RNAi keeps Atf1-bound stress response genes in check at nuclear pores

Abstract

RNAi pathways are prevalent throughout the eukaryotic kingdom and are well known to regulate gene expression on a post-transcriptional level in the cytoplasm. Less is known about possible functions of RNAi in the nucleus. In the fission yeast Schizosaccharomyces pombe, RNAi is crucial to establish and maintain centromeric heterochromatin and functions to repress genome activity by a chromatin silencing mechanism referred to as cotranscriptional gene silencing (CTGS). Mechanistic details and the physiological relevance of CTGS are unknown. Here we show that RNAi components interact with chromatin at nuclear pores to keep stress response genes in check. We demonstrate that RNAi-mediated CTGS represses stress-inducible genes by degrading mRNAs under noninduced conditions. Under chronic heat stress conditions, a Dicer thermoswitch deports Dicer to the cytoplasm, thereby disrupting CTGS and enabling expression of genes implicated in the acquisition of thermotolerance. Taken together, our work highlights a role for nuclear pores and the stress response transcription factor Atf1 in coordinating the interplay between the RNAi machinery and the S. pombe genome and uncovers a novel mode of RNAi regulation in response to an environmental cue.

Functions of double-stranded RNA-binding domains in nucleocytoplasmic transport

“…As a result, Dcr1 localizes in the cytoplasm at elevated temperature, with important consequences for silencing and RNAi-mediated response to stress conditions. 29 Additionally, cytoplasmic retention mediated by dsRBDs has also been reported in a few proteins. For instance, in mammalian Staufen1, dsRBD3 plays critical roles in the cytoplasmic retention of the protein.…”

“…28 It will therefore be interesting to investigate whether the localization of human Dicer is sensitive to variation of external conditions, a layer of regulation that was shown to enable a rapid response to stress conditions in the fission yeast. 29 We recently uncovered the molecular basis for the dsRBD-mediated nuclear import of the RNA-editing enzyme ADAR1. 9 Mammalian ADAR1 is a nucleocytoplasmic shuttling protein containing 3 dsRBDs.…”

RNAi in fission yeast finds new targets and new ways of targeting at the nuclear periphery: Figure 1.

“…+ siRNAs are generated Woolcock et al (2012). Here, deletion of Ago1, the mediator of small RNA-guided sequence specificity, does not inhibit Dcr1 and Rdp1 recruitment to chromatin.…”

“…A new study by Bü hler and colleagues (Woolcock et al 2012) offers exciting new insights into both of these questions. By probing the genome-wide localization of RNAi factors using the highly sensitive DNA adenine methyltransferase identification (DamID) technique, they uncover a role for RNAi in the regulation of a class of stress response genes associated with the DNA-binding protein Atf1 and nuclear pores.…”

Subnuclear relocalization and silencing of a chromosomal region by an ectopic ribosomal DNA repeat

“…The rDNA repeats merge opposite to the SPB to form the nucleolus, where rDNA genes are transcribed and ribosomes preassembled (25). Much has been learned regarding the biogenesis and composition of S. pombe chromatin (26), but with few exceptions (20)(21)(22)(23)(24)(27)(28)(29), the molecular processes discovered to date have not been studied in this spatial context.We gained insight into effects exerted through the spatial organization of chromatin in S. pombe by searching for genomic elements capable of restoring silencing in a fragilized matingtype region. Heterochromatin in the mating-type region spans ∼20 kb.…”