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Series GSE41985 Query DataSets for GSE41985
Status Public on Nov 20, 2014
Title Transcriptome analysis in mouse late spermatocyte deficient in pachytene piRNAs (Miwi+/- and -/-)
Organism Mus musculus
Experiment type Expression 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 Late spermatocyte mRNA profiles of Miwi+/- and -/- were analyzed by deep sequencing, in triplicate, using Illumina HiSeq.
Contributor(s) Watanable T, Zhong M, Cheng E, Lin H
Citation(s) 25480952
Submission date Nov 01, 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 (6)
GSM1029528 Miwi+/- late sc rep1
GSM1029529 Miwi+/- late sc rep2
GSM1029530 Miwi+/- late sc rep3
This SubSeries is part of SuperSeries:
GSE42004 Spermatogenesis
BioProject PRJNA178747
SRA SRP016955

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Supplementary file Size Download File type/resource
GSE41985_processed_file_Miwi_late_spermatocyte.txt.gz 459.7 Kb (ftp)(http) TXT
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