转录组测序技术在生物学研究中的现状及展望
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摘要
高通量测序技术在当前生物学研究中占据了越来越重要的地位,而转录组学的研究更是占据了很大区域。本文针对Illumnina测序对转录组测序的应用前景、发展概况以及存在的问题进行综述,并对Pacbio测序原理进行剖析,对Nanopore公司开发的MinlON四代测序进行展望,阐述整个转录组测序技术的发展。
The high throughput sequencing technology has been playing an increasingly important role in current biological research,in which transcriptome research has occupied a large area.In this paper,the application prospect,development and existing problems of Illumnina sequencing are reviewed.The principle of Pacbio sequencing is analyzed,and the MinlON 4 thgeneration sequencing of the Nanopore Company is prospected,and the development of the whole sequence of the transcriptional sequence is described.
The high throughput sequencing technology has been playing an increasingly important role in current biological research,in which transcriptome research has occupied a large area.In this paper,the application prospect,development and existing problems of Illumnina sequencing are reviewed.The principle of Pacbio sequencing is analyzed,and the MinlON 4 thgeneration sequencing of the Nanopore Company is prospected,and the development of the whole sequence of the transcriptional sequence is described.
引文
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[35]Tang F,Barbacioru C,Wang Y,et al.mRNA-Seq whole-transcriptome analysis of a single cell[J].Nature methods,2009,6(5):377-382.
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[40]岳建宇,费忠安,郎小强,等.基于全基因组预测莱茵衣藻的新miRNA及其靶基因[J].应用与环境生物学报,2015,21(01):68-74.
[41]Chen X,Xie D,Zhao Q,et al.MicroRNAs and complex diseases:from experimental results to computational models[J].Briefings in Bioinformatics,2016,18(4):558.
[42]Li M,Xia Y,Gu Y,et al.MicroRNAome of porcine pre-and postnatal development[J].PloS one,2010,5(7):e11541.
[43]Sultan M,Schulz M H,Richard H,et al.A global view of gene activity and alternative splicing by deep sequencing of the humantranscriptome[J].Science,2008,321(5891):956-960.
[44]Ozsolak F,Milos P M.RNA sequencing:advances,challenges and opportunities[J].Nature reviews genetics,2011,12(2):87-98.
[45]张烨华.杂交盘羊尾部抑制性消减文库的构建与转录组初步分析[D].石河子:石河子大学,2015.
[46]胡海岩.基于新一代测序技术的三种髓系血液细胞系转录组研究及杂色鲍微卫星富集文库构建和多态性验证[D].北京:中国科学院北京基因组研究所,2011.
[47]Kapranov P,Willingham A T,Gingeras T R.Genome-wide transcription and the implications for genomic organization[J].Nature Reviews Genetics,2007,8(6):413-423.
[48]Dutrow N,Nix D A,Holt D,et al.Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping[J].Nature genetics,2008,40(8):977-986.
[49]Robinson M D,Oshlack A.A scaling normalization method for differential expression analysis of RNA-seq data[J].Genome Biol,2010,11(3):R25.
[50]Li R,Li Y,Kristiansen K,et al.SOAP:short oligonucleotide alignmentprogram[J].Bioinformatics,2008,24(5):713-714.
[51]Tao Zhao,Hong-Shuai Zhang,Hao Tang,Jian-Hui Jiang.Nanopore biosensor for sensitive and label-free nucleic acid detection based on hybridization chain reaction amplification[J].Talanta,2017,175:121-126.
[2]Costa V,Angelini C,De Feis I,et al.Uncovering the complexity of transcriptomes with RNA-Seq[J].BioMed Research International,2010,2010.
[3]Wang Z,Gerstein M,Snyder M.RNA-Seq:a revolutionary tool for transcriptomics[J].Nature Reviews Genetics,2009,10(1):57-63.
[4]Mardis E R.A decade’sperspective on DNA sequencing technology[J].Nature,2011,470(7333):198-203.
[5]Metzker M L.Sequencing technologies-the next generation[J].Nature reviews genetics,2010,11(1):31-46.
[6]Bentley D R,Balasubramanian S,Swerdlow H P,et al.Accurate whole human genome sequencing using reversible terminator chemistry[J].nature,2008,456(7218):53-59.
[7]Margulies M,Egholm M,Altman W E,et al.Genome sequencing in microfabricated high-density picolitre reactors[J].Nature,2005,437(7057):376-380.
[8]Smith D R,Quinlan A R,Peckham H E,et al.Rapid whole-genome mutational profiling using next-generation sequencing technologies[J].Genome research,2008,18(10):1638-1642.
[9]Mardis E R.The impact of next-generation sequencing technology on genetics[J].Trends in genetics,2008,24(3):133-141.
[10]Shendure J,Ji H.Next-generation DNA sequencing[J].Nature biotechnology,2008,26(10):1135-1145.
[11]Mardis E R.Next-generation DNA sequencing methods[J].Annu.Rev.Genomics Hum.Genet.,2008,9:387-402.
[12]Ozsolak F,Milos P M.RNA sequencing:advances,challenges and opportunities[J].Nature reviews genetics,2011,12(2):87-98.
[13]Maher C A,Palanisamy N,Brenner J C,et al.Chimeric transcript discovery by paired-end transcriptome sequencing[J].Proceedings of the National Academy of Sciences,2009,106(30):12353-12358.
[14]Au K F,Jiang H,Lin L,et al.Detection of splice junctions from paired-end RNA-seq data by SpliceMap[J].Nucleic acids research,2010,38(14):4570-4578.
[15]Edgren H,Murumagi A,Kangaspeska S,et al.Identification of fusion genes in breast cancer by paired-end RNA-sequencing[J].Genome Biol,2011,12(1):R6.
[16]Dobin A,Davis C A,Schlesinger F,et al.STAR:ultrafast universal RNA-seq aligner[J].Bioinformatics,2013,29(1):15-21.
[17]Ghosh S,Chan C K.Analysis of RNA-Seq Data Using Top Hat and Cufflinks[M]//Plant Bioinformatics.Springer New York,2016:339-361.
[18]Yang-Ming S I,Xing Y Q,Cai L.Differential splicing event analysis of liver tumor-educated blood platelets RNA-seq data with Hisat2 and MISO[J].Journal of Inner Mongolia University of Science&Technology,2016,35(3):274-279.
[19]Ghosh S,Chan C K.Analysis of RNA-Seq Data Using Top Hat and Cufflinks[M]//Plant Bioinformatics.Springer New York,2016:339-61.
[20]Pertea M,Pertea G M,Antonescu C M,et al.String Tie enables improved reconstruction of a transcriptome from RNA-seq reads[J].Nature Biotechnology,2015,33(3):290-295.
[21]Love M I,Huber W,Anders S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J].Genome Biology,2014,15(12):550.
[22]AnthonyRhoads,Kin Fai Au.PacBio Sequencing and Its Applications[J].Genomics,Proteomics&Bioinformatics,2015,13(05):278-289.
[23]RocheDiagnosticsCorporation.GSFLX+system,
[24]Li H,Ruan J,Durbin R.Mapping short DNA sequencing reads and calling variants using mapping quality scores[J].Genome research,2008,18(11):1851-1858.
[25]Ingolia N T,Ghaemmaghami S,Newman J R S,et al.Genomewide analysis in vivo of translation with nucleotide resolution using ribosome profiling[J].science,2009,324(5924):218-223.
[26]Forrest A RR.Stem cell transcriptome profiling via massive-scale mRNA sequencing[J].Nat Methods,2008.5(7):613-619.
[27]David L,Huber W,Granovskaia M,et al.A high-resolution map of transcription in the yeast genome[J].Proceedings of the National Academy of Sciences,2006,103(14):5320-5325.
[28]Marioni J C,Mason C E,Mane S M,et al.RNA-seq:an assessment of technical reproducibility and comparison with gene expression arrays[J].Genome research,2008,18(9):1509-1517.
[29]Nagalakshmi U,Wang Z,Waern K,et al.The transcriptional landscape of the yeast genome defined by RNA sequencing[J].Science,2008,320(5881):1344-1349.
[30]高阳,薛大伟,钱前,等.二代测序技术在水稻基因组学和转录组学研究中的应用[J].中国水稻科学,2015,29(2):208-214.
[31]陈柳,华清泉.转录组在肿瘤中的应用及进展[J].中国医药导报,2016,13(06):58-61.
[32]Zhang G,Guo G,Hu X,et al.Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome[J].Genome research,2010,20(5):646-654.
[33]Shah S P,Morin R D,Khattra J,et al.Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution[J].Nature,2009,461(7265):809-813.
[34]Zhang G,Guo G,Hu X,et al.Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome[J].Genome research,2010,20(5):646-654.
[35]Tang F,Barbacioru C,Wang Y,et al.mRNA-Seq whole-transcriptome analysis of a single cell[J].Nature methods,2009,6(5):377-382.
[36]Mortazavi A,Williams B A,Mc Cue K,et al.Mapping and quantifying mammalian transcriptomes by RNA-Seq[J].Nature methods,2008,5(7):621-628.
[37]Clamp M,Fry B,Kamal M,et al.Distinguishing protein-coding and noncoding genes in the humangenome[J].Proceedings of the National Academy of Sciences,2007,104(49):19428-19433.
[38]韩雪.拟南芥miR156介导种子成熟调控机制的初步研究[D].长春:吉林大学,2017.
[39]Metzker M L.Sequencing technologies-the next generation[J].Nature reviews genetics,2010,11(1):31-46.
[40]岳建宇,费忠安,郎小强,等.基于全基因组预测莱茵衣藻的新miRNA及其靶基因[J].应用与环境生物学报,2015,21(01):68-74.
[41]Chen X,Xie D,Zhao Q,et al.MicroRNAs and complex diseases:from experimental results to computational models[J].Briefings in Bioinformatics,2016,18(4):558.
[42]Li M,Xia Y,Gu Y,et al.MicroRNAome of porcine pre-and postnatal development[J].PloS one,2010,5(7):e11541.
[43]Sultan M,Schulz M H,Richard H,et al.A global view of gene activity and alternative splicing by deep sequencing of the humantranscriptome[J].Science,2008,321(5891):956-960.
[44]Ozsolak F,Milos P M.RNA sequencing:advances,challenges and opportunities[J].Nature reviews genetics,2011,12(2):87-98.
[45]张烨华.杂交盘羊尾部抑制性消减文库的构建与转录组初步分析[D].石河子:石河子大学,2015.
[46]胡海岩.基于新一代测序技术的三种髓系血液细胞系转录组研究及杂色鲍微卫星富集文库构建和多态性验证[D].北京:中国科学院北京基因组研究所,2011.
[47]Kapranov P,Willingham A T,Gingeras T R.Genome-wide transcription and the implications for genomic organization[J].Nature Reviews Genetics,2007,8(6):413-423.
[48]Dutrow N,Nix D A,Holt D,et al.Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping[J].Nature genetics,2008,40(8):977-986.
[49]Robinson M D,Oshlack A.A scaling normalization method for differential expression analysis of RNA-seq data[J].Genome Biol,2010,11(3):R25.
[50]Li R,Li Y,Kristiansen K,et al.SOAP:short oligonucleotide alignmentprogram[J].Bioinformatics,2008,24(5):713-714.
[51]Tao Zhao,Hong-Shuai Zhang,Hao Tang,Jian-Hui Jiang.Nanopore biosensor for sensitive and label-free nucleic acid detection based on hybridization chain reaction amplification[J].Talanta,2017,175:121-126.