Both H4K20 mono-methylation and H3K56 acetylation mark transcription-dependent histone turnover in fission yeast

Yang, Hanna; Kwon, Chang Seob; Choi, Yuni; Lee, Daeyoup

doi:10.1016/j.bbrc.2016.05.155

Cited by 13 publications

(14 citation statements)

References 38 publications

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“…It is known that nucleosome loss during transcription stimulates incorporation of new histones, especially histones H3 and H4, and thus is associated with DNA replication-independent exchange of histone H3 and H4 (refs 8 , 38 ). Scatterplot analysis revealed that the levels of histone H3 occupancy changes at transcribing regions of fft3Δ cells positively correlate with the rates of histone H3 exchange in wild-type cells 39 ( r =0.41; Fig. 4b ), indicating that Fun30 Fft3 -mediated nucleosome loss at transcribing regions is related to histone exchange and, by extension, to nucleosome loss at transcribing regions during transcription.…”

Section: Resultsmentioning

confidence: 93%

Chromatin remodeller Fun30Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation

et al. 2017

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Previous studies have revealed that nucleosomes impede elongation of RNA polymerase II (RNAPII). Recent observations suggest a role for ATP-dependent chromatin remodellers in modulating this process, but direct in vivo evidence for this is unknown. Here using fission yeast, we identify Fun30Fft3 as a chromatin remodeller, which localizes at transcribing regions to promote RNAPII transcription. Fun30Fft3 associates with RNAPII and collaborates with the histone chaperone, FACT, which facilitates RNAPII elongation through chromatin, to induce nucleosome disassembly at transcribing regions during RNAPII transcription. Mutants, resulting in reduced nucleosome-barrier, such as deletion mutants of histones H3/H4 themselves and the genes encoding components of histone deacetylase Clr6 complex II suppress the defects in growth and RNAPII occupancy of cells lacking Fun30Fft3. These data suggest that RNAPII utilizes the chromatin remodeller, Fun30Fft3, to overcome the nucleosome barrier to transcription elongation.

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Section: Resultsmentioning

confidence: 93%

Chromatin remodeller Fun30Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation

et al. 2017

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“…No striking enrichment at GR-bound regions was observed for histone modifications associated with either transcriptionally inactive regions (H3K9me3 and H3K27me3) or with transcriptional elongation (H3K36me3, H3K79me2). Interestingly, we found that H4K20me1, a histone mark linked to transcription-linked histone turn-over (30) and Polycomb repression (31), showed a marked enrichment at GR-bound regions in IMR90 and K562 cells, whereas no enrichment was observed in A549 cells (Figure 1C), indicative of a possible role of H4K20me1 in generating cell type-specific GR binding patterns.…”

Section: Resultsmentioning

confidence: 97%

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation

Love

Huska

Jurk

et al. 2016

Nucleic Acids Research

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The genomic loci bound by the glucocorticoid receptor (GR), a hormone-activated transcription factor, show little overlap between cell types. To study the role of chromatin and sequence in specifying where GR binds, we used Bayesian modeling within the universe of accessible chromatin. Taken together, our results uncovered that although GR preferentially binds accessible chromatin, its binding is biased against accessible chromatin located at promoter regions. This bias can only be explained partially by the presence of fewer GR recognition sequences, arguing for the existence of additional mechanisms that interfere with GR binding at promoters. Therefore, we tested the role of H3K9ac, the chromatin feature with the strongest negative association with GR binding, but found that this correlation does not reflect a causative link. Finally, we find a higher percentage of promoter–proximal GR binding for genes regulated by GR across cell types than for cell type-specific target genes. Given that GR almost exclusively binds accessible chromatin, we propose that cell type-specific regulation by GR preferentially occurs via distal enhancers, whose chromatin accessibility is typically cell type-specific, whereas ubiquitous target gene regulation is more likely to result from binding to promoter regions, which are often accessible regardless of cell type examined.

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“…Promoter-proximal nucleosomes flanking active genes are highly acetylated (Rufiange et al, 2007; Yang et al, 2016) and display rapid, replication-independent nucleosome turnover (Dion et al, 2007; Rufiange et al, 2007; Yang et al, 2016). These results suggest that enhanced nucleosome dynamics and histone acetylation are generally beneficial for transcription.…”

Section: Discussionmentioning

confidence: 99%

Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability

Feldman

Peterson

2019

Cell Reports

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SUMMARY The mammalian sirtuin, SIRT6, is a key tumor suppressor that maintains genome stability and regulates transcription, though how SIRT6 family members control genome stability is unclear. Here, we use multiple genome-wide approaches to demonstrate that the yeast SIRT6 homologs, Hst3 and Hst4, prevent genome instability by tuning levels of both coding and noncoding transcription. While nascent RNAs are elevated in the absence of Hst3 and Hst4, a global impact on steady-state mRNAs is masked by the nuclear exosome, indicating that sirtuins and the exosome provide two levels of regulation to maintain transcription homeostasis. We find that, in the absence of Hst3 and Hst4, increased transcription is associated with excessive DNA-RNA hybrids (R-loops) that appear to lead to new DNA double-strand breaks. Importantly, dissolution of R-loops suppresses the genome instability phenotypes of hst3 hst4 mutants, suggesting that the sirtuins maintain genome stability by acting as a rheostat to prevent promiscuous transcription.

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Both H4K20 mono-methylation and H3K56 acetylation mark transcription-dependent histone turnover in fission yeast

Cited by 13 publications

References 38 publications

Chromatin remodeller Fun30Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation

Chromatin remodeller Fun30Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation

Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability

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