Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation

Qiu, Hongfang; Chereji, Răzvan V.; Hu, Cuihua; Cole, Hope A.; Rawal, Yashpal; Clark, David; Hinnebusch, Alan G.

doi:10.1101/gr.196337.115

Cited by 50 publications

(84 citation statements)

References 73 publications

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“…In conclusion, our data clearly show that H2B and H4 are generally heavily depleted from promoters. In addition, our H3 ChIP-seq data (Qiu et al, 2016) and those of Fan et al (2010), obtained using a polyclonal antibody, confirm that H3 is also depleted from promoter NDRs.…”

Section: Discussionsupporting

confidence: 73%

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

2017

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SUMMARY Micrococcal nuclease (MNase) is commonly used to map nucleosomes genome-wide, but nucleosome maps are affected by the degree of digestion. It has been proposed that many yeast promoters are not nucleosome-free but instead occupied by easily digested, unstable, “fragile” nucleosomes. We analyzed the histone content of all MNase-sensitive complexes by MNase-ChIP-seq and sonication-ChIP-seq. We find that yeast promoters are predominantly bound by non-histone protein complexes, with little evidence for fragile nucleosomes. We do detect MNase-sensitive nucleosomes elsewhere in the genome, including at transcription termination sites. However, they have high A/T content, suggesting that MNase sensitivity does not indicate instability, but rather the preference of MNase for A/T-rich DNA, such that A/T-rich nucleosomes are digested faster than G/C-rich nucleosomes. We confirm our observations by analyzing ChIP-exo, chemical mapping, and ATAC-seq data from other laboratories. Thus, histone ChIP-seq experiments are essential to distinguish nucleosomes from other DNA-binding proteins that protect against MNase.

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Section: Discussionsupporting

confidence: 73%

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

2017

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“…Rows show Gcn4 targets (genes that exhibit >2-fold increase in RNA Pol2 occupancy in (Qiu et al, 2016)) for all mutants, sorted as in (C).…”

Section: Figurementioning

confidence: 99%

Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation

et al. 2017

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SUMMARY Covalent nucleotide modifications in noncoding RNAs affect a plethora of biological processes, and new functions continue to be discovered even for well-known modifying enzymes. To systematically compare the functions of a large set of ncRNA modifications in gene regulation, we carried out ribosome profiling in budding yeast to characterize 57 nonessential genes involved in tRNA modification. Deletion mutants exhibited a range of translational phenotypes, with enzymes known to modify anticodons, or non-tRNA substrates such as rRNA, exhibiting the most dramatic translational perturbations. Our data build on prior reports documenting translational upregulation of the nutrient-responsive transcription factor Gcn4 in response to numerous tRNA perturbations, and identify many additional translationally-regulated mRNAs throughout the yeast genome. Our data also uncover unexpected roles for tRNA modifying enzymes in regulation of TY retroelements, and in rRNA 2′-O-methylation. This dataset should provide a rich resource for discovery of additional links between tRNA modifications and gene regulation.

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“…Histone modification and Htz1 ChIP-seq data was obtained from GSE61888 (Weiner et al 2015). Histone H3 data are from GSE74787 (Qiu et al 2016). Pioneer factor ChECseq data are from GSE67453 (Zentner et al 2015).…”

Section: Analysis Of Previously Published Datasetsmentioning

confidence: 99%

“…As in (C), but here each p-value was divided by the H3 ChIP-seq signal below the summit of the Hsf1 peak under NHS conditions (H3 ChIP-seq data from Qiu et al 2016).…”

Section: D)mentioning

confidence: 99%

Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome

Pincus

Anandhakumar

Thiru

et al. 2018

Preprint

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Heat Shock Factor 1 (Hsf1) is the master transcriptional regulator of molecular chaperones and binds to the same cis-acting element -Heat Shock Element (HSE)across the eukaryotic lineage. In budding yeast, Hsf1 drives transcription of ~20 genes essential to maintain proteostasis under basal conditions, yet its specific targets and extent of inducible binding during heat shock remain unclear. Here we combine Hsf1ChIP-seq, nascent RNA-seq and Hsf1 nuclear depletion to quantify Hsf1 binding and transcription across the yeast genome. Hsf1 binds 74 loci during acute heat shock, 46 of which are linked to genes with strong Hsf1-dependent transcription. Most of these targets show detectable Hsf1 binding under basal conditions, but basal occupancy and heat shock-inducible binding both vary over two orders of magnitude. Notably, Hsf1's induced DNA binding leads to a disproportionate (up to 50-fold) increase in nascent transcription. While variation in basal Hsf1 occupancy poorly correlates with the strength of the HSE, promoters with high basal Hsf1 occupancy have nucleosome-depleted regions due to the presence of 'pioneer' factors. Such accessible chromatin may be critical for Hsf1 occupancy of its genomic sites as the activator is incapable of binding HSEs embedded within a stable nucleosome in vitro. In response to heat shock, however, Hsf1 is able to gain access to nucleosomal sites and promotes chromatin remodeling with the RSC complex playing a key role. We propose that the interplay between nucleosome occupancy, HSE strength and active Hsf1 levels allows cells to precisely tune expression of the proteostasis network.

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Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation

Cited by 50 publications

References 73 publications

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation

Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome

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