Interplay between small RNA pathways shapes chromatin landscapes in C. elegans

Abstract

The nematode Caenorhabditis elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both ‘silencing’ siRNAs bound by Worm-specific Argonautes (WAGO) and ‘activating’ siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here, we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partially rescued null mutant strain (WM193), this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements and an increased number of small RNAs that match enhancers in both drh-3 and csr-1 mutants. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to sites with increased silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.

DOT1L complex suppresses transcription from enhancer elements and ectopic RNAi in Caenorhabditis elegans

“…Furthermore, we link DOT1L-mediated transcriptional control to suppression of dsRNA formation and small RNA generation. Notably, we have recently described enhancer-matching small RNAs likely produced through dsRNA and/or eRNA degradation in C. elegans and correlated their production with H3K9me3 deposition at enhancers (Gushchanskaia et al 2019). We hypothesize that the ZFP-1/DOT-1.1 complex controls generation of such small RNAs, and it will be important to directly test this in the future.…”

Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility

“…These collective findings point to a consistent pool of CSR-1b present in the nucleus and/or associated with germ cell chromatin, despite the fact that the bulk of CSR-1b protein is present within the cytoplasm and germ granules (Claycomb et al, 2009). This pool of CSR-1b can be passed from parent to progeny via sperm or oocyte chromatin and presents the possibility for epigenetically marking chromosomes, influencing chromatin landscapes, and reinforcing patterns of transcription in progeny (Gushchanskaia et al, 2019;Conine et al, 2013;She et al, 2009).…”

“…Second, CSR-1 licenses the expression of germline GFP transgenes in opposition to the silencing effects of the piRNA pathway, in a process related to paramutation, termed RNA activation (RNAa) (Seth et al, 2013;Wedeles et al, 2013b). CSR-1 also promotes the formation of euchromatin at its numerous target gene loci throughout the genome, and loss of csr-1 leads to aberrant accumulation of heterochromatic histone modifications and decreased transcription at target gene loci (Gushchanskaia et al, 2019;Cecere et al, 2014).…”

Translation and codon usage regulate Argonaute slicer activity to trigger small RNA biogenesis

“…7 ). Mutation in the CSR-1 pathway was also shown to cause changes in the epigenetic landscape 52 , 53 . Given that HRDE-1 is known to promote the deposition of histone modifications associated with gene silencing, the effects observed upon mutation in components of the CSR-1 pathway might be the results of CSR-1 anti-silencing function.…”