Gushchanskaia, E. | bioRxiv Science

bioRxiv2018

DOT1L suppresses nuclear RNAi originating from enhancer elements in Caenorhabditis elegans

Methylation of histone H3 on lysine 79 (H3K79) by DOT1L is associated with actively transcribed genes. Earlier, we described that DOT-1.1, the Caenorhabditis elegans DOT1L homologue, cooperates with the chromatin-binding protein ZFP-1 (AF10 homologue) to negatively modulate transcription of highly and widely expressed target genes. Also, reduction in ZFP-1 levels has long been associated with lower efficiency of RNA interference (RNAi) triggered by exogenous double-stranded RNA (dsRNA), but the reason for this is not clear. Here, we demonstrate that DOT1L suppresses bidirectional transcription, including that producing enhancer RNAs, thereby preventing dsRNA formation and ectopic RNAi. This ectopic elevation of endogenous dsRNA may engage the Dicer complex and, therefore, limit efficiency of exogenous RNAi. Our insight provides a novel perspective on the underlying mechanisms of DOT1L function in development, neural activity, and cancer.

genomics↗

bioRxiv2018

The interplay between small RNA pathways shapes chromatin landscape in C. elegans

The nematode C. 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 partial loss-of-function mutant this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements in both drh-3 and csr-1 partial loss-of-function mutants and describe small RNAs matching enhancers. 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 increase in silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.

molecular biology↗