Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes

Tianxiong Yu, Kaili Fan, Deniz M. Özata, Gen Zhang, Yu Fu, William E. Theurkauf (), Phillip D. Zamore () and Zhiping Weng ()
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Tianxiong Yu: Tongji University
Kaili Fan: Tongji University
Deniz M. Özata: University of Massachusetts Medical School
Gen Zhang: University of Massachusetts Medical School
Yu Fu: University of Massachusetts Medical School
William E. Theurkauf: University of Massachusetts Medical School
Phillip D. Zamore: University of Massachusetts Medical School
Zhiping Weng: Tongji University

Nature Communications, 2021, vol. 12, issue 1, 1-17

Abstract: Abstract In the male germ cells of placental mammals, 26–30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. In mice, pachytene piRNAs derive from ~100 discrete autosomal loci that produce canonical RNA polymerase II transcripts. These piRNA clusters bear 5′ caps and 3′ poly(A) tails, and often contain introns that are removed before nuclear export and processing into piRNAs. What marks pachytene piRNA clusters to produce piRNAs, and what confines their expression to the germline? We report that an unusually long first exon (≥ 10 kb) or a long, unspliced transcript correlates with germline-specific transcription and piRNA production. 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 clusters. Furthermore, a highly methylated promoter, often containing a low or intermediate level of CG dinucleotides, correlates with germline expression and somatic silencing of pachytene piRNA clusters. Pachytene piRNA precursor transcripts bind THOC1 and THOC2, THO complex subunits known to promote transcriptional elongation and mRNA nuclear export. Together, these features may explain why the major sources of pachytene piRNA clusters specifically generate these unique small RNAs in the male germline of placental mammals.

Date: 2021
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DOI: 10.1038/s41467-020-20345-3

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