Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs

Abstract

PIWI-interacting small RNAs (piRNAs) protect the germline genome and are essential for fertility. Previously, we showed that ribosomes guide the biogenesis of piRNAs from long non-coding RNAs (lncRNAs) after translating the short open reading frames (ORFs) near their 5′ cap. It remained unclear, however, how ribosomes proceed downstream of ORFs and how piRNA precursors distinguish from other RNAs. It is thus important to test whether a short ORF length is required for substrate recognition for ribosome guided-piRNA biogenesis. Here, we characterized a poorly understood class of piRNAs that originate from the 3′ untranslated regions (3′UTRs) of protein coding genes in mice and chickens. We demonstrate that their precursors are full-length mRNAs and that post-termination 80S ribosomes guide piRNA production on 3′UTRs after translation of upstream long ORFs. Similar to non-sense mediated decay (NMD), piRNA biogenesis degrades mRNA right after pioneer rounds of translation and fine-tunes protein production from mRNAs. Interestingly, however, we found that NMD, along with other surveillance pathways for ribosome recycling are temporally sequestered during the pachytene stage to allow for robust piRNA production. Although 3′UTR piRNA precursor mRNAs code for distinct proteins in mice and chickens, they all harbor embedded transposable elements (TEs) and produce piRNAs that cleave TEs, suggesting that TE suppression, rather than the function of proteins, is the primary evolutionary force maintaining a subset of mRNAs as piRNA precursors. Altogether, we discover a function of the piRNA pathway in fine-tuning protein production and reveal a conserved, general piRNA biogenesis mechanism that recognizes translating RNAs regardless of their ORF length in amniotes.

UHRF1 interacts with snRNAs and regulates alternative splicing in mouse spermatogonial stem cells

“…Interestingly, in addition to the enrichment of 116 UHRF1-interacting proteins on the snRNP spliceosome, this study also found that some other co-immunoprecipitating proteins are enriched for the ribosome. On one hand, ribosomedirected pachytene piRNA formation is a breakthrough discovery that significantly enhances the theory of piRNA biogenesis (Sun et al, 2020(Sun et al, , 2021. On the other hand, we previously showed that 25-to 32-bp reads of pachytene piRNAs were reduced by $80% in Uhrf1 cKO (Stra8-Cre induced) mice (Dong et al, 2019).…”

A pathway to produce non-coding piRNAs from endogenous protein-coding regions supports Drosophila spermatogenesis

“…Nonetheless, unique sequence piRNAs can be provided by endogenous proteincoding genes (Robine et al, 2009;Saito et al, 2009). A defining characteristic of these genic piRNAs is their production from transcript 3' untranslated regions (3'UTRs) (Ishizu et al, 2015(Ishizu et al, , 2019Sun et al, 2021;Takase et al, 2022). As exemplified by traffic jam (tj) that is one of representative host genes, 3'UTR-piRNAs bind Piwi and exert regulatory effects in gonadal soma (Saito et al, 2009).…”