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Series GSE70891 Query DataSets for GSE70891
Status Public on Jul 20, 2017
Title The effect of the Pld6 and Dnmt3l mutations on DNA methylation and expression of retrotransposons in mouse male germ cells
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Mammalian genomes harbor millions of retrotransposon copies, some of which are transpositionally active. In mouse prospermatogonia, PIWI-interacting small RNAs called piRNAs combat retrotransposon activity. The piRNA system guides de novo DNA methylation at retrotransposon promoters, but it remains unclear whether DNA methylation is involved in retrotransposon silencing in prospermatogonia. We performed a genome-wide study of DNA methylation and RNA abundance for retrotransposons in developing mouse male germ cells, using Pld6/Mitopld and Dnmt3l knockout (KO) mice deficient in piRNA biogenesis and de novo DNA methylation, respectively. The Dnmt3l mutation greatly reduced DNA methylation at most retrotransposons but its effect on their RNA abundance was low in prospermatogonia. In the Pld6 mutants, only few retrotransposons exhibited reduced DNA methylation but many were more upregulated at the RNA level than in the Dnmt3l mutants. Moreover, the retrotransposon upregulation by the Pld6 mutation was observed even in the Dnmt3l KO background. Thus, in prospermatogonia, post-transcriptional RNA digestion by the piRNA system plays a more important role in retrotransposon regulation than transcriptional silencing by DNA methylation. However, their relative importance was changed in meiotic spermatocytes where hypomethylation of retrotransposons increased their expression by up to 100-fold in both mutants. Interestingly, retrotransposon activation disrupted the transcriptome integrity because intergenic and intronic retrotransposon sequences, in particular, the antisense promoter of LINE-1, drive expression of nearby genes.
Overall design To study the effect of the Pld6 and Dnmt3l mutations on retrotransposon regulation, we determined the DNA methylation levels in the mutant spermatogonia and the RNA expression levels of retrotransposons in the mutant testes at P0 (containing prospermatogonia) and mutant leptotene/zygotene spermatocytes using bowtie2 (both are available as supplementary tables in the original article). We also determined genome-wide DNA methylation map (using bismark) and the levels of gene expression (using Tophat and Cuffdiff), which are available as processed files here. We also analyzed small RNAs in spermatogonia, spermatocytes and round spermatids to analyze the population of piRNAs in these cells.
Citation(s) 28749988
Submission date Jul 14, 2015
Last update date May 15, 2019
Contact name Kota Inoue
Phone +8192-642-6760
Organization name Kyushu University
Department Medical Institute of Bioregulation
Lab Division of Epigenomics and Development
Street address 3-1-1 Maidashi, Higashiku
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (37)
GSM1821362 BS_seq: WT
GSM1821363 BS_seq: Pld6 KO
GSM1821364 BS_seq: Dnmt3L KO
This SuperSeries is composed of the following SubSeries:
GSE70888 Whole-genome DNA methylation analysis for purified WT, Pld6 KO, and Dnmt3l KO spermatogonia
GSE70889 Gene and retrotransposon expression analysis for WT, Pld6 KO, and Dnmt3l KO male germ cells during spermatogenesis
GSE70890 Small RNA sequencing analysis for male germ cells during spermatogenesis
BioProject PRJNA289866

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Supplementary file Size Download File type/resource
GSE70891_RAW.tar 440.3 Mb (http)(custom) TAR (of CSV, TXT)
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