A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis

Abstract

Several developmental stages of spermatogenesis are transcriptionally quiescent which presents major challenges associated with the regulation of gene expression. Here we identify that the zygotene to pachytene transition is not only associated with the resumption of transcription but also a wave of programmed mRNA degradation that is essential for meiotic progression. We explored whether terminal uridydyl transferase 4- (TUT4-) or TUT7-mediated 3′ mRNA uridylation contributes to this wave of mRNA degradation during pachynema. Indeed, both TUT4 and TUT7 are expressed throughout most of spermatogenesis, however, loss of either TUT4 or TUT7 does not have any major impact upon spermatogenesis. Combined TUT4 and TUT7 (TUT4/7) deficiency results in embryonic growth defects, while conditional gene targeting revealed an essential role for TUT4/7 in pachytene progression. Loss of TUT4/7 results in the reduction of miRNA, piRNA and mRNA 3′ uridylation. Although this reduction does not greatly alter miRNA or piRNA expression, TUT4/7-mediated uridylation is required for the clearance of many zygotene-expressed transcripts in pachytene cells. We find that TUT4/7-regulated transcripts in pachytene spermatocytes are characterized by having long 3′ UTRs with length-adjusted enrichment for AU-rich elements. We also observed these features in TUT4/7-regulated maternal transcripts whose dosage was recently shown to be essential for sculpting a functional maternal transcriptome and meiosis. Therefore, mRNA 3′ uridylation is a critical determinant of both male and female germline transcriptomes. In conclusion, we have identified a novel requirement for 3′ uridylation-programmed zygotene mRNA clearance in pachytene spermatocytes that is essential for male meiotic progression.

Reproductive phasiRNAs regulate reprogramming of gene expression and meiotic progression in rice

“…Notably, although phasiRNAs in rice and piRNAs in mice can eliminate mRNAs during sporogenesis, they function according to different working models: piRNAs in animals are mainly involved in the non-selective elimination of mRNAs at the late spermatogenesis stage at which meiosis has already finished 34 , whereas rice phasiRNAs eliminate specific categories of genes during meiotic prophase I. In mice, mRNA elimination during meiotic prophase I might be regulated by other mechanisms, such as mRNA uridylation 38 . It is intriguing that plants and animals might have evolved different mechanisms to regulate genes during meiotic prophase.…”

“…Second, in addition to the cleavage principle, the method by which reproductive phasiRNAs targeted genes differed from that of most plant sRNAs, since other plant sRNAs usually target only one gene or several genes of the same gene family 38 . The degradome data here showed that reproductive phasiRNAs cleave their targets in a regulatory manner such that one phasiRNA can target more than one gene, and the target genes of one phasiRNA often belong to different gene families.…”

Poly(A) inclusive RNA isoform sequencing (PAIso−seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails

“…Recently, there are two methods, PAL-seq (poly(A) tail length profiling by sequencing) and TAIL-seq, developed by using custom poly(T) (the reverse complement strand of poly(A) sequenced as poly(T) on Illumina platforms) base-calling algorithm to detect transcriptome-wide poly(A) tail length 1,8 . These methods have yielded rich knowledge of poly(A) tail length dynamics in germinal vesicle (GV) oocytes, spermatocytes, mouse embryonic fibroblast (MEFs), embryonic stem cells (ESCs), bone marrow, yeast, mouse liver, Arabidopsis leaves, Drosophila embryos, frog embryos, and zebrafish embryos 1,4,8,10–13 . PAL-seq utilizes a customized sequencing recipe that is only available on the discontinued Illumina Genome Analyzer II sequencer.…”

Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases

“…The same mechanism occurs for mRNAs that are targeted for nonsense‐mediated decay in eukaryotes (Kurosaki, Miyoshi, Myers, & Maquat, 2018). Recent work with a conditional knockout mouse model strongly suggests that the TUT4/7‐mediated regulation of mRNA stability is particularly important during gametogenesis and early embryonic development (Chang et al, 2018; Morgan et al, 2019, 2017). The deletion of TUT4 and TUT7 leads to infertility and alterations of the transcriptome of germ cells, whereas the effect on somatic cells is minimal.…”