Genome-Wide Mapping of Histone Modifications and Mass Spectrometry Reveal H4 Acetylation Bias and H3K36 Methylation at Gene Promoters in Fission Yeast

Sinha, Indranil; Buchanan, Luke; Rönnerblad, Michelle; Bonilla, Carolina; Durand-Dubief, Mickaël; Shevchenko, Andrej; Grunstein, Michael; Stewart, Aengus; Ekwall, Karl

doi:10.2217/epi.10.18

Cited by 23 publications

(21 citation statements)

References 51 publications

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“…We note that increased pho1 + transcription is also evident in expression profiling data from set2Δ cells (47). In addition, pho1 + mRNA levels similarly accumulated in cells lacking the activity of Clr6CII Rpd3S (p st2Δ or alp13Δ ), Spt6 ( spt6-1 ) and FACT ( spt16-18 or pob3Δ ) (Figure 6E, and Supplementary Figure S2).…”

Section: Resultsmentioning

confidence: 66%

Transcription-coupled changes to chromatin underpin gene silencing by transcriptional interference

Ard

Allshire

2016

Nucleic Acids Res

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Long non-coding RNA (lncRNA) transcription into a downstream promoter frequently results in transcriptional interference. However, the mechanism of this repression is not fully understood. We recently showed that drug tolerance in fission yeast Schizosaccharomyces pombe is controlled by lncRNA transcription upstream of the tgp1+ permease gene. Here we demonstrate that transcriptional interference of tgp1+ involves several transcription-coupled chromatin changes mediated by conserved elongation factors Set2, Clr6CII, Spt6 and FACT. These factors are known to travel with RNAPII and establish repressive chromatin in order to limit aberrant transcription initiation from cryptic promoters present in gene bodies. We therefore conclude that conserved RNAPII-associated mechanisms exist to both suppress intragenic cryptic promoters during genic transcription and to repress gene promoters by transcriptional interference. Our analyses also demonstrate that key mechanistic features of transcriptional interference are shared between S. pombe and the highly divergent budding yeast Saccharomyces cerevisiae. Thus, transcriptional interference is an ancient, conserved mechanism for tightly controlling gene expression. Our mechanistic insights allowed us to predict and validate a second example of transcriptional interference involving the S. pombe pho1+ gene. Given that eukaryotic genomes are pervasively transcribed, transcriptional interference likely represents a more general feature of gene regulation than is currently appreciated.

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Section: Resultsmentioning

confidence: 66%

Transcription-coupled changes to chromatin underpin gene silencing by transcriptional interference

Ard

Allshire

2016

Nucleic Acids Res

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“…In contrast, there are no homologs of Dot1 or detectable levels of H3K79me in the fission yeast Schizosaccharomyces pombe (Sinha et al 2010). Thus, while gene expression at the heterochromatin of S. pombe is also known to be (D) at ADE2-TEL05R and native TEL06R using the cultures described in B.…”

Section: Discussionmentioning

confidence: 97%

Mechanism for epigenetic variegation of gene expression at yeast telomeric heterochromatin

et al. 2012

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Yeast contains heterochromatin at telomeres and the silent mating-type loci (HML/HMR). Genes positioned within the telomeric heterochromatin of Saccharomyces cerevisiae switch stochastically between epigenetically bistable ON and OFF expression states. Important aspects of the mechanism of variegated gene expression, including the chromatin structure of the natural ON state and the mechanism by which it is maintained, are unknown. To address this issue, we developed approaches to select cells in the ON and OFF states. We found by chromatin immunoprecipitation (ChIP) that natural ON telomeres are associated with Rap1 binding and, surprisingly, also contain known characteristics of OFF telomeres, including significant amounts of Sir3 and H4K16 deacetylated nucleosomes. Moreover, we found that H3K79 methylation (H3K79me), H3K4me, and H3K36me, which are depleted from OFF telomeres, are enriched at ON telomeres. We demonstrate in vitro that H3K79me, but not H3K4me or H3K36me, disrupts transcriptional silencing. Importantly, H3K79me does not significantly reduce Sir complex binding in vivo or in vitro. Finally, we show that maintenance of H3K79me at ON telomeres is dependent on transcription. Therefore, although Sir proteins are required for silencing, we propose that epigenetic variegation of telomeric gene expression is due to the bistable enrichment/depletion of H3K79me and not the fluctuation in the amount of Sir protein binding to nucleosomes.

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“…Histones were purified following a previously described purification protocol with some modification (Sinha et al, 2010). A 150 mL culture was inoculated to a density of 1.4 × 10 6 cells/mL in 4X YES media from a starter culture grown overnight in 4X YES at 25°C.…”

Section: Methodsmentioning

confidence: 99%

“…Native WCE and chromatin enrichment (NIB buffer) . Cell lysates were fractionated using a method modified from (Ekwall et al, 1997; Sinha et al, 2010). Briefly, cell pellets from 50 ml cultures in YES were washed with NIB [0.25 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl 2 , 1 mM CaCl 2 , 2.5 mM spermidine, 20 mM HEPES, 10 mM N-butyric acid, 0.8% Triton X-100 (w/v) with 1:1000 protease inhibitors (Sigma (P8215)) and 1 mM phenylmethylsulfonyl fluoride (PMSF)] and resuspended in 1 ml NIB.…”

Section: Methodsmentioning

confidence: 99%

Histone H3G34R mutation causes replication stress, homologous recombination defects and genomic instability in S. pombe

Yadav

Jablonowski

Fernandez

et al. 2017

eLife

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Recurrent somatic mutations of H3F3A in aggressive pediatric high-grade gliomas generate K27M or G34R/V mutant histone H3.3. H3.3-G34R/V mutants are common in tumors with mutations in p53 and ATRX, an H3.3-specific chromatin remodeler. To gain insight into the role of H3-G34R, we generated fission yeast that express only the mutant histone H3. H3-G34R specifically reduces H3K36 tri-methylation and H3K36 acetylation, and mutants show partial transcriptional overlap with set2 deletions. H3-G34R mutants exhibit genomic instability and increased replication stress, including slowed replication fork restart, although DNA replication checkpoints are functional. H3-G34R mutants are defective for DNA damage repair by homologous recombination (HR), and have altered HR protein dynamics in both damaged and untreated cells. These data suggest H3-G34R slows resolution of HR-mediated repair and that unresolved replication intermediates impair chromosome segregation. This analysis of H3-G34R mutant fission yeast provides mechanistic insight into how G34R mutation may promote genomic instability in glioma.DOI: http://dx.doi.org/10.7554/eLife.27406.001

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Genome-Wide Mapping of Histone Modifications and Mass Spectrometry Reveal H4 Acetylation Bias and H3K36 Methylation at Gene Promoters in Fission Yeast

Abstract: Histone modification patterns could be linked to gene expression in fission yeast.

Cited by 23 publications

References 51 publications

Transcription-coupled changes to chromatin underpin gene silencing by transcriptional interference

Transcription-coupled changes to chromatin underpin gene silencing by transcriptional interference

Mechanism for epigenetic variegation of gene expression at yeast telomeric heterochromatin

Histone H3G34R mutation causes replication stress, homologous recombination defects and genomic instability in S. pombe

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