转录组测序技术的研究和应用进展
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摘要
转录组(Transcriptome)是指特定细胞或组织中全部转录产物,包括信使RNA,核糖体RNA、转运RNA以及非编码RNA。高通量测序技术的快速发展,为从整体水平系统地研究转录组学研究提供快捷可靠的平台。综述了当前主流的高通量测序技术及其在转录组学研究中的应用,并讨论了转录组数据分析中一些值得关注的问题,以及转录组测序技术在生物学研究中的应用方向。
The transcriptome is the set of all RNA molecules in the specific tissue or cell,including message RNA,ribosome RNA,transfer RNA and non-coding RNAs. The rapid development of high-throughput sequencing technology provides a fast and reliable platform for the systematic study of transcriptome. Here we reviewed the current high-throughput sequencing technology and its application in transcriptome research,and discussed some issues worthy of attention in transcriptome data analysis,as well as the application direction of transcriptome sequencing technology in biological research.
The transcriptome is the set of all RNA molecules in the specific tissue or cell,including message RNA,ribosome RNA,transfer RNA and non-coding RNAs. The rapid development of high-throughput sequencing technology provides a fast and reliable platform for the systematic study of transcriptome. Here we reviewed the current high-throughput sequencing technology and its application in transcriptome research,and discussed some issues worthy of attention in transcriptome data analysis,as well as the application direction of transcriptome sequencing technology in biological research.
引文
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[6]Hutvagner G, Zamore PD. A microRNA in a multiple-turnover RNAi enzyme complex[J]. Science, 2002, 297(5589):2056-2060.
[7]Lam MT, Li W, et al. Enhancer RNAs and regulated transcriptional programs[J]. Trends Biochem Sci, 2014, 39(4):170-182.
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[9]Ashwal-Fluss R, Meyer M, et al. circRNA biogenesis competes with pre-mRNA splicing[J]. Mol Cell, 2014, 56(1):55-66.
[10]Abe N, Matsumoto K, et al. Rolling circle translation of circular RNA in living human cells[J]. Sci Rep, 2015, 5:16435.
[11]Kristensen LS, Hansen TB, Veno MT, et al. Circular RNAs in cancer:opportunities and challenges in the field[J]. Oncogene,2018, 37(5):555-565.
[12]Eberwine J, Yeh H, et al. Analysis of gene expression in single live neurons[J]. Proc Natl Acad Sci USA, 1992, 89(7):3010-3014.
[13]Brady G, Barbara M, Iscove NN. Representative in vitro cDNA amplification from individual hemopoietic cells and colonies[J].Methads in Molecular and Cellular Biology, 1990, 1(2):17-25.
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[15]Levin JZ, Yassour M, Adiconis X, et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods[J]. Nat Methods, 2010, 7(9):709-715.
[16]Bolger AM, Lohse M, Usadel B. Trimmomatic:a flexible trimmer for Illumina sequence data[J]. Bioinformatics, 2014, 30(15):2114-2120.
[17]Wang L, Wang S, Li W. RSeQC:quality control of RNA-seq experiments[J]. Bioinformatics, 2012, 28(16):2184-2185.
[18]Langmead B, Trapnell C, Pop M, et al. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome[J]. Genome Biol, 2009, 10(3):R25.
[19]Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie2[J]. Nat Methods, 2012, 9(4):357-359.
[20]Dobin A, Davis CA, Schlesinger F, et al. STAR:ultrafast universal RNA-seq aligner[J]. Bioinformatics, 2013, 29(1):15-21.
[21]Kim D, Langmead B, et al. HISAT:a fast spliced aligner with low memory requirements[J]. Nat Methods, 2015, 4:357-360.
[22]Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2009, 25(14):1754-1760.
[23]Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks[J]. Nat Protoc, 2012, 7(3):562-578.
[24]Guttman M, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs[J]. Nat Biotechnol, 2010, 28(5):503-510.
[25]Grabherr MG, Haas BJ, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J].Nat Biotechnol, 2011, 29(7):644-652.
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[28]Haas BJ, et al. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis[J]. Nat Protoc, 2013, 8(8):1494-1512.
[29]Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expressionanalysesforRNA-sequencingandmicroarray studies[J]. Nucleic Acids Res, 2015, 43(7):e47.
[30]Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J]. Nat Biotechnol,2010, 28(5):511-515.
[31]Anders S, Huber W. Differential expression analysis for sequence count data[J]. Genome Biol, 2010, 11(10):R106-R118.
[32]Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome Biol,2014, 15(12):550-571.
[33]Robinson MD, Mccarthy DJ, Smyth GK. edgeR:a Bioconductor package for differential expression analysis of digital gene expression data[J]. Bioinformatics, 2010, 26(1):139-140.
[34]Kharchenko PV, Silberstein L, Scadden DT. Bayesian approach to single-cell differential expression analysis[J]. Nat Methods,2014, 11(7):740-742.
[35]Bacher R, Kendziorski C. Design and computational analysis of single-cell RNA-sequencing experiments[J]. Genome Biol,2016, 17:63.
[36]Machnicka MA, Milanowska K, et al. MODOMICS:a database of RNA modification pathways-2013 update[J]. Nucleic acids research, 2013, 41(Database issue):D262-D267.
[37]Li H, Handsaker B, et al. The sequence alignment/map format and SAMtools[J]. Bioinformatics, 2009, 25(16):2078-2079.
[38]Li H. A statistical framework for SNP calling, mutation discovery,association mapping and population genetical parameter estimation from sequencing data[J]. Bioinformatics, 2011, 27(21):2987-2993.
[39]Mckenna A, Hanna M, et al. The genome analysis toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data[J]. Genome Res, 2010, 20(9):1297-1303.
[40]Klepikova AV, Kasianov AS, Gerasimov ES, et al. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling[J]. Plant J, 2016, 88(6):1058-1070.
[41]Kozomara A, Birgaoanu M, Griffiths-Jones S. miRBase:from microRNA sequences to function[J]. Nucleic Acids Res, 2019,47(D1):D155-D162.
[42]Liu XX, Mei WB, Soltis PS, et al. Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome[J]. Molecular Ecology Resources,2017, 17(6):1243-1256.
[43]Wang B, Regulski M, Tseng E, et al. A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing[J]. Genome Research, 2018, 28(6):921-932.
[44]Zhao X, Li J, Lian B, et al. Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA[J]. Nat Commun, 2018, 9(1):5056.
[45]RéDA, Lang PLM, Yones C, et al. Alternative use of miRNAbiogenesisco-factorsinplantsat lowtemperatures[J].Development, 2019, 146(5). pii:dev1721932.
[46]Haque A, Engel J, Teichmann SA, et al. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications[J]. Genome Med, 2017, 9(1):75.
[47]Levitin HM, Yuan J, et al. Single-cell transcriptomic analysis of tumor heterogeneity[J]. Trends Cancer, 2018, 4(4):264-268.
[48]Moffitt JR, Bambah-Mukku D, et al. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region[J]. Science, 2018, 362(6416). pii:eaau5324..
[2]MccarthyA.ThirdgenerationDNAsequencing:pacific biosciences’ single molecule real time technology[J]. Chem Biol,2010, 17(7):675-676.
[3]Branton D, Deamer DW, Marziali A, et al. The potential and challenges of nanopore sequencing[J]. Nat Biotechnol, 2008, 26(10):1146-1153.
[4]Wenger AM, Peluso P, Rowell WJ, et al. Highly-accurate longread sequencing improves variant detection and assembly of ahumangenome[J].bioRxiv,2019:doi:https://doi.org/10.1101/519025.
[5]ChuY,CoreyDR.RNAsequencing:platformselection,experimental design, and data interpretation[J]. Nucleic Acid Ther, 2012, 22(4):271-274.
[6]Hutvagner G, Zamore PD. A microRNA in a multiple-turnover RNAi enzyme complex[J]. Science, 2002, 297(5589):2056-2060.
[7]Lam MT, Li W, et al. Enhancer RNAs and regulated transcriptional programs[J]. Trends Biochem Sci, 2014, 39(4):170-182.
[8]Barrett SP, Salzman J. Circular RNAs:analysis, expression and potential functions[J]. Development, 2016, 11:1838-1847.
[9]Ashwal-Fluss R, Meyer M, et al. circRNA biogenesis competes with pre-mRNA splicing[J]. Mol Cell, 2014, 56(1):55-66.
[10]Abe N, Matsumoto K, et al. Rolling circle translation of circular RNA in living human cells[J]. Sci Rep, 2015, 5:16435.
[11]Kristensen LS, Hansen TB, Veno MT, et al. Circular RNAs in cancer:opportunities and challenges in the field[J]. Oncogene,2018, 37(5):555-565.
[12]Eberwine J, Yeh H, et al. Analysis of gene expression in single live neurons[J]. Proc Natl Acad Sci USA, 1992, 89(7):3010-3014.
[13]Brady G, Barbara M, Iscove NN. Representative in vitro cDNA amplification from individual hemopoietic cells and colonies[J].Methads in Molecular and Cellular Biology, 1990, 1(2):17-25.
[14]Tang F, BarbacioruC, Wang Y,et al. mRNA-Seqwholetranscriptome analysis of a single cell[J]. Nat Methods, 2009, 6(5):377-382.
[15]Levin JZ, Yassour M, Adiconis X, et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods[J]. Nat Methods, 2010, 7(9):709-715.
[16]Bolger AM, Lohse M, Usadel B. Trimmomatic:a flexible trimmer for Illumina sequence data[J]. Bioinformatics, 2014, 30(15):2114-2120.
[17]Wang L, Wang S, Li W. RSeQC:quality control of RNA-seq experiments[J]. Bioinformatics, 2012, 28(16):2184-2185.
[18]Langmead B, Trapnell C, Pop M, et al. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome[J]. Genome Biol, 2009, 10(3):R25.
[19]Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie2[J]. Nat Methods, 2012, 9(4):357-359.
[20]Dobin A, Davis CA, Schlesinger F, et al. STAR:ultrafast universal RNA-seq aligner[J]. Bioinformatics, 2013, 29(1):15-21.
[21]Kim D, Langmead B, et al. HISAT:a fast spliced aligner with low memory requirements[J]. Nat Methods, 2015, 4:357-360.
[22]Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2009, 25(14):1754-1760.
[23]Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks[J]. Nat Protoc, 2012, 7(3):562-578.
[24]Guttman M, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs[J]. Nat Biotechnol, 2010, 28(5):503-510.
[25]Grabherr MG, Haas BJ, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J].Nat Biotechnol, 2011, 29(7):644-652.
[26]Robertson G, Schein J, et al. De novo assembly and analysis of RNA-seq data[J]. Nat Methods, 2010, 7(11):909-912.
[27]Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies[J]. Current Protocols In Bioinformatics,2010, Chapter 11:Unit-11. 5.
[28]Haas BJ, et al. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis[J]. Nat Protoc, 2013, 8(8):1494-1512.
[29]Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expressionanalysesforRNA-sequencingandmicroarray studies[J]. Nucleic Acids Res, 2015, 43(7):e47.
[30]Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J]. Nat Biotechnol,2010, 28(5):511-515.
[31]Anders S, Huber W. Differential expression analysis for sequence count data[J]. Genome Biol, 2010, 11(10):R106-R118.
[32]Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome Biol,2014, 15(12):550-571.
[33]Robinson MD, Mccarthy DJ, Smyth GK. edgeR:a Bioconductor package for differential expression analysis of digital gene expression data[J]. Bioinformatics, 2010, 26(1):139-140.
[34]Kharchenko PV, Silberstein L, Scadden DT. Bayesian approach to single-cell differential expression analysis[J]. Nat Methods,2014, 11(7):740-742.
[35]Bacher R, Kendziorski C. Design and computational analysis of single-cell RNA-sequencing experiments[J]. Genome Biol,2016, 17:63.
[36]Machnicka MA, Milanowska K, et al. MODOMICS:a database of RNA modification pathways-2013 update[J]. Nucleic acids research, 2013, 41(Database issue):D262-D267.
[37]Li H, Handsaker B, et al. The sequence alignment/map format and SAMtools[J]. Bioinformatics, 2009, 25(16):2078-2079.
[38]Li H. A statistical framework for SNP calling, mutation discovery,association mapping and population genetical parameter estimation from sequencing data[J]. Bioinformatics, 2011, 27(21):2987-2993.
[39]Mckenna A, Hanna M, et al. The genome analysis toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data[J]. Genome Res, 2010, 20(9):1297-1303.
[40]Klepikova AV, Kasianov AS, Gerasimov ES, et al. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling[J]. Plant J, 2016, 88(6):1058-1070.
[41]Kozomara A, Birgaoanu M, Griffiths-Jones S. miRBase:from microRNA sequences to function[J]. Nucleic Acids Res, 2019,47(D1):D155-D162.
[42]Liu XX, Mei WB, Soltis PS, et al. Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome[J]. Molecular Ecology Resources,2017, 17(6):1243-1256.
[43]Wang B, Regulski M, Tseng E, et al. A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing[J]. Genome Research, 2018, 28(6):921-932.
[44]Zhao X, Li J, Lian B, et al. Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA[J]. Nat Commun, 2018, 9(1):5056.
[45]RéDA, Lang PLM, Yones C, et al. Alternative use of miRNAbiogenesisco-factorsinplantsat lowtemperatures[J].Development, 2019, 146(5). pii:dev1721932.
[46]Haque A, Engel J, Teichmann SA, et al. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications[J]. Genome Med, 2017, 9(1):75.
[47]Levitin HM, Yuan J, et al. Single-cell transcriptomic analysis of tumor heterogeneity[J]. Trends Cancer, 2018, 4(4):264-268.
[48]Moffitt JR, Bambah-Mukku D, et al. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region[J]. Science, 2018, 362(6416). pii:eaau5324..