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

Ryan Ard,Robin C Allshire

doi:10.1093/nar/gkw801

Ryan Ard, Robin C Allshire

Open Access

https://doi.org/10.1093/nar/gkw801

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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.

Highlights

The organization of DNA into chromatin poses a significant physical challenge to eukaryotic transcription
Pervasive eukaryotic transcription implies that transcriptional interference mediated by intergenic Long non-coding RNA (lncRNA) transcription might be a much more general feature of gene regulation in higher eukaryotes than is currently appreciated
The genetic disease alpha thalassemia is caused by an intergenic single nucleotide polymorphism that creates a new promoter and initiates novel transcription that interferes with the expression of the alpha globin gene downstream [61]

Summary

INTRODUCTION

The organization of DNA into chromatin poses a significant physical challenge to eukaryotic transcription. Histone deacetylase complexes (HDACs) remove acetyl groups from histone tails, while other HMTs deposit repressive histone marks (e.g. H3K9me2/3) Such activities create a much less accessible chromatin environment that silences gene expression, termed heterochromatin [9]. Several individual lncRNAs have been reported to interact with and/or direct chromatin-modifiers to control gene expression, while others have been proposed to recruit transcriptional activators, repressors, or components of the transcription machinery itself [27]. We show that numerous conserved transcriptional elongation factors (including Set, the Rpd3S homolog Clr6CII, and histone chaperones Spt and FACT) are required to establish a repressive chromatin environment over the tgp1+ promoter in the wake of upstream initiating lncRNA transcription. Upstream lncRNA transcription-coupled changes in promoter chromatin status underpin gene silencing by transcriptional interference in two evolutionarily distant eukaryotes

MATERIALS AND METHODS

RESULTS

DISCUSSION