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A conserved role of the RSC chromatin remodeler in the establishment of nucleosome-depleted regions

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ABSTRACT

The occupancy of nucleosomes governs access to the eukaryotic genomes and results from a combination of biophysical features and the effect of ATP-dependent remodelling complexes. Most promoter regions show a conserved pattern characterized by a nucleosome-depleted region (NDR) flanked by nucleosomal arrays. The conserved RSC remodeler was reported to be critical to establish NDR in vivo in budding yeast but other evidences suggested that this activity may not be conserved in fission yeast. By reanalysing and expanding previously published data, we propose that NDR formation requires, at least partially, RSC in both yeast species. We also discuss the most prominent biological role of RSC and the possibility that non-essential subunits do not define alternate versions of the complex.

No MeSH data available.


Average nucleosome occupancy nearby the TSS in fission and budding yeasts. a Average nucleosome signals centered on two different fission yeast TSS annotations. b Average nucleosome signals centered on TSS in fission yeast and budding yeasts
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Fig1: Average nucleosome occupancy nearby the TSS in fission and budding yeasts. a Average nucleosome signals centered on two different fission yeast TSS annotations. b Average nucleosome signals centered on TSS in fission yeast and budding yeasts

Mentions: One of the early difficulties in comparing the two model yeast species (the budding yeast Saccharomyces cerevisiae, hereafter S. cerevisiae, and the fission yeast Schizosaccharomyces pombe, hereafter S. pombe) was the very poor annotation of the transcription start sites in S. pombe. This is an issue when plotting the average nucleosome signal obtained from MNase-Seq experiments to transcripts coordinates. Very recently, several groups (Booth et al. 2016; Eser et al. 2016; Li et al. 2015) have used different approaches to address that issue and Fig. 1a shows a comparison of the average nucleosome signal when plotted to the Pombase annotation (the reference of the community working on fission yeast) and the most recent work performed by the Lis laboratory using precision run-on 5′ cap sequencing (PRO-cap) (Booth et al. 2016), which corresponds to the annotation used in this manuscript. Comparing the overlay of MNase-Seq data after alignment at the TSS between the two yeast species confirms previous observations from the pioneer work of the Korber laboratory in fission yeast, namely the absence of a clearly positioned −1 nucleosome and shorter nucleosome spacing in S. pombe (Lantermann et al. 2009). In addition, the +1 nucleosome is positioned further away from the TSS and there are clear, albeit weak nucleosome arrays upstream of NDR in fission yeast (Fig. 1b). Importantly, the low amplitude of the peaks and the absence of a positioned −1 nucleosome were previously shown to result from the larger variation in the size of individual NDRs in fission yeast (Soriano et al. 2013). Therefore, nucleosomal arrays emanate bidirectionally from the NDRs in fission yeast as well.Fig. 1


A conserved role of the RSC chromatin remodeler in the establishment of nucleosome-depleted regions
Average nucleosome occupancy nearby the TSS in fission and budding yeasts. a Average nucleosome signals centered on two different fission yeast TSS annotations. b Average nucleosome signals centered on TSS in fission yeast and budding yeasts
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC5383693&req=5

Fig1: Average nucleosome occupancy nearby the TSS in fission and budding yeasts. a Average nucleosome signals centered on two different fission yeast TSS annotations. b Average nucleosome signals centered on TSS in fission yeast and budding yeasts
Mentions: One of the early difficulties in comparing the two model yeast species (the budding yeast Saccharomyces cerevisiae, hereafter S. cerevisiae, and the fission yeast Schizosaccharomyces pombe, hereafter S. pombe) was the very poor annotation of the transcription start sites in S. pombe. This is an issue when plotting the average nucleosome signal obtained from MNase-Seq experiments to transcripts coordinates. Very recently, several groups (Booth et al. 2016; Eser et al. 2016; Li et al. 2015) have used different approaches to address that issue and Fig. 1a shows a comparison of the average nucleosome signal when plotted to the Pombase annotation (the reference of the community working on fission yeast) and the most recent work performed by the Lis laboratory using precision run-on 5′ cap sequencing (PRO-cap) (Booth et al. 2016), which corresponds to the annotation used in this manuscript. Comparing the overlay of MNase-Seq data after alignment at the TSS between the two yeast species confirms previous observations from the pioneer work of the Korber laboratory in fission yeast, namely the absence of a clearly positioned −1 nucleosome and shorter nucleosome spacing in S. pombe (Lantermann et al. 2009). In addition, the +1 nucleosome is positioned further away from the TSS and there are clear, albeit weak nucleosome arrays upstream of NDR in fission yeast (Fig. 1b). Importantly, the low amplitude of the peaks and the absence of a positioned −1 nucleosome were previously shown to result from the larger variation in the size of individual NDRs in fission yeast (Soriano et al. 2013). Therefore, nucleosomal arrays emanate bidirectionally from the NDRs in fission yeast as well.Fig. 1

View Article: PubMed Central - PubMed

ABSTRACT

The occupancy of nucleosomes governs access to the eukaryotic genomes and results from a combination of biophysical features and the effect of ATP-dependent remodelling complexes. Most promoter regions show a conserved pattern characterized by a nucleosome-depleted region (NDR) flanked by nucleosomal arrays. The conserved RSC remodeler was reported to be critical to establish NDR in vivo in budding yeast but other evidences suggested that this activity may not be conserved in fission yeast. By reanalysing and expanding previously published data, we propose that NDR formation requires, at least partially, RSC in both yeast species. We also discuss the most prominent biological role of RSC and the possibility that non-essential subunits do not define alternate versions of the complex.

No MeSH data available.