Accumulation of RNA on chromatin disrupts heterochromatic silencing

Abstract

Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochromatin is lost at transcribed regions in the absence of RNA degradation. We show that heterochromatic RNAs are retained on chromatin, form DNA: RNA hybrids, and need to be degraded by the Ccr4-Not complex or RNAi to maintain heterochromatic silencing. The Ccr4-Not complex is localized to chromatin independently of H3K9me and degrades chromatin-associated transcripts, which is required for transcriptional silencing. Overexpression of heterochromatic RNA, but not euchromatic RNA, leads to chromatin localization and loss of silencing of a distant ade6 reporter in wild-type cells. Our results demonstrate that chromatin-bound RNAs disrupt heterochromatin organization and need to be degraded in a process of heterochromatin formation.

The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast

“…As such, these RNAs are more likely to correspond to dsRNAs rather than R-loops. We speculate that at least a fraction of these dsRNAs remain associated with chromatin as was suggested previously for heterochromatin transcripts [24], which might explain why they have been previously detected using DRIP. Interestingly, lack of a significant enrichment for R-loops at terminator regions was also recently observed in A. thaliana [9].…”

The affinity of the S9.6 antibody for double-stranded RNAs impacts the mapping of R-loops in fission yeast

“…As such, these RNAs are more likely to correspond to dsRNAs rather than R-loops. We speculate that at least a fraction of these dsRNAs remain associated with chromatin as was suggested previously for heterochromatin transcripts (Bronner et al 2017), which might explain why they have been previously detected using DRIP. Interestingly, lack of a significant enrichment for R-loops at terminator regions was also recently observed in Arabidopsis thaliana (Xu et al 2017).…”

Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control

“…MTREC, which is functionally related to mammalian PAXT 20 , and its associated proteins promote RNA degradation by the 3’→5’ exosome exonuclease (Rrp6) 17,19 . Additionally, the RNAi machinery including Argonaute (Ago1), Dicer (Dcr1) and the RNA-dependent RNA polymerase (Rdp1), as well as the CCR4-NOT complex that plays diverse roles in RNA metabolism from synthesis to decay 21 , target various mRNAs for degradation 17,18,22–27 (see also Supplementary Fig. 1).…”

“…In addition to RNA degradation, RNA processing factors mediate RNA-dependent targeting of heterochromatin 5,14,17,22,25,26,28–30 . The RNA interference (RNAi) machinery targets facultative heterochromatin assembly at regulated genes 17,26,29,31 , in addition to constitutive heterochromatin assembly at centromeric repeats 27,32 .…”