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Series GSE147724 Query DataSets for GSE147724
Status Public on Oct 24, 2020
Title Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes
Organisms Macaca mulatta; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary In the male germ cells of eutherian animals, 26–30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. These pachytene piRNAs derive from ~100 discrete autosomal loci resemble canonical protein-coding genes and long non-coding RNA-producing genes—they are transcribed by RNA polymerase II, bearing 5´ caps and 3´ poly(A) tails, and their transcripts often contain introns that are removed before nuclear export and processing into piRNAs. However, it is unclear which genic and epigenetic features distinguish pachytene piRNA genes from other types of genes and dictate their germline-specific expression. We report that an unusually long first exon (≥ 10 kb) or a long gene absent of introns altogether is highly correlated with both the germline-specific production of piRNA precursor transcripts from mouse pachytene piRNA loci. We also found that these precursor transcripts are enriched in the binding by THOC1 (also known as HPR1) and THOC2, subunits of the THO complex critical for transcription elongation and nuclear export of mRNAs. Our integrative analysis of transcriptome, piRNA, and epigenome datasets across multiple species reveals that a long first exon is an evolutionarily conserved feature of pachytene piRNA loci. We further found that a highly methylated promoter, often containing a low or intermediate level of CG dinucleotides, correlates with germline expression and somatic silencing of pachytene piRNA loci.
Overall design RIPseq for adult mouse testis and ChIPseq for adult rhesus testis
Contributor(s) Yu T, Fan K, Zhang G, Ozata DM, Zamore PD, Weng Z
Citation(s) 33397987
Submission date Mar 30, 2020
Last update date Jan 19, 2021
Contact name Tianxiong Yu
Organization name Umass Med
Street address 364 Plantation St
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21120 Illumina NextSeq 500 (Macaca mulatta)
Samples (19)
GSM4443820 ChIPseq-H3K27ac-Rhesus-Testis
GSM4443821 ChIPseq-Input-Rhesus-Testis
GSM4443822 RIPseq-mouseIgG-Mouse-Testis-rep1
BioProject PRJNA616264
SRA SRP254547

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Supplementary file Size Download File type/resource
GSE147724_RAW.tar 5.7 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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