Modeling of Genome-Wide Polyadenylation Signals in Xenopus tropicalis
Modeling of Genome-Wide Polyadenylation Signals in Xenopus tropicalis
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热带爪蟾全基因组多腺苷酸化信号的建模
DOI：
10.3389/fgene.2019.00647
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发表时间：
2019
影响因子：
3.7
通讯作者：
Ji Guoli
中科院分区：
文献类型：
--
作者：
Zhu Sheng;Wu Xiaohui;Fu Hongjuan;Ye Congting;Chen Moliang;Jiang Zhihua;Ji Guoli
选择性多聚腺苷酸化（阿帕）是一种重要的转录后修饰事件，用于处理信使RNA（mRNA）的转录终止、转运和翻译。在本研究中，我们使用来自16，511个蛋白质编码基因的70，918个高度可信的poly（A）位点来表征热带爪蟾中的poly（A）信号，以了解它们在胚胎发育和性别差异调节中的作用。我们研究了可能影响阿帕患病率的潜在因素，包括基因长度、基因中内含子的数量和内含子长度。我们观察到12个突出的poly（A）信号模式，约占92%的总阿帕网站在热带爪蟾。其中，有三种模式是X所特有的.因此，它们在其他动物如人类或小鼠中不存在。我们根据阿帕位点的基因组区域对其进行编目，并开发了一个生物信息学管道来识别每个类别的过度代表信号模式。提出了阿帕位点在每个基因组区域的顺式元件模式。更重要的是，阿帕的使用是显着动态的胚胎沿着五个发展阶段，并与母合子过渡事件协调。我们使用了基于熵的方法来确定特定的发育阶段的阿帕网站，并确定了显着的信号模式周围的特定网站和组成型网站。我们发现阿帕在不同基因组区域的频率随发育阶段而变化，位于内含子或编码序列区域的位点对发育阶段基因表达的动态变化贡献最大。本研究揭示了X染色体上典型阿帕位点和非典型阿帕位点在不同发育阶段和性别二态性中的特征和poly（A）信号模式。tropicalis，提供了新的见解远端和近端阿帕的动态调节。
Alternative polyadenylation (APA) is an important post-transcriptional modification event to process messenger RNA (mRNA) for transcriptional termination, transport, and translation. In the present study, we characterized poly(A) signals in Xenopus tropicalis using 70,918 highly confident poly(A) sites derived from 16,511 protein-coding genes to understand their roles in the regulation of embryo development and gender difference. We examined potential factors, including the gene length, the number of introns in a gene, and the intron length, that may affect the prevalence of APA. We observed 12 prominent poly(A) signal patterns, which accounted for approximately 92% of total APA sites in Xenopus tropicalis. Among them, three patterns are specific to X. tropicalis, so they are absent in other animals such as humans or mice. We catalogued APA sites based on their genomic regions and developed a bioinformatics pipeline to identify over-represented signal patterns for each class. Then the schema of cis elements for APA sites in each genomic region was proposed. More importantly, APA usage is dramatically dynamic in embryos along five developmental stages and well-coordinated with the maternal-to-zygotic transition event. We used an entropy-based method to identify developmental stage-specific APA sites and identified significant signal patterns around specific sites and constitutive sites. We found that the APA frequency in different genomic regions varies with developmental stages and that those sites located in intron or coding sequence regions contribute most to the dynamics of gene expression during developmental stages. This study deciphers the characteristics and poly(A) signal patterns for both canonical APA sites and non-canonical APA sites across different developmental stages and gender dimorphisms in X. tropicalis, providing new insights into the dynamic regulation of distal and proximal APA.