time points (8,55,56) could be linked phenomena that can be rationalized by our proposed mechanistic model.…”

Section: Discussionmentioning

confidence: 90%

“…Although the temporal phenomenon of fewer and larger γH2AX/53BP1 foci being observed over time is well-established (8,55,56), the existence of DNA DSBs at persistent γH2AX foci has been inferred but not demonstrated (57). Because in situ DNA-PK activity requires DNA termini, we used DNA-PK activity to probe fixed chromatin for DNA termini at persistent γH2AX foci.…”

Section: Resultsmentioning

confidence: 99%

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An autonomous chromatin/DNA-PK mechanism for localized DNA damage signaling in mammalian cells

Muñoz

Kawahara

Yannone

2013

Nucleic Acids Research

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Rapid phosphorylation of histone variant H2AX proximal to DNA breaks is an initiating event and a hallmark of eukaryotic DNA damage responses. Three mammalian kinases are known to phosphorylate H2AX in response to DNA damage. However, the mechanism(s) for damage-localized phosphorylation remains incompletely understood. The DNA-dependent protein kinase (DNA-PK) is the most abundant H2AX-modifying kinases and uniquely activated by binding DNA termini. Here, we have developed a novel approach to examine enzyme activity and substrate properties by executing biochemical assays on intact cellular structures. We apply this approach to examine the mechanisms of localized protein modification in chromatin within fixed cells. DNA-PK retains substrate specificity and independently generates break-localized γH2AX foci in chromatin. In situ DNA-PK activity recapitulates localization and intensity of in vivo H2AX phosphorylation and requires no active cellular processes. Nuclease treatments or addition of exogenous DNA resulted in genome-wide H2AX phosphorylation, showing that DNA termini dictated the locality of H2AX phosphorylation in situ. DNA-PK also reconstituted focal phosphorylation of structural maintenance of chromatin protein 1, but not activating transcription factor 2. Allosteric regulation of DNA-PK by DNA termini protruding from chromatin constitutes an autonomous mechanism for break-localized protein phosphorylation that generates sub-nuclear foci. We discuss generalized implications of this mechanism in localizing mammalian DNA damage responses.

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Section: Resultssupporting

confidence: 86%

Section: Discussionmentioning

confidence: 90%

Section: Resultsmentioning

confidence: 99%

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An autonomous chromatin/DNA-PK mechanism for localized DNA damage signaling in mammalian cells

Muñoz

Kawahara

Yannone

2013

Nucleic Acids Research

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“…H3.3 does not influence overall nucleosome positioning in IGVL H3.3 has been proposed to influence nucleosome positioning (Thakar et al, 2009;Le et al, 2010), which could in turn affect the formation of single-stranded DNA. Further, strong nucleosome positioning sequences have been shown to impair diversification (Kodgire et al, 2012).…”

Section: Aid Localisation and Enzymatic Activity Are Unaffected By Lomentioning

confidence: 99%

Histone H3.3 promotes IgV gene diversification by enhancing formation of AID ‐accessible single‐stranded DNA

et al. 2016

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Immunoglobulin diversification is driven by activation‐induced deaminase (AID), which converts cytidine to uracil within the Ig variable (IgV) regions. Central to the recruitment of AID to the IgV genes are factors that regulate the generation of single‐stranded DNA (ssDNA), the enzymatic substrate of AID. Here, we report that chicken DT40 cells lacking variant histone H3.3 exhibit reduced IgV sequence diversification. We show that this results from impairment of the ability of AID to access the IgV genes due to reduced formation of ssDNA during IgV transcription. Loss of H3.3 also diminishes IgV R‐loop formation. However, reducing IgV R‐loops by RNase HI overexpression in wild‐type cells does not affect IgV diversification, showing that these structures are not necessary intermediates for AID access. Importantly, the reduction in the formation of AID‐accessible ssDNA in cells lacking H3.3 is independent of any effect on the level of transcription or the kinetics of RNAPII elongation, suggesting the presence of H3.3 in the nucleosomes of the IgV genes increases the chances of the IgV DNA becoming single‐stranded, thereby creating an effective AID substrate.

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“…Pf H2B.Z may also aid targeting of Pf H2A.Z nucleosomes to particular regions. A precedent for this possibility exists in humans where H3.3 confers a preference for CA/TG dinucleotide repeats on H3.3/ H2A.Z nucleosomes, suggesting that H3.3 may position the H2A.Z-containing nucleosomes where they can affect chromatin structure and gene expression (Le et al, 2010).…”

Section: Pf H2az and Pf H2bz -A Faithful Pairmentioning

confidence: 99%

H2A.Z and H2B.Z double‐variant nucleosomes define intergenic regions and dynamically occupy var gene promoters in the malaria parasite Plasmodium falciparum

Petter

Selvarajah

Lee

et al. 2013

Molecular Microbiology

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SummaryHistone variants are important components of eukaryotic chromatin and can alter chromatin structure to confer specialized functions. H2B variant histones are rare in nature but have evolved independently in the phyla Apicomplexa and Trypanasomatida. Here, we investigate the apicomplexan-specific Plasmodium falciparum histone variant Pf H2B.Z and show that within nucleosomes Pf H2B.Z dimerizes with the H2A variant Pf H2A.Z and that Pf H2B.Z and Pf H2A.Z occupancy correlates in the subset of genes examined. These double-variant nucleosomes also carry common markers of euchromatin like H3K4me3 and histone acetylation. Pf H2B.Z levels are elevated in intergenic regions across the genome, except in the var multigene family, where Pf H2A.Z/Pf H2B.Z doublevariant nucleosomes are only enriched in the promoter of the single active var copy and this enrichment is developmentally regulated. Importantly, this pattern seems to be specific for var genes and does not apply to other heterochromatic gene families involved in red blood cell invasion which are also subject to clonal expression. Thus, Pf H2A.Z/Pf H2B.Z double-variant nucleosomes appear to have a highly specific function in the regulation of P. falciparum virulence.

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Sequence-dependent histone variant positioning signatures

Cited by 6 publications

References 59 publications

An autonomous chromatin/DNA-PK mechanism for localized DNA damage signaling in mammalian cells

An autonomous chromatin/DNA-PK mechanism for localized DNA damage signaling in mammalian cells

Histone H3.3 promotes IgV gene diversification by enhancing formation of AID ‐accessible single‐stranded DNA

H2A.Z and H2B.Z double‐variant nucleosomes define intergenic regions and dynamically occupy var gene promoters in the malaria parasite Plasmodium falciparum

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