The balance of poly(U) polymerase activity ensures germline identity, survival and development in Caenorhabditis elegans

Screening by deep sequencing reveals mediators of microRNA tailing in C. elegans

microRNAs are frequently modified by addition of untemplated nucleotides to the 3' end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailing in vivo, using Caenorhabditis elegans. MicroRNA tailing in C. elegans consists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2-here named GLD-2-related 2 (GLDR-2)-is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median = 20.7 h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay in C. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.

Meiotic H3K9me2 distribution is influenced by the ALG-3 and ALG-4 pathway and by poly(U) polymerase activity

Histone modifications influence gene expression and chromosome dynamics by altering chromatin structure and recruitment of nonhistone proteins. Dimethylation of histone H3 on lysine 9 (H3K9me2) is a conserved modification often found within heterochromatin. During first meiotic prophase when homologous chromosomes undergo pairing and synapsis, immunolabeling of C. elegans male germ cells detects a relatively high H3K9me2 level on the single X chromosome and a relatively low H3K9me2 level on synapsed autosomes. This H3K9me2 distribution is influenced by several components of the small RNA machinery, including: EGO-1 RNA-directed RNA polymerase (RdRP); DRH-3 helicase; EKL-1, a Tudor domain protein; CSR-1 Argonaute; and RRF-3 RdRP. EGO-1, DRH-3, and EKL-1 function together to generate/stabilize 22G RNAs in the germ line. A subset of these 22G RNAs function together with CSR-1 to ensure correct gene expression. RRF-3 RdRP functions in biogenesis of 26G RNAs that feed into two germline regulatory mechanisms mediated by ERGO-1 Argonaute and the redundant ALG-3 and ALG-4 Argonaute proteins. Here, we report that meiotic H3K9me2 distribution is influenced by ALG-3 and ALG-4, as well as by two other factors required for 26G RNA synthesis, ERI-1 and ERI-5. Moreover, meiotic H3K9me2 distribution is influenced by activity of the poly(U) polymerases, PUP-1 (aka CDE-1, CID-1) and PUP-2.

CDE-1 suppresses the production of risiRNA by coupling polyuridylation and degradation of rRNA

BACKGROUND

Modification of RNAs, particularly at the terminals, is critical for various essential cell processes; for example, uridylation is implicated in tumorigenesis, proliferation, stem cell maintenance, and immune defense against viruses and retrotransposons. Ribosomal RNAs can be regulated by antisense ribosomal siRNAs (risiRNAs), which downregulate pre-rRNAs through the nuclear RNAi pathway in Caenorhabditis elegans. However, the biogenesis and regulation of risiRNAs remain obscure. Previously, we showed that 26S rRNAs are uridylated at the 3'-ends by an unknown terminal polyuridylation polymerase before the rRNAs are degraded by a 3' to 5' exoribonuclease SUSI-1(ceDIS3L2).

RESULTS

Here, we found that CDE-1, one of the three C.elegans polyuridylation polymerases (PUPs), is specifically involved in suppressing risiRNA production. CDE-1 localizes to perinuclear granules in the germline and uridylates Argonaute-associated 22G-RNAs, 26S, and 5.8S rRNAs at the 3'-ends. Immunoprecipitation followed by mass spectrometry (IP-MS) revealed that CDE-1 interacts with SUSI-1(ceDIS3L2). Consistent with these results, both CDE-1 and SUSI-1(ceDIS3L2) are required for the inheritance of RNAi.

CONCLUSIONS

This work identified a rRNA surveillance machinery of rRNAs that couples terminal polyuridylation and degradation.

Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases

Termini often determine the fate of RNA molecules. In recent years, 3' ends of almost all classes of RNA species have been shown to acquire nontemplated nucleotides that are added by terminal nucleotidyltransferases (TENTs). The best-described role of 3' tailing is the bulk polyadenylation of messenger RNAs in the cell nucleus that is catalyzed by canonical poly(A) polymerases (PAPs). However, many other enzymes that add adenosines, uridines, or even more complex combinations of nucleotides have recently been described. This review focuses on metazoan TENTs, which are either noncanonical PAPs or terminal uridylyltransferases with varying processivity. These enzymes regulate RNA stability and RNA functions and are crucial in early development, gamete production, and somatic tissues. TENTs regulate gene expression at the posttranscriptional level, participate in the maturation of many transcripts, and protect cells against viral invasion and the transposition of repetitive sequences. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.