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Series GSE43735 Query DataSets for GSE43735
Status Public on Nov 20, 2014
Title Transcriptome analysis in mouse late spermatocyte deficient in pachytene piRNAs (Mov10l1 fl/+ and Mov10l1 s fl/-)
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 Mov10l1 fl/+ and Mov10l1 s fl/- were analyzed by deep sequencing, in triplicate, using Illumina HiSeq.
Contributor(s) Watanabe T, Zhong M, Cheng E, Lin H
Citation(s) 25480952
Submission date Jan 24, 2013
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)
GSM1070044 Mov10l1 fl/+ rep1
GSM1070045 Mov10l1 fl/+ rep2
GSM1070046 Mov10l1 fl/+ rep3
This SubSeries is part of SuperSeries:
GSE42004 Spermatogenesis
SRA SRP018131
BioProject PRJNA187986

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE43735_processed_file_Mov10l1_late_spermatocyte.txt.gz 499.0 Kb (ftp)(http) TXT
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Processed data are available on Series record

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