Li Wencheng, Park Ji Yeon, Zheng Dinghai, Hoque Mainul, Yehia Ghassan, Tian Bin
Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA.
Transgenic Core Facility, Rutgers New Jersey Medical School, Newark, NJ, USA.
BMC Biol. 2016 Jan 22;14:6. doi: 10.1186/s12915-016-0229-6.
Most mammalian genes display alternative cleavage and polyadenylation (APA). Previous studies have indicated preferential expression of APA isoforms with short 3' untranslated regions (3'UTRs) in testes.
By deep sequencing of the 3' end region of poly(A) + transcripts, we report widespread shortening of 3'UTR through APA during the first wave of spermatogenesis in mouse, with 3'UTR size being the shortest in spermatids. Using genes without APA as a control, we show that shortening of 3'UTR eliminates destabilizing elements, such as U-rich elements and transposable elements, which appear highly potent during spermatogenesis. We additionally found widespread regulation of APA events in introns and exons that can affect the coding sequence of transcripts and global activation of antisense transcripts upstream of the transcription start site, suggesting modulation of splicing and initiation of transcription during spermatogenesis. Importantly, genes that display significant 3'UTR shortening tend to have functions critical for further sperm maturation, and testis-specific genes display greater 3'UTR shortening than ubiquitously expressed ones, indicating functional relevance of APA to spermatogenesis. Interestingly, genes with shortened 3'UTRs tend to have higher RNA polymerase II and H3K4me3 levels in spermatids as compared to spermatocytes, features previously known to be associated with open chromatin state.
Our data suggest that open chromatin may create a favorable cis environment for 3' end processing, leading to global shortening of 3'UTR during spermatogenesis. mRNAs with shortened 3'UTRs are relatively stable thanks to evasion of powerful mRNA degradation mechanisms acting on 3'UTR elements. Stable mRNAs generated in spermatids may be important for protein production at later stages of sperm maturation, when transcription is globally halted.
大多数哺乳动物基因表现出可变剪接和多聚腺苷酸化（APA）。先前的研究表明，在睾丸中，具有短3'非翻译区（3'UTR）的APA异构体优先表达。
通过对poly(A)+转录本的3'末端区域进行深度测序，我们报道了在小鼠精子发生的第一波过程中，通过APA广泛缩短了3'UTR，其中精子细胞中的3'UTR大小最短。以没有APA的基因为对照，我们表明3'UTR的缩短消除了不稳定元件，如富含U的元件和转座元件，这些元件在精子发生过程中似乎具有很强的作用。我们还发现内含子和外显子中的APA事件受到广泛调控，这可能影响转录本的编码序列以及转录起始位点上游反义转录本的全局激活，提示精子发生过程中剪接和转录起始的调控。重要的是，显示出显著3'UTR缩短的基因往往具有对精子进一步成熟至关重要的功能，并且睾丸特异性基因比普遍表达的基因表现出更大程度的3'UTR缩短，表明APA与精子发生具有功能相关性。有趣的是，与精母细胞相比，3'UTR缩短的基因在精子细胞中往往具有更高的RNA聚合酶II和H3K4me3水平，这些特征先前已知与开放染色质状态相关。
我们的数据表明，开放染色质可能为3'末端加工创造有利的顺式环境，导致精子发生过程中3'UTR的全局缩短。由于避开了作用于3'UTR元件的强大mRNA降解机制，具有缩短3'UTR的mRNA相对稳定。精子细胞中产生的稳定mRNA对于精子成熟后期的蛋白质产生可能很重要，此时转录全局停止。
