An integrative piRNA analysis of mouse gametes and zygotes reveals new potential origins and gene regulatory roles

Scientific Reports
Eduardo Larriba, Jesús del Mazo

Abstract

Piwi-interacting RNAs (piRNAs) are a subclass of the small non-coding RNAs (sncRNAs). Their main reported function was to exert control over transposable elements (TEs) in mammalian germline. In this study undertaking a deeper bioinformatics analysis of piRNAs present in mouse oocytes, sperm cells and zygotes, we first elaborated a new piRNA database based on sequences identified as piRNAs by immunoprecipitation with PIWI proteins. Our bioinformatics analysis revealed that, at least in gametes and zygotes, piRNAs could encompass multifunctional cell-dependent regulatory molecules. Indeed, genome analysis of the piRNA mapping density (reads/kb) evidenced in all samples an enrichment of intron-derived piRNAs. Further, piRNA population was classified into sequences not associated to TEs or repeats (NRapiRNAs) and associated to repetitive genome elements (RapiRNAs). In oocytes most of the NRapiRNAs mapped to the 5'UTRs of coding mRNAs, while higher proportion of NRapiRNAs was detected in sperm cells associated to the 3'UTRs of mRNAs. This piRNA complementarity to mRNA UTRs suggests key post-transcriptional regulatory roles over mRNAs such as those encoding MHC genes. In addition, a striking association of RapiRNA with long non-codi...Continue Reading

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Citations

Feb 14, 2020·Systems Biology in Reproductive Medicine·Stewart J RussellClifford Librach
Sep 3, 2020·Marine Biotechnology·Maria PapadakiElena Sarropoulou
Dec 21, 2019·PLoS Genetics·Eliska TaborskaPetr Svoboda
Mar 8, 2021·Journal of Animal Science·Lauren G ChukrallahElizabeth M Snyder

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Datasets Mentioned

BETA
SRX648519-21

Methods Mentioned

BETA
RNAs-seq
immunoprecipitation
RNA-Seq
sncRNA-Seq

Software Mentioned

Integrative Genomics Viewer ( IGV )
RapiRNA
DAVID
Ipdb
BedTools
Ensembl
Bowtie
db
RapiRNAs
DESeq

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