Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in <i>Saccharomyces cerevisiae</i>

Martin, Benjamin J E; McBurney, Kristina L.; Maltby, Vicki E.; Jensen, Kristoffer N.; Brind’Amour, Julie; Howe, LeAnn

doi:10.1534/genetics.116.199422

Cited by 24 publications

(30 citation statements)

References 59 publications

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“…We note however that this observation could not be generalized to other chromatin-modifying enzymes, as the occupancy of the H3K4 methyltransferase, Set1, positively correlated with H3K4me3 ( Figure 3B and S4B). Thus, specifically for HATs, we observe poor correspondence between HAT localization and histone acetylation, which is consistent with previous suggestions that regulation of HAT activity, following chromatin binding, is a major determinant of histone acetylation genome-wide 21,26,37,38 .…”

Section: The Activity Of Histone Acetyltransferases Is Regulated Postsupporting

confidence: 91%

The majority of histone acetylation is a consequence of transcription

Martin

Brind’Amour

Jensen

et al. 2019

Preprint

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Histone acetylation is a ubiquitous hallmark of transcriptional activity, but whether the link is of a causal or consequential nature is still a matter of debate. In this study we resolve this question. Using both immunoblot analysis and chromatin immunoprecipitation-sequencing (ChIP-seq) in S. cerevisiae, we show that the majority of histone acetylation is dependent on transcription. Loss of histone H4 acetylation upon transcription inhibition is partially explained by depletion of histone acetyltransferases (HATs) from gene bodies, implicating transcription in HAT targeting. Despite this, HAT occupancy alone poorly predicts histone acetylation, suggesting that HAT activity is regulated at a step postrecruitment. Collectively, these data show that the majority of histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases.

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Section: The Activity Of Histone Acetyltransferases Is Regulated Postsupporting

confidence: 91%

The majority of histone acetylation is a consequence of transcription

Martin

Brind’Amour

Jensen

et al. 2019

Preprint

Self Cite

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“…Sequencing libraries were prepared as described previously (Maltby et al 2012;Martin et al 2017). Briefly, 2 ng of ChIP or input material were end-repaired, A-tailed, and adapters ligated, before PCR amplification with indexed primers.…”

Section: Spt16 Chromatin Immunoprecipitation Sequencingmentioning

confidence: 99%

Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes inSaccharomyces cerevisiae

2018

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The FACT (FAcilitates Chromatin Transactions) complex is a conserved complex that maintains chromatin structure on transcriptionally active genes. Consistent with this, FACT is enriched on highly expressed genes, but how it is targeted to these regions is unknown. In vitro, FACT binds destabilized nucleosomes, supporting the hypothesis that FACT is targeted to transcribed chromatin through recognition of RNA polymerase (RNAP)-disrupted nucleosomes. In this study, we used high-resolution analysis of FACT occupancy in Saccharomyces cerevisiae to test this hypothesis. We demonstrate that FACT interacts with nucleosomes in vivo and that its interaction with chromatin is dependent on transcription by any of the three RNAPs. Deep sequencing of micrococcal nucleaseresistant fragments shows that FACT-bound nucleosomes exhibit differing nuclease sensitivity compared to bulk chromatin, consistent with a modified nucleosome structure being the preferred ligand for this complex. Interestingly, a subset of FACT-bound nucleosomes may be "overlapping dinucleosomes," in which one histone octamer invades the 147-bp territory normally occupied by the adjacent nucleosome. While the differing nuclease sensitivity of FACT-bound nucleosomes could also be explained by the demonstrated ability of FACT to alter nucleosome structure, transcription inhibition restores nuclease resistance, suggesting that it is not due to FACT interaction alone. Collectively, these results are consistent with a model in which FACT is targeted to transcribed genes through preferential interaction with RNAP-disrupted nucleosomes.

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“…Sequencing libraries were prepared as described previously (M altby et al . 2012; M artin et al . 2017).…”

Section: Methodsmentioning

confidence: 99%

Transcription promotes the interaction of the FAcilitates Chromatin Transactions (FACT) complex with nucleosomes inS. cerevisiae

Howe

Martin

Chruscicki

2018

Preprint

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1The FACT (FAcilitates Chromatin Transactions) complex is enriched on highly 2 expressed genes, where it facilitates transcription while maintaining chromatin structure. 3How it is targeted to these regions is unknown. In vitro, FACT binds destabilized 4 nucleosomes, supporting the hypothesis that FACT is targeted to transcribed chromatin 5 through recognition of RNA polymerase-disrupted nucleosomes. In this study, we used 6 high resolution analysis of FACT occupancy in S. cerevisiae to test this hypothesis. We 7 demonstrate that FACT interacts with unstable nucleosomes in vivo and its interaction 8 with chromatin is dependent on transcription by any of the three RNA polymerases. Deep 9 sequencing of micrococcal nuclease-resistant fragments shows that FACT-bound 10 nucleosomes exhibit differences in micrococcal nuclease sensitivity compared to bulk 11 chromatin, consistent with a modified nucleosome structure being the preferred ligand for 12 this complex. While the presence of altered nucleosomes associated with FACT can also 13 be explained by the known ability of this complex to modulate nucleosome structure, 14 transcription inhibition alleviates this effect indicating that it is not due to FACT 15 interaction alone. Collectively these results suggest that FACT is targeted to transcribed 16 genes through preferential interaction with RNA polymerase disrupted nucleosomes.

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Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

Cited by 24 publications

References 59 publications

The majority of histone acetylation is a consequence of transcription

The majority of histone acetylation is a consequence of transcription

Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes inSaccharomyces cerevisiae

Transcription promotes the interaction of the FAcilitates Chromatin Transactions (FACT) complex with nucleosomes inS. cerevisiae

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