The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans

Abstract

Proper regulation of germline gene expression is essential for fertility and maintaining species integrity. In the C. elegans germline, a diverse repertoire of regulatory pathways promote the expression of endogenous germline genes and limit the expression of deleterious transcripts to maintain genome homeostasis. Here we show that the conserved TRIM-NHL protein, NHL-2, plays an essential role in the C. elegans germline, modulating germline chromatin and meiotic chromosome organization. We uncover a role for NHL-2 as a co-factor in both positively (CSR-1) and negatively (HRDE-1) acting germline 22G-small RNA pathways and the somatic nuclear RNAi pathway. Furthermore, we demonstrate that NHL-2 is a bona fide RNA binding protein and, along with RNA-seq data point to a small RNA independent role for NHL-2 in regulating transcripts at the level of RNA stability. Collectively, our data implicate NHL-2 as an essential hub of gene regulatory activity in both the germline and soma.

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

“…To assess this, we performed metagene analysis, examining the density of sRNAs along the set of CSR-1a vs. CSR-1b protein coding gene targets, after normalizing for gene length (Figure 5F ). CSR-1b -associated sRNAs displayed a pattern consistent with previous reports, in which sRNAs were enriched at the 3′ end of the target transcripts ( 72 ). However, we observed a distinct pattern of sRNAs associated with CSR-1a, in which sRNAs were distributed along the entire length of the target transcripts.…”

smalldisco, a pipeline for siRNA discovery and 3’ tail identification

“…Although most C. elegans siRNAs are generated as direct single-strand RNA products of RNA-directed RNA polymerase and do not require Dicer activity, we were interested in comparing sRNA discovery by the two programs. We analyzed the Davis et al (2018) dataset (see Methods) with each program and noted several major differences in output. First, smalldisco analyzed our sample input dataset in ~2.5 hr, whereas segmentSeq required ~2.5 weeks.…”

“…Finally, to benchmark smalldisco’s performance against another sRNA discovery tool, segmentSeq (Hardcastle et al . 2011), we analyzed two samples from Davis et al . (2018), each with three replicates (SRR5931601, SRR5931602, SRR5931603, SRR5931604, SRR5931605, SRR5931606), and compared runtime, number of identified siRNA “loci,” and resolution of siRNA region sizes.…”

“…To normalize our siRNA library as executed by Scheer et al, we created a library by counting reads that map to exons, combined this library with the smalldisco siRNA output, and normalized to CPM. Finally, to benchmark smalldisco's performance against another sRNA discovery tool, segmentSeq (Hardcastle et al 2011), we analyzed two samples from Davis et al (2018), each with three replicates (SRR5931601, SRR5931602, SRR5931603, SRR5931604, SRR5931605, SRR5931606), and compared runtime, number of identified siRNA "loci," and resolution of siRNA region sizes.…”

Fraternity of old‐timers: How ubiquitin regulates miRNA functions

“…[100] NHL-2 in germinal cells is also known to modulate the action of another class of short RNAs, 22G-RNAs, which are only found in nematodes. [101,102] We expect that further study of TRIM family proteins will expand our understanding of their involvement in the regulation of not only miRNAs but possibly other types of short non-coding RNAs as well.…”