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Series GSE42004 Query DataSets for GSE42004
Status Public on Nov 20, 2014
Title Spermatogenesis
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary In animal germline cells, Piwi-interacting RNAs (piRNAs) silence retrotransposons through post-transcriptional and transcriptional mechanisms. However, little is known, especially in mammals, about the functions of piRNAs beyond retrotransposon suppression1-5. In mammalian spermatocytes, piRNAs are known to be abundantly expressed6-10. Here, we show that a subset of coding and noncoding RNAs in mouse spermatocytes is degraded by the piRNA pathway. By analyzing the germline trasnscriptome of mice deficient in piRNA biogenesis, we identify hundreds of mRNAs as direct targets of piRNAs. Remarkably, the 3' untranslated region (UTR) of the mRNAs up-regulated in the piRNA pathway mutants are highly enriched with retrotransposon sequenes, implying that these sequences serve as regulatory elements for piRNA-mediated regulation. Furthermore, deficiencies of piRNAs derived from pseudogenes result in increased mRNA levels of their cognate genes, indicating that pseudogenes regulate their functional cognates via piRNAs. Moreover, we identify a large population of testis-enriched long intergenic noncoding RNAs (lincRNAs), some of which are also degraded by the piRNA pathway. Collectively, our results reveal that the piRNA pathway regulates the expression of both mRNAs and lincRNAs in addition to retrotransposon RNAs during meiosis and the key role of retrotransposons and pseudogenes, two major types of genomic sequences, in this regulation by acting as piRNA sources and/or regulatory elements in target RNAs.
Overall design Refer to individual Series
Citation(s) 25480952
Submission date Nov 02, 2012
Last update date May 15, 2019
Contact name Toshiaki Watanabe
Phone 81-55-981-6796
Organization name Yale University
Street address 10 Amistad
City NewHaven
State/province CT
ZIP/Postal code 06511
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (44)
GSM1029381 Miwi+/- early RS rep1
GSM1029382 Miwi+/- early RS rep2
GSM1029383 Miwi+/- early RS rep3
This SuperSeries is composed of the following SubSeries:
GSE41974 Transcriptome analysis in mouse early round spermatids deficient in pachytene piRNAs (Miwi+/- and -/-)
GSE41976 Transcriptome analysis during mouse spermatogenic cell development
GSE41977 piRNA analysis in Stambp-ps1 mutant mouse testes
BioProject PRJNA178741

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Supplementary file Size Download File type/resource
GSE42004_RAW.tar 128.9 Mb (http)(custom) TAR (of TXT)
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