MicroRNAs control mRNA fate by compartmentalizing mRNAs based on 3’UTR length

ABSTRACT: Introduction: we conduct comprehensive transcriptomic profiling analyses on three spermatogenic cell types (pachytene spermatocytes, round and elongating spermatids) purified from adult mouse testes using RNA-seq, and we determined not only the levels of both mRNAs and all known sncRNA species, but their cytoplasmic compartmentalization as well. Method: Pachytene spermatocytes, round and elongating/elongated spermatids were purified from adult mouse testes using the STA-PUT method. We fractionated the purified spermatogenic cells into RNP, monoribosome, and polyribosome fractions using a continuous sucrose gradient ultracentrifugation method, as described. Large RNAs were isolated using the AquaRNA RNA Purification Kit (Cat#5001MT, Mo Bi Tec, Inc.), whereas small RNAs were prepared by the mirPremier™ microRNA Isolation Kit (Cat#SNC10, Sigma). Constructions of mRNA and sncRNA libraries were conducted following our published protocols (Refs) and the next-gen sequencing was performed on a Hi-Seq 2000 sequencer with SE50 at the Genomics Microarray Core Facility of the UT Southwestern Medical Center (Dallas, TX). Result:Bioinformatics analyses revealed miRNAs were mostly enriched in RNPs and RNP-enriched miRNAs preferentially target RNP-enriched mRNAs. More interestingly, we found that miRNAs could distinguish shorter and longer 3’UTR transcript based on the distance between their binding sites and the stop codon. Conclusions:Overall, our genome-wide transcriptomic and bioinformatics analyses have revealed a highly likely mechanism through which miRNAs shape the haploid male germ cell-specific transcriptome characterized by RNP-enrichment of transcripts with shorter 3’UTRs.

ORGANISM(S): Mus musculus

PROVIDER: GSE80353 | GEO | 2016/04/18

SECONDARY ACCESSION(S): PRJNA318649

REPOSITORIES: GEO