Yu Zhibo, Hong Liwei, Li Qingshun Q
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China.
Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States.
Front Genet. 2022 Apr 26;13:863253. doi: 10.3389/fgene.2022.863253. eCollection 2022.
Alternative polyadenylation (APA) of pre-mRNA is an important co-transcriptional mechanism that modulates gene expression, leading to transcriptomic and functional diversities. The role of APA in leaf development, however, remains elusive. We applied a poly(A)-tag sequencing (PAT-seq) technique to characterize APA-mediated regulation events in cotyledon and in five stages of true leaf development. Over 60% APA was identified in genes expressed in leaves, consistent with the results in previous publications. However, a reduced APA level was detected in younger leaves, reaching 44% in the 18th true leaf. Importantly, we also found that >70% of the poly(A) site usages were altered in the second true leaf relative to the cotyledon. Compared with the cotyledon, more genes in the second true leaf tended to use the distal site of 3'UTR, but this was not found in pairwise comparison among other true leaves. In addition, a significant APA gene was found to be decreased in a pairwise comparison among true leaves, including differentially expressed genes. The APA genes identified herein were associated with specific biological processes, including metabolic and cellular processes and response to stimuli and hormones. These results provide a new insight into the regulation of leaf development through APA.
前体mRNA的可变聚腺苷酸化（APA）是一种重要的共转录机制，可调节基因表达，导致转录组和功能多样性。然而，APA在叶片发育中的作用仍不清楚。我们应用了聚（A）标签测序（PAT-seq）技术来表征子叶和真叶发育五个阶段中APA介导的调控事件。在叶片中表达的基因中鉴定出超过60%的APA，这与先前出版物中的结果一致。然而，在较年轻的叶片中检测到APA水平降低，在第18片真叶中降至44%。重要的是，我们还发现，相对于子叶，第二片真叶中>70%的聚（A）位点使用发生了改变。与子叶相比，第二片真叶中更多的基因倾向于使用3'UTR的远端位点，但在其他真叶的两两比较中未发现这种情况。此外，在真叶的两两比较中发现一个显著的APA基因减少，包括差异表达基因。本文鉴定的APA基因与特定的生物学过程相关，包括代谢和细胞过程以及对刺激和激素的反应。这些结果为通过APA调控叶片发育提供了新的见解。
