Alternative cleavage and polyadenylation in spermatogenesis coordinates chromatin regulation and post-transcriptional control

Most mammalian genes display alternative cleavage and polyadenylation (APA). Previous studies have indicated preferential expression of APA isoforms with short 3'UTRs in testes. Here we show widespread shortening of 3'UTR by APA during the first wave of spermatogenesis in mouse, with 3'UTRs being the shortest in spermatids. Shortening of 3'UTR eliminates destabilizing elements, such as U-rich elements and transposable elements, which appear to be highly potent for transcript elimination during spermatogenesis. We additionally found widespread regulation of APA in introns and global activation of upstream antisense transcripts during spermatogenesis. Interestingly, genes that display 3'UTR shortening tend to have higher levels of H3K4me3, consistent with the open chromatin feature previously observed in spermatids. Since genes with 3'UTR shortening tend to have functions important for further sperm development after spermatids, when transcription is halted, this result indicates that expression of short, stable mRNAs may serve the purpose of mRNA storage for later translation. Thus, APA in spermatogenesis connects regulation of chromatin status with post-transcriptional control, and impacts sperm maturation. 3'READS of 1 week to 6 week of testis development绝大多数哺乳动物基因均可发生可变切割与多聚腺苷酸化（alternative cleavage and polyadenylation，APA）现象。既往研究表明，在睾丸组织中，带有短3'非翻译区（3' untranslated region，3'UTR）的APA亚型更易优势表达。本研究揭示，在小鼠精子发生（spermatogenesis）的第一波过程中，APA可广泛介导3'UTR缩短，且精子细胞（spermatids）中的3'UTR长度最短。3'UTR的缩短可去除诸如富U元件（U-rich elements）与转座因子（transposable elements）等不稳定元件，而这些元件在精子发生过程中对转录本消除（transcript elimination）具有极强的调控效力。此外，本研究还发现，在精子发生过程中，内含子（introns）区域的APA调控现象广泛存在，且上游反义转录本（upstream antisense transcripts）呈现全局性激活状态。有趣的是，发生3'UTR缩短的基因往往具有更高水平的组蛋白H3赖氨酸4三甲基化（H3K4me3）修饰，这与此前在精子细胞中观察到的开放染色质特征相符。由于发生3'UTR缩短的基因，其功能多与精子细胞形成后进一步的精子发育相关，而此时转录过程已发生停滞；该结果表明，短而稳定的mRNA的表达可起到mRNA储存的作用，以供后续翻译使用。因此，精子发生过程中的APA将染色质状态调控与转录后调控联系起来，并对精子成熟产生重要影响。本数据集包含1至6周龄小鼠睾丸发育样本的3'READS测序数据。