Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
Biomed Res Int. 2020 Mar 16;2020:2626584. doi: 10.1155/2020/2626584. eCollection 2020.
Many increasing documents have proved that alternative polyadenylation (APA) events with different polyadenylation sites (PAS) contribute to posttranscriptional regulation. However, little is known about the detailed molecular features of PASs and its role in porcine fast and slow skeletal muscles through microRNAs (miRNAs) and RNA binding proteins (RBPs). In this study, we combined single-molecule real-time sequencing and Illumina RNA-seq datasets to comprehensively analyze polyadenylation in pigs. We identified a total of 10,334 PASs, of which 8734 were characterized by reference genome annotation. 32.86% of PAS-associated genes were determined to have more than one PAS. Further analysis demonstrated that tissue-specific PASs between fast and slow muscles were enriched in skeletal muscle development pathways. In addition, we obtained 1407 target genes regulated by APA events through potential binding 69 miRNAs and 28 RBPs in variable 3' UTR regions and some are involved in myofiber transformation. Furthermore, the de novo motif search confirmed that the most common usage of canonical motif AAUAAA and three types of PASs may be related to the strength of motifs. In summary, our results provide a useful annotation of PASs for pig transcriptome and suggest that APA may serve as a role in fast and slow muscle development under the regulation of miRNAs and RBPs.
许多研究表明，具有不同多聚腺苷酸化位点（PAS）的可变多聚腺苷酸化（APA）事件有助于转录后调控。然而，对于 PAS 的详细分子特征及其通过 microRNAs（miRNAs）和 RNA 结合蛋白（RBPs）在猪快肌和慢肌中的作用知之甚少。在这项研究中，我们结合单分子实时测序和 Illumina RNA-seq 数据集，全面分析了猪的多聚腺苷酸化。我们共鉴定了 10334 个 PAS，其中 8734 个通过参考基因组注释进行了特征描述。32.86%的 PAS 相关基因被确定具有多个 PAS。进一步分析表明，快肌和慢肌之间的组织特异性 PAS 富集在骨骼肌发育途径中。此外，我们通过可变 3'UTR 区域中潜在结合的 69 个 miRNAs 和 28 个 RBPs，获得了 1407 个受 APA 事件调控的靶基因，其中一些与肌纤维转化有关。此外，从头 motif 搜索证实，最常见的使用规范 motif AAUAAA 和三种 PAS 类型可能与 motif 的强度有关。总之，我们的研究结果为猪转录组提供了有用的 PAS 注释，并表明 APA 可能在 miRNA 和 RBPs 的调控下在快肌和慢肌发育中发挥作用。
