The principle of dRNA-seq and its applications in prokaryotic tran-scriptome analyses
Received date: 2013-03-20
Revised date: 2013-05-16
Online published: 2013-08-25
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
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(Beijing), 2013 , 35(8) : 983 -991 . DOI: 10.3724/SP.J.1005.2013.00983
[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
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