Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
Nat Commun. 2021 Jan 4;12(1):73. doi: 10.1038/s41467-020-20345-3.
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.
在胎盘哺乳动物的精母细胞中，当精母细胞进入减数分裂的粗线期时，会出现 26-30 个核苷酸长的 PIWI 相互作用 RNA (piRNA)。在小鼠中，粗线期 piRNA 来源于约 100 个离散的常染色体位点，这些位点产生典型的 RNA 聚合酶 II 转录本。这些 piRNA 簇带有 5'帽和 3'多聚(A)尾，通常含有内含子，这些内含子在核输出和加工成 piRNA 之前被切除。是什么标记粗线期 piRNA 簇产生 piRNA，又是什么将它们的表达局限于生殖系？我们报告说，异常长的第一外显子（≥10kb）或长的、未剪接的转录本与生殖系特异性转录和 piRNA 产生相关。我们对多个物种的转录组、piRNA 和表观基因组数据集的综合分析表明，长的第一外显子是粗线期 piRNA 簇的一个进化保守特征。此外，一个高度甲基化的启动子，通常含有低或中等水平的 CG 二核苷酸，与生殖系表达和粗线期 piRNA 簇的体细胞沉默相关。粗线期 piRNA 前体转录本与 THOC1 和 THOC2 结合，THOC 复合物亚基已知可促进转录延伸和 mRNA 核输出。这些特征共同解释了为什么粗线期 piRNA 簇的主要来源特异性地在胎盘哺乳动物的雄性生殖细胞中产生这些独特的小 RNA。
