Transcription-coupled changes to chromatin underpin gene silencing by transcriptional interference

Abstract

Long non-coding RNA (lncRNA) transcription into a downstream promoter frequently results in transcriptional interference. However, the mechanism of this repression is not fully understood. We recently showed that drug tolerance in fission yeast Schizosaccharomyces pombe is controlled by lncRNA transcription upstream of the tgp1+ permease gene. Here we demonstrate that transcriptional interference of tgp1+ involves several transcription-coupled chromatin changes mediated by conserved elongation factors Set2, Clr6CII, Spt6 and FACT. These factors are known to travel with RNAPII and establish repressive chromatin in order to limit aberrant transcription initiation from cryptic promoters present in gene bodies. We therefore conclude that conserved RNAPII-associated mechanisms exist to both suppress intragenic cryptic promoters during genic transcription and to repress gene promoters by transcriptional interference. Our analyses also demonstrate that key mechanistic features of transcriptional interference are shared between S. pombe and the highly divergent budding yeast Saccharomyces cerevisiae. Thus, transcriptional interference is an ancient, conserved mechanism for tightly controlling gene expression. Our mechanistic insights allowed us to predict and validate a second example of transcriptional interference involving the S. pombe pho1+ gene. Given that eukaryotic genomes are pervasively transcribed, transcriptional interference likely represents a more general feature of gene regulation than is currently appreciated.

Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus inDrosophila melanogaster

“…H3K36me3 is a co-transcriptionally established modification that occurs in regions downstream of active promoters (Xiao et al, 2003;Bannister et al, 2005;Mikkelsen et al, 2007). In yeast, H3K36me3 is associated with a decrease in spurious transcription initiation from within the body of transcribed genes and repression of gene promoters (Hampsey and Reinberg, 2003;Carrozza et al, 2005;Keogh et al, 2005;Houseley et al, 2008;Kim and Buratowski, 2009;Govind et al, 2010;Kim et al, 2012;van Werven et al, 2012;Ard and Allshire, 2016;Chia et al, 2017). We observed an increase in H3K36me3 enrichment downstream of the Adh DIST transcription start site in the two Adh UAS lines in which the abundance of the Adh DIST transcript and the degree of Adh PROX repression were most pronounced: UAS/UAS and UAS/+; GAL4/bal ( Figure 3D).…”

“…These mechanisms are not mutually exclusive and in fact have been shown to act in concert (van Werven et al, 2012;Chia et al, 2017). In the case of chromatin state changes, co-transcriptional histone modifications such as histone 3 lysine 36 trimethylation (H3K36me3) have been associated with nucleosome stabilization and repression of the downstream promoter (Hampsey and Reinberg, 2003;Carrozza et al, 2005;Keogh et al, 2005;Houseley et al, 2008;Kim and Buratowski, 2009;Govind et al, 2010;Kim et al, 2012;van Werven et al, 2012;Ard and Allshire, 2016;Chia et al, 2017). While these studies have been conducted extensively in yeast, the link between H3K36me3 and transcription-coupled repression has been less clear in metazoans.…”

Transcription levels of a long noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast

“…Examples from yeasts and other eukaryotes have demonstrated that transcription through promoters of protein coding genes exerts repression (Ard et al, 2014;Bumgarner et al, 2009;Latos et al, 2012;Martens et al, 2004;Rom et al, 2019;van Werven et al, 2012). At these loci, chromatin regulators such as facilitator of chromatin transcription (FACT), Set2-dependent deposition of lysine 36 methylation, Set3 mediated histone de-acetylation and others mediate transcriptional repression evoked by lncRNA transcription (Ard and Allshire, 2016;Hainer et al, 2011;Kim et al, 2012;van Werven et al, 2012). Conversely, lncRNA transcription can also stimulate opening of chromatin and promote coding gene transcription, which involves increased histone acetylation and disassembly of nucleosomes locally (Hirota et al, 2008;Takemata et al, 2016).…”

Intragenic transcriptional interference regulates the human immune ligand MICA

“…Transcriptional interference is thought to occur when a traversing RNA polymerase elongation complex, arising from one promoter, encounters and displaces a transcription initiation complex, which has formed transiently at a different promoter (Shearwin et al, 2005;Palmer et al, 2011). In some cases, epigenetic changes of transcriptional elongation have been associated with transcriptional interference (Houseley et al, 2008;Hainer et al, 2011;Ard & Allshire, 2016). Transcriptional interference is well characterized in lower eukaryotes with compact genomes where the transcriptional path of one gene runs on into the promoter of another gene (Greger et al, 2000;Martens et al, 2005;Hongay et al, 2006;Petruk et al, 2006;Gummalla et al, 2012;Ard et al, 2014).…”