dRNA-seq原理及其在原核生物转录组学研究中的应用

doi:10.3724/SP.J.1005.2013.00983

遗传 ›› 2013, Vol. 35 ›› Issue (8): 983-991.doi: 10.3724/SP.J.1005.2013.00983

dRNA-seq原理及其在原核生物转录组学研究中的应用

侯志伟^{1, 2}, 王赟³, 高宏¹, 侯圣伟 ¹

1. 中国科学院水生生物研究所, 淡水生态与生物技术国家重点实验室, 武汉 430072 2. 中国科学院大学, 北京 100049 3. 河南城建学院生物工程系, 平顶山 467036

收稿日期:2013-03-20 修回日期:2013-05-16 出版日期:2013-08-20 发布日期:2013-08-25
通讯作者: 高宏 E-mail:whihb2006@gmail.com
基金资助:
国家自然科学基金项目(编号：31270132)资助

The principle of dRNA-seq and its applications in prokaryotic tran-scriptome analyses

HOU Zhi-Wei^1,2, WANG Yun³, GAO Hong¹, HOU Sheng-Wei¹

1. The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China 2. University of Chinese Academy of Sciences, Beijing 100049, China 3. Department of Bioengineering, Henan University of Urban Construction, Pingdingshan 467036, China

Received:2013-03-20 Revised:2013-05-16 Online:2013-08-20 Published:2013-08-25

摘要/Abstract

摘要：

第二代测序技术不仅推进了基因组学的研究, 而且也广泛应用到转录组学的研究中。原核生物转录组学的研究方法主要有Tiling芯片和RNA-seq, 后者因其较高的覆盖率和分辨率以及越来越低廉的成本而逐渐被更多的研究单位采用。根据对mRNA富集方法或rRNA去除方法的不同, 目前RNA-seq方法主要有6种, 其中dRNA-seq由于采用了5′单磷酸依赖的外切酶, 可以特异性地降解加工过的转录本, 从而使初始转录本得到富集, 已被广泛应用到原核生物转录起始位点、小的调控RNA、启动子及操纵子等研究中。文章对dRNA-seq的原理、技术流程及其在原核生物转录组学研究中的应用进行了综述, 并对这一研究方法在现阶段应用的优势和局限性进行了讨论, 也进一步对该方法在未来的发展和应用进行了展望, 期望为国内相关领域研究人员提供参考。

关键词: 转录起始位点, 小RNA, 非编码RNA, dRNA-seq, 转录组测序

Abstract:

The genomic and transcriptomic studies have been greatly accelerated by the next-generation sequencing technology. Currently, there are two main methods in transcriptomic studies, namely, Tiling microarray and RNA-seq. Comparatively, because of its overwhelming superiority in transcript coverage and resolution, as well as decrease of costs, RNA-seq has been employed in transcriptome analyses by an increasing number of research institutes. According to the mRNA enrichment or rRNA depletion methods, RNA-seq can be performed in six ways. Among them, dRNA-seq can descriminate the original transcripts from the processed RNAs based on a differential exonuclease treatment. This kind of method has been broadly applied in studies of prokaryotic transcriptional start sites, small regulatory RNAs, promoters and operons, etc. Here, we reviewed the detailed principle and technical process of dRNA-seq and its applications in prokaryotic transcriptome analyses. Besides, we also summarized the advantages and limitations of dRNA-seq at present stage, and then gave our perspective of its future development and potential applications, expecting to present useful references for civil researchers in related fields.

Key words: dRNA-seq, sRNA, transcriptome sequencing, TSS, ncRNA

侯志伟王赟高宏侯圣伟. dRNA-seq原理及其在原核生物转录组学研究中的应用[J]. 遗传, 2013, 35(8): 983-991.

HOU Zhi-Wei WANG Yun GAO Hong HOU Sheng-Wei. The principle of dRNA-seq and its applications in prokaryotic tran-scriptome analyses[J]. HEREDITAS, 2013, 35(8): 983-991.

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dRNA-seq原理及其在原核生物转录组学研究中的应用

The principle of dRNA-seq and its applications in prokaryotic tran-scriptome analyses

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