A single-cell genomic strategy for alternative transcript start sites identification

文献类型： 外文期刊

第一作者： Peng, Yanling

作者： Peng, Yanling;Huang, Qitong;Liu, Danli;Kong, Siyuan;Zhang, Yubo;Huang, Qitong;Kamada, Rui;Ozato, Keiko;Zhang, Yubo;Zhu, Jun;Zhang, Yubo;Zhu, Jun

作者机构：

关键词： analytical biotechnology; bioinformatics

期刊名称：BIOTECHNOLOGY JOURNAL （ 影响因子：4.7； 五年影响因子：4.5 ）

ISSN： 1860-6768

年卷期： 2024 年 19 卷 3 期

页码：

收录情况： SCI

摘要： Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. We report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. In the method, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNAs, then dual priming oligonucleotide system to specifically enrich TSSs for genomic analysis. We apply this method to a genome-wide study of alternative TSSs identification in two different IFN-beta stimulated mouse embryonic fibroblasts (MEFs). The data clearly discriminate two IFN-beta stimulated MEFs. Moreover, our results indicate 81% expressed genes in these two cell types containing multiple TSSs, which is much higher than previous predictions based on Cap-Analysis Gene Expression (CAGE) (58%) or empirical determination (54%) in various cell types. This indicates that alternative TSSs are more pervasive than expected and implies our strategy could position them at an unprecedented sensitivity. It would be helpful for elucidating their biological insights in future. We developed a single cell method for detecting alternative transcript start sites. P5, Nextera XT illumina P5 primers; DPO P7, custom-made DPO P7 primers. DPO, dual priming oligonucleotides; scTSS-seq, single cell TSSs sequencing. image

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