GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE37150 Query DataSets for GSE37150
Status Public on Sep 11, 2012
Title Alkbh1/Tzfp Repress a Non-Repeat piRNA Cluster in Pachytene Spermatocytes
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Piwi proteins and Piwi-interacting small RNAs (piRNAs) have known functions in transposon silencing in the male germline of fetal and newborn mice. Both are also necessary for spermatogenesis in adult testes, however, their function here remains a mystery. Here, we use germ cell isolations and small RNA sequencing to show that most piRNAs in meiotic spermatocytes originate from clusters in intergenic non-repeat regions of DNA. The regulation of these piRNA clusters, including the processing of the precursor transcripts into individual piRNAs, is accomplished through mostly unknown processes. We present evidence for a regulatory mechanism for one such cluster, named cluster 1082B, located on chromosome 7 in the mouse genome, containing 788 unique piRNAs. The precursor transcript and individual piRNAs within the cluster are repressed by the Alkbh1 dioxygenase and the transcription repressor Tzfp, which are believed to be interaction partners in testis. We observe more than a thousand-fold upregulation of individual piRNAs in pachytene spermatocytes isolated from Alkbh1-/- and TzfpGTi/GTi testes. Repression is further supported by the identification of a 10 bp Tzfp recognition sequence contained within the precursor transcript. Downregulation of long interspersed elements 1 (LINE1) and intracisternal A-particle (IAP) transcripts in the Alkbh1-/- and TzfpGTi/GTi testes leads us to propose a potential role for the 1082B-encoded piRNAs in transposon silencing.
Overall design Characterization of small RNAs in mouse pachytene spermatocytes for wild-type (WT) and Alkbh1-/- and TzfpGTi/GTi, and mRNA in mouse pachytene spermatocytes for wild-type (WT) and Alkbh1-/-
Contributor(s) Nordstrand LM, Furu K, Paulsen J, Rognes T, Klungland A
Citation(s) 22965116
Submission date Apr 10, 2012
Last update date May 15, 2019
Contact name Jonas Paulsen
Organization name Oslo University Hospital
Department Radium Hospital
Lab Institute for Medical Informatics
Street address Montebello
City Oslo
State/province Foreign
ZIP/Postal code N-0310
Country Norway
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (6)
GSM912540 WT rep1
GSM912541 KO Alkbh1-/-
GSM912542 WT rep2
BioProject PRJNA158427
SRA SRP012147

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE37150_RAW.tar 240.0 Kb (http)(custom) TAR (of BED)
GSE37150_mRNA_table.txt.gz 129.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap