Role of Ccr4-Not complex in heterochromatin formation at meiotic genes and subtelomeres in fission yeast

Abstract

BackgroundHeterochromatin is essential for chromosome segregation, gene silencing and genome integrity. The fission yeast Schizosaccharomyces pombe contains heterochromatin at centromeres, subtelomeres, and mating type genes, as well as at small islands of meiotic genes dispersed across the genome. This heterochromatin is generated by partially redundant mechanisms, including the production of small interfering RNAs (siRNAs) that are incorporated into the RITS protein complex (RNAi-Induced Transcriptional Silencing). The assembly of heterochromatin islands requires the function of the RNA-binding protein Mmi1, which recruits RITS to its mRNA targets and to heterochromatin islands. In addition, Mmi1 directs its targets to an exosome-dependent RNA elimination pathway.ResultsCcr4-Not is a conserved multiprotein complex that regulates gene expression at multiple levels, including RNA degradation and translation. We show here that Ccr4-Not is recruited by Mmi1 to its RNA targets. Surprisingly, Ccr4 and Caf1 (the mRNA deadenylase catalytic subunits of the Ccr4-Not complex) are not necessary for the degradation or translation of Mmi1 RNA targets, but are essential for heterochromatin integrity at Mmi1-dependent islands and, independently of Mmi1, at subtelomeric regions. Both roles require the deadenylase activity of Ccr4 and the Mot2/Not4 protein, a ubiquitin ligase that is also part of the complex. Genetic evidence shows that Ccr4-mediated silencing is essential for normal cell growth, indicating that this novel regulation is physiologically relevant. Moreover, Ccr4 interacts with components of the RITS complex in a Mmi1-independent manner.ConclusionsTaken together, our results demonstrate that the Ccr4-Not complex is required for heterochromatin integrity in both Mmi1-dependent and Mmi1-independent pathways.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-015-0018-4) contains supplementary material, which is available to authorized users.

Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast

“…6A as DSRx3-2). Tandem DSRs promote the selective degradation of meiotic mRNAs expressed during vegetative growth of fission yeast, via their recognition by the YTHdomain protein Mmi1 (Harigaya et al 2006;Yamashita et al 2012), which interacts with the nuclear exosome and with the Ccr4-Not complex (Cotobal et al 2015;Ukleja et al 2016). During meiosis, Mmi1 is sequestered by a DSR-containing lncRNA transcribed at the sme2 locus (Harigaya et al 2006;Shichino et al 2014), allowing stabilization of DSR-containing meiotic mRNAs.…”

Accumulation of RNA on chromatin disrupts heterochromatic silencing

“…At the same time, heterochromatic transcripts are degraded by RNAi. A link between various RNA degradation machineries and H3K9me at meiotic genes was also recently reported (Hiriart et al 2012;Zofall et al 2012;Egan et al 2014;Chalamcharla et al 2015;Cotobal et al 2015;Tucker et al 2016). Several of those studies suggested a direct recruitment of the H3K9 methyltransferase by different RNA degradation machineries to deposit H3K9me.…”

A twist of fate: How a meiotic protein is providing new perspectives on germ cell development

“…XND-1 protein sequence provides no hints as its function, although its localization to autosomes in the developing and adult germ cells hints at a role as a chromatin regulator. The association of Nanos proteins with the CCR4/ NOT complex that recently was shown to regulate heterochromatic loci in Saccromyces pombe 35 raises the tantalizing possibility that Nanos family members may accordingly facilitate heterochromatinization of the germ line.…”