Wen Qiuhan, Wang Zhen, Bao Qi, Ding Tianli, Zhang Haihan, Li Jianbo, Liu Zhuang, Huang Jieping, Yi Guoqiang
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
Genome Res. 2025 Sep 2;35(9):2116-2129. doi: 10.1101/gr.280095.124.
As an important posttranscriptional modification mechanism, alternative polyadenylation (APA) plays a crucial role in gene regulation and phenotypic diversity. Whereas extensive studies have explored the global APA landscape using bulk RNA-seq data, in-depth analyses of APA events at the single-cell level remain limited-particularly in farm animals. In this study, we construct a comprehensive APA atlas for 261 cell types across 19 porcine tissues based on single-nucleus RNA sequencing (snRNA-seq) data. This analysis reveals tissue- and cell type-specific patterns of APA. We find that many genes display a clear correlation between the average length of 3' untranslated regions (3' UTRs) and expression levels in various cell types, with most showing a negative correlation. Early cell types within the developmental lineage, such as spermatogonia and satellite cells, display longer 3' UTRs, especially for spermatogenesis, where 3' UTR lengths show significant decreasing trends along the differentiation trajectory. Notably, we find that variable 3' UTR lengths in the and genes might be critical regulators during spermatogenesis and myogenesis, respectively, potentially through modulation of RNA-binding protein and miRNA binding sites. Furthermore, the SNP rs323354626, located in the 3' UTR of the gene, significantly impacts gene splicing and is strongly associated with reproductive phenotypes. Additionally, we observe that neuronal cells generally possess longer 3' UTRs-a pattern conserved across humans, mice, fruit flies, and pigs. Together, these findings enrich the single-cell atlas of pigs by adding a layer of posttranscriptional regulation to the existing gene expression data, highlighting the significant role of cell type-specific 3' UTR lengths in cell commitment and complex trait regulation.
作为一种重要的转录后修饰机制，可变聚腺苷酸化（APA）在基因调控和表型多样性中起着关键作用。尽管已有大量研究利用批量RNA测序（RNA-seq）数据探索了全球APA图谱，但在单细胞水平上对APA事件的深入分析仍然有限，尤其是在农场动物中。在本研究中，我们基于单核RNA测序（snRNA-seq）数据构建了一个涵盖19种猪组织中261种细胞类型的综合APA图谱。该分析揭示了APA的组织和细胞类型特异性模式。我们发现，许多基因在不同细胞类型中的3'非翻译区（3'UTR）平均长度与表达水平之间存在明显的相关性，大多数呈负相关。发育谱系中的早期细胞类型，如精原细胞和卫星细胞，显示出更长的3'UTR，特别是在精子发生过程中，3'UTR长度沿分化轨迹呈现显著下降趋势。值得注意的是，我们发现 和 基因中可变的3'UTR长度可能分别是精子发生和肌发生过程中的关键调节因子，可能是通过调节RNA结合蛋白和miRNA结合位点来实现的。此外，位于 基因3'UTR中的单核苷酸多态性（SNP）rs323354626显著影响基因剪接，并与生殖表型密切相关。此外，我们观察到神经元细胞通常具有更长的3'UTR，这一模式在人类、小鼠、果蝇和猪中都是保守的。总之，这些发现通过在现有的基因表达数据中增加一层转录后调控，丰富了猪的单细胞图谱，突出了细胞类型特异性3'UTR长度在细胞分化和复杂性状调控中的重要作用。
