Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast

Abstract

Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites genome-wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation, specific to S. pombe, that requires the conserved elongation factor subunit Spt4 and resembles promoter-proximal pausing in metazoans. PRO-seq profiles in strains lacking Spt4 reveal globally elevated levels of transcribing RNA Polymerase II (Pol II) within genes in both species. Messenger RNA abundance, however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.

Native elongating transcript sequencing reveals global anti-correlation between sense and antisense nascent transcription in fission yeast

“…Metagene analysis highlighted several fundamental features of sense and antisense transcription in fission yeast ( Fig. 1F): (i) It confirms the recent observation made using precision run-on sequencing (Booth et al 2016) that transcription in fission yeast extends far beyond the mRNA 3 ′ end; (ii) it reveals that the genes with antisense transcription globally display a peak of nascent antisense signal in the 3 ′ region; (iii) these genes are globally less transcribed than those without antisense (P < 2.2 × 10 −16 , Wilcoxon ranksum test), which is consistent with previous observations based on RNA labeling (Eser et al 2016).…”

“…Some of them, such as four-thiouracil sequencing (Eser et al 2016) and global/precision run-on sequencing (Booth et al 2016), use metabolic labeling of nascent RNA, followed by sequencing of the labeled transcripts. However, although the labeling times are short, the labeled transcripts remain sensitive to post-transcriptional degradation.…”

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

“…TSS annotations for S. pombe were obtained from pombase (http://www.pombase.org/, ASM294v2.26) and (Booth et al 2016). TSS annotation for S. cerevisiae was obtained from (Ganguli et al 2014).…”

“…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.…”

“…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).…”