Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast

Abstract

Most genomes, including yeast Saccharomyces cerevisiae, are pervasively transcribed producing numerous non-coding RNAs, many of which are unstable and eliminated by nuclear or cytoplasmic surveillance pathways. We previously showed that accumulation of PHO84 antisense RNA (asRNA), in cells lacking the nuclear exosome component Rrp6, is paralleled by repression of sense transcription in a process dependent on the Hda1 histone deacetylase (HDAC) and the H3K4 histone methyl transferase Set1. Here we investigate this process genome-wide and measure the whole transcriptome of various histone modification mutants in a Δrrp6 strain using tiling arrays. We confirm widespread occurrence of potentially antisense-dependent gene regulation and identify three functionally distinct classes of genes that accumulate asRNAs in the absence of Rrp6. These classes differ in whether the genes are silenced by the asRNA and whether the silencing is HDACs and histone methyl transferase-dependent. Among the distinguishing features of asRNAs with regulatory potential, we identify weak early termination by Nrd1/Nab3/Sen1, extension of the asRNA into the open reading frame promoter and dependence of the silencing capacity on Set1 and the HDACs Hda1 and Rpd3 particularly at promoters undergoing extensive chromatin remodelling. Finally, depending on the efficiency of Nrd1/Nab3/Sen1 early termination, asRNA levels are modulated and their capability of silencing is changed.

Coordination of Cell Cycle Progression and Mitotic Spindle Assembly Involves Histone H3 Lysine 4 Methylation by Set1/COMPASS

“…Based on these observations we propose that H3K4 methylation contributes to the coordination of cell-cycle progression, which links regulation at G1/S to the metaphase-anaphase transition during mitosis. The role of H3K4 methylation in regulation of gene expression is now well established (Margaritis et al 2012;Weiner et al 2012;Castelnuovo et al 2014) but the impact of this regulation on the implementation of biological function remains unclear. We synchronized WT and Dset1 cells with alpha-factor pheromone and collected gene expression data of cells following their release into the cell cycle.…”

“…The predominant effect of methylated H3K4 in gene expression appears to involve repressive mechanisms, which are relying on noncoding antisense RNA transcription (Margaritis et al 2012;Weiner et al 2012, Castelnuovo et al 2014. We therefore asked whether benomyl resistance of Dset1 was modulated by the 39-59 exonuclease Rrp6, the main activity involved in the turnover of unstable noncoding RNA (ncRNA) (Wyers et al 2005).…”

“…H3K4 dimethylation recruits deacetylase complexes to antagonize nucleosome acetylation and remodelling downstream of promoters (Kim and Buratowski 2009;Pinskaya et al 2009). Repressive function frequently involves regulation of antisense transcription (Margaritis et al 2012;Castelnuovo et al 2014).…”

Saccharomyces cerevisiae Sen1 Helicase Domain Exhibits 5′- to 3′-Helicase Activity with a Preference for Translocation on DNA Rather than RNA

“…Although we have not examined the in vivo origin of the Sen1-HD-associated RNAs in detail, we note that of the top 21 matches to the (CAN) 4 consensus, 18 correspond to the antisense strand of annotated protein-coding genes and only three correspond to the sense strand. This skewed distribution is intriguing, because one function of Sen1 in S. cerevisiae is silencing of genes via cotranscriptional association with their antisense transcripts (6,26,27). Conceivably, engagement of Sen1-HD with antisense transcripts in E. coli protects it from degradation, whereas the mutant versions of Sen1-HD that expressed poorly are not functionally engaged and therefore are degraded.…”

Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF

“…In addition, transcription termination sites (TTSs) possess a promoter architecture sufficient to permit transcription initiation (Whitehouse et al 2007;Murray et al 2012;Castelnuovo et al 2014). The mechanisms that regulate transcription start site (TSS)-associated ncRNA expression have recently been examined by several groups (Huang and Workman 2013).…”