The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans

Abstract

Eukaryotic cells regulate 5' triphosphorylated (ppp-) RNAs to promote cellular functions and prevent recognition by antiviral RNA sensors. For example, RNA capping enzymes possess triphosphatase domains that remove the γ phosphates of ppp-RNAs during RNA capping. Members of the closely related PIR1 family of RNA polyphosphatases remove both the β and γ phosphates from ppp-RNAs. Here we show that C. elegans PIR-1 dephosphorylates ppp-RNAs made by cellular RdRPs and is required for the maturation of 26G-RNAs, Dicer-dependent small RNAs that regulate thousands of genes during spermatogenesis and embryogenesis. PIR-1 also regulates the CSR-1 22G-RNA pathway and has critical functions in both somatic and germline development. Our findings suggest that PIR-1 modulates both Dicer-dependent and -independent Argonaute pathways, and provide insight into how cells and viruses use a conserved RNA phosphatase to regulate and respond to ppp-RNA species.

Small RNA Plays Important Roles in Virus–Host Interactions

“…These observations are consistent with the functions of mammalian PIR1 on the maturation of viral miRNAs [76,77]. Interestingly, here the PIR-1 and Dicer complex utilizes a non-processive but phased manner (finite fraction) to generate 26G-RNAs [74,83]. Technically, this biogenesis manner is equivalent to those used in normal antiviral RNAi pathways, which generate phased siRNAs (23mer siRNAs) processively from long dsRNAs (Figure 3D) (see below) [66].…”

“…Unlike its paralogs, including the triphosphatase domains of RNA capping enzymes, PIR-1 as an RNA polyphosphatase removes both the β and γ phosphates rather than just the γ phosphate of triphosphorylated RNAs (ppp-RNA) (Figure 3A) [69][70][71][72][73][74][75]. As a result, PIR-1-treated RNAs are usually destined for destruction or further processing instead of for protection/translation as in mRNA capping [76,77].…”

“…elegans PIR-1 interacts with Dicer [78] and is required for the biogenesis of 26G-RNAs (26G) [74], which regulate thousands of genes in spermatogenesis and embryogenesis [79][80][81][82]. In this biogenesis pathway, PIR-1 recognizes triphosphorylated short dsRNAs generated by worm RNA dependent RNA polymerase (RdRP) RRF-3, recruits Dicer for dsRNA cleavage (generating 26G-RNA precursors) and promotes the loading of 26G-RNAs (26 nts long and preferentially starting with G) to Argonautes by dephosphorylating the triphosphorylated 26G-RNA precursors (Figure 3C) [74]. These observations are consistent with the functions of mammalian PIR1 on the maturation of viral miRNAs [76,77].…”

Small RNAs in epigenetic inheritance: from mechanisms to trait transmission

“…DCR-1 is instead required for the biogenesis of primary endo-siRNAs called 26G-RNAs, which are 26nt with a bias for a monophosphorylated 5 0 guanosine [67,78]. These monophosphate 26G-RNAs are originated from a dsRNA precursor generated by the RdRP, which is then cleaved by Dicer and converted in monophosphate by a pyrophosphatase [140,141]. The 26G-RNAs are loaded by specific Argonaute proteins and trigger the production of secondary 22G-RNAs.…”

Nematode Small RNA Pathways in the Absence of piRNAs

“…Much lower abundance 5-monophosphate 22G-RNAs are also present. Their relationship to the triphosphate 22G-RNAs could be as primary siRNAs or dephosphorylated triphosphate 22G-RNAs [72]. Argonaute IP from tissues where an Argonaute is expressed at low levels generates small RNA profiles reflecting the input or are random as seen in the ovary, and 4-cell IP of AsALG-4 (Figure 2A) or WAGO-2 and WAGO-3 in the testis (Figure 4, M6-M7), suggesting non-specific background for these IPs.…”