利用三代测序技术识别小鼠早期胚胎等位基因特异的转录本和剪切事件  

Using Third-Generation Sequencing to Identify Allele-Spe⁃cific Transcripts and Splicing Events in Early Mouse Em⁃bryogenesis

作　　者：袁杰 李敏 黄诗圣 舒文杰 任超 YUAN Jie;LI Min;HUANG Shi-Sheng;SHU Wen-Jie;REN Chao(Institute of Radiation Medicine,Academy of Military Medical Sciences,Beijing 100850;Precise Genome Engi-neering Center,School of Life Sciences,Guangzhou University,Guangzhou 510006;School of Life Science and Technology,ShanghaiTech University,Shanghai 201210,China)

机构地区：[1]军事医学研究院辐射医学研究所,北京100850 [2]广州大学生命科学学院精准基因编辑工程中心,广东广州510006 [3]上海科技大学生命科学与技术学院,上海201210

出　　处：《生物技术通讯》2020年第6期659-669,共11页Letters in Biotechnology

基　　金：国家自然科学基金(61873276)。

摘　　要：目的:探究三代测序技术在研究小鼠早期胚胎发育过程中等位基因特异的转录组和可变剪切中的优势。方法:收集已发表文献中小鼠早期胚胎的测序数据,用这些数据识别等位基因特异的转录本和可变剪切事件以及差异可变剪切事件,比较二代测序数据和三代测序数据识别的结果。结果:小鼠早期胚胎7个阶段的三代测序数据中分别识别出1288、759、734、955、976、953和834个等位基因特异的转录本,值得注意的是50%~94%的等位基因特异的转录本无法被二代测序数据所识别。与二代测序技术相比,三代测序在鉴别可变剪切事件方面具有更高的潜力,并且三代数据可以鉴别出大量准确且特异的剪切结。另外,在每个阶段平均鉴定出650个等位基因特异的可变剪切事件和26个差异可变剪切事件。结论:三代测序技术有助于发现新的等位基因特异的转录本和可变剪切事件以及差异可变剪切事件,从而为早期胚胎发育研究领域提供宝贵的注释资源。Objective:To explore the advantages of third-generation sequencing technology in studying allele-spe⁃cific transcriptomes and alternative splicing during early mouse embryonic development.Methods:We collected the sequencing data of mouse early embryos in the previously published literature,and utilized these data to identi⁃fy allele-specific transcripts and alternative splicing events as well as differential alternative splicing events.And then compared the results identified from next-generation sequencing and third-generation sequencing datasets re⁃spectively.Results:The 1288,759,734,955,976,953 and 834 allele-specific transcripts were identified in the third-generation sequencing data of seven stages of embryogenesis.Notably,50%~94%of these allele-specific tran⁃scripts were not able to be identified from short-read data of early embryogenesis.The third-generation sequenc⁃ing has greater potential for identifying novel alternative splicing events than next-generation sequencing,and a large number of accurate and unique splicing junctions were identified with third-generation sequencing.In addi⁃tion,there were an average of 650 allele-specific splicing events and 26 differential splicing events identified in each stage examined.Conclusion:Third-generation sequencing technology can facilitate the discovery of novel al⁃lele-specific transcripts and alternative splicing events as well as differential alternative splicing events,thereby providing a valuable resource to the field of early embryo development.

关 键 词：三代测序技术 等位基因特异 可变剪切 早期胚胎 

分 类 号：Q786[生物学—分子生物学]