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.

参考文献

[1] 李湘龙, 柏斌, 吴俊, 邓启云, 周波. 第二代测序技术用于水稻和稻瘟菌互作早期转录组的分析. 遗传, 2012, 34(1): 102-112.

[2] 梁烨, 陈双燕, 刘公社. 新一代测序技术在植物转录组研究中的应用. 遗传, 2011, 33(12): 1317-1326.

[3] Gregory BD, Yazaki J, Ecker JR. Utilizing tiling microarrays for whole-genome analysis in plants. Plant J, 2008, 53(4): 636-644.

[4] Yazaki J, Gregory BD, Ecker JR. Mapping the genome landscape using tiling array technology. Curr Opin Plant Biol, 2007, 10(5): 534-542.

[5] Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res, 2008, 18(9): 1509-1517.

[6] 祁云霞, 刘永斌, 荣威恒. 转录组研究新技术: RNA- Seq及其应用. 遗传, 2011, 33(11): 1191-1202.

[7] Westermann AJ, Gorski SA, Vogel J. Dual RNA-seq of pathogen and host. Nat Rev Microbiol, 2012, 10(9): 618-630.

[8] Sorek R, Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet, 2009, 11(1): 9-16.

[9] Yoder-Himes DR, Chain PSG, Zhu Y, Wurtzel O, Rubin E, Tiedje JM, Sorek R. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci USA, 2009, 106(10): 3976-3981.

[10] Stewart FJ, Ottesen EA, DeLong EF. Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J, 2010, 4(7): 896-907.

[11] Ottesen EA, Young CR, Eppley JM, Ryan JP, Chavez FP, Scholin CA, DeLong EF. Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc Natl Acad Sci USA, 2013, 110(6): E488-E497.

[12] Dodd D, Moon YH, Swaminathan K, Mackie RI, Cann IK. Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic Bacteroidetes. J Biol Chem, 2010, 285(39): 30261-30273.

[13] Chen ZT, Duan XP. Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications. Methods Mol Biol, 2011, 733:93-103.

[14] Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Ward D V, Nusbaum C, Birren B W, Gnirke A. Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol, 2012, 13(3): r23.

[15] Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, Shah JK, Dey J, Rohl CA, Johnson JM. Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat Methods, 2009, 6(9): 647-649.

[16] Bogdanova EA, Shagin DA, Lukyanov SA. Normalization of full-length enriched cDNA. Mol Biosyst, 2008, 4(3): 205-212.

[17] Yi H, Cho YJ, Won S, Lee JE, Yu HJ, Kim S, Schroth GP, Luo S, Chun J. Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq. Nucleic Acids Res, 2011, 39(20): e140-e140.

[18] Frias-Lopez J, Shi YM, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, DeLong EF. Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA, 2008, 105(10): 3805-3810.

[19] Warnecke F, Hess M. A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol, 2009, 142(1): 91-95.

[20] Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet, 2008, 4(8): e1000163.

[21] Zhang AX, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S. Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol, 2003, 50(4): 1111-1124.

[22] He SM, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R. Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods, 2010, 7(10): 807-812.

[23] Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermü

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

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

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	韩熙, 罗富成. 单细胞转录组测序在少突胶质谱系细胞异质性与神经系统疾病中的应用[J]. 遗传, 2023, 45(3): 198-211.
[2]	吕雪, 李帮洁, 徐寒梅. 功能性微肽通量发现和功能验证的研究进展[J]. 遗传, 2022, 44(6): 478-490.
[3]	熊婉迪, 徐开宇, 陆林, 李家立. 长链非编码RNA在阿尔茨海默病中的研究进展[J]. 遗传, 2022, 44(3): 189-197.
[4]	崔浩亮, 史佩华, 高锦春, 张新博, 赵顺然, 陶晨雨. 细胞重编程过程中核小体定位改变研究进展[J]. 遗传, 2022, 44(3): 208-215.
[5]	程敏, 张静, 曹鹏博, 周钢桥. 缺氧相关长链非编码RNA作为肝癌预后预测标志物的潜在价值[J]. 遗传, 2022, 44(2): 153-167.
[6]	陈相颖, 李梦玮, 王颖, 陈权, 徐寒梅. 小开放阅读框编码微肽的研究进展[J]. 遗传, 2021, 43(8): 737-746.
[7]	马剑峰, 甘麦邻, 朱砺, 沈林園. 转运RNA衍生的小RNA功能及其研究方法[J]. 遗传, 2021, 43(12): 1107-1120.
[8]	梁文权,侯豫,赵存友. 精神分裂症相关单核苷酸多态性调控microRNA功能研究进展[J]. 遗传, 2019, 41(8): 677-685.
[9]	张競文,续倩,李国亮. 癌症发生发展中的表观遗传学研究[J]. 遗传, 2019, 41(7): 567-581.
[10]	张华伟, 孟星宇, 李连峰, 杨玉莹, 仇华吉. 长链非编码RNA——抗病毒天然免疫应答的新兴调控因子[J]. 遗传, 2018, 40(7): 525-533.
[11]	周瑞,王以鑫,龙科任,蒋岸岸,金龙. LncRNA调控骨骼肌发育的分子机制及其在家养动物中的研究进展[J]. 遗传, 2018, 40(4): 292-304.
[12]	李恩惠,赵欣,张策,刘威. 脆性X智力低下蛋白参与非编码RNA通路的研究进展[J]. 遗传, 2018, 40(2): 87-94.
[13]	任岚,肖茹丹,张倩,娄晓敏,张昭军,方向东. KLF1和KLF9对K562细胞红系分化的协同调控作用[J]. 遗传, 2018, 40(11): 998-1006.
[14]	叶仲杰,刘启鹏,岑山,李晓宇. LINE-1编码的逆转录酶在肿瘤形成过程中的作用[J]. 遗传, 2017, 39(5): 368-376.
[15]	魏凯,马磊. 高通量测序时代下持家基因定义的发展[J]. 遗传, 2017, 39(2): 127-134.