Whole-transcriptome splicing profiling of E7.5 mouse primary germ layers reveals frequent alternative promoter usage during mouse early embryogenesis
Whole-transcriptome splicing profiling of E7.5 mouse primary germ layers reveals frequent alternative promoter usage during mouse early embryogenesis
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E7.5小鼠初级胚层的全转录组剪接分析揭示了小鼠早期胚胎发生过程中频繁使用的替代启动子
DOI：
10.1242/bio.032508
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发表时间：
2018-03
期刊：
影响因子：
2.4
通讯作者：
Li Lei
中科院分区：
文献类型：
--
作者：
Lu Xukun;Zhao Zhen-Ao;Wang Xiaoqing;Zhang Xiaoxin;Zhai Yanhua;Deng Wenbo;Yi Zhaohong;Li Lei
选择性剪接（AS）和选择性启动子（AP）的使用扩大了哺乳动物转录组谱的库，从而使基因功能多样化。然而，我们的知识的程度和功能的AS和AP的使用在小鼠早期胚胎发育仍然难以捉摸。在这里，通过高通量下一代测序进行全转录组剪接分析，我们报告说AS广泛发生在胚胎（E）7.5天的小鼠初级胚层，并可能参与多个发育过程。此外，许多RNA剪接因子在三个胚层中差异表达和选择性剪接，这意味着AS机制在塑造早期胚胎发生中的潜在重要性。值得注意的是，在这个阶段，AP的使用非常频繁，占显著不同AS事件总数的四分之一以上（430/1，648）。产生430个AP事件的基因参与许多生物学过程，包括小鼠早期胚胎发生所必需的重要调节因子，这表明AP的使用被广泛使用，可能与小鼠胚层特化有关。我们的数据强调了AP在小鼠原肠胚形成中的潜在意义，为理解哺乳动物早期发育的调控机制提供了丰富的数据来源并开辟了另一个维度。总结：本研究旨在捕捉小鼠原肠胚形成过程中的选择性剪接景观，强调在哺乳动物早期胚胎发生中使用选择性启动子的潜在重要性。
ABSTRACT Alternative splicing (AS) and alternative promoter (AP) usage expand the repertories of mammalian transcriptome profiles and thus diversify gene functions. However, our knowledge about the extent and functions of AS and AP usage in mouse early embryogenesis remains elusive. Here, by performing whole-transcriptome splicing profiling with high-throughput next generation sequencing, we report that AS extensively occurs in embryonic day (E) 7.5 mouse primary germ layers, and may be involved in multiple developmental processes. In addition, numerous RNA splicing factors are differentially expressed and alternatively spliced across the three germ layers, implying the potential importance of AS machinery in shaping early embryogenesis. Notably, AP usage is remarkably frequent at this stage, accounting for more than one quarter (430/1,648) of the total significantly different AS events. Genes generating the 430 AP events participate in numerous biological processes, and include important regulators essential for mouse early embryogenesis, suggesting that AP usage is widely used and might be relevant to mouse germ layer specification. Our data underline the potential significance of AP usage in mouse gastrulation, providing a rich data source and opening another dimension for understanding the regulatory mechanisms of mammalian early development. Summary: This study seeks to capture the alternative splicing landscape during mouse gastrulation, underlining the potential importance of alternative promoter usage in mammalian early embryogenesis.
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影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
14.9
作者：
通讯作者：
--
影响因子：
4.6
作者：
Verdier-Pinard P;Salaun D;Bouguenina H;Shimada S;Pophillat M;Audebert S;Agavnian E;Coslet S;Charafe-Jauffret E;Tachibana T;Badache A
通讯作者：
Badache A
DOI：
10.1083/jcb.200712086
发表时间：
2008-09-22
期刊：
The Journal of cell biology
影响因子：
--
作者：
Hirano M;Hashimoto S;Yonemura S;Sabe H;Aizawa S
通讯作者：
Aizawa S
影响因子：
4.1
作者：
Warzecha CC;Shen S;Xing Y;Carstens RP
通讯作者：
Carstens RP