| 7,116 | 42 | 156 |
| 下载次数 | 被引频次 | 阅读次数 |
同一组织中的细胞往往被认为是具有相同状态的功能单位,传统的检测手段分析的是细胞群体的总体平均反应。然而通过对单个细胞的DNA或RNA进行测序,表明组织系统层面的功能是由异质性细胞构成的。单细胞测序以单个细胞为单位,通过全基因组或转录组扩增,进行高通量测序,能够揭示单个细胞的基因结构和基因表达状态,反映细胞间的异质性,在肿瘤、发育生物学、微生物学、神经科学等领域发挥重要作用,正成为生命科学研究的焦点。单细胞测序的难点是单个细胞的分离、单细胞基因组和转录组的扩增。本文主要介绍和分析了单细胞测序技术中常用的单细胞分离技术、单细胞基因组扩增技术和转录组扩增技术及其优缺点,并对当前已经取得成果的应用领域进行了阐述,为单细胞测序技术的研究与应用提供参考。
Abstract：Individual cells of the same phenotype are commonly viewed as identical functional units of a tissue.The analysis of traditional detection method always bases on the overall average reaction of cells. However, the sequencing of DNA or RNA from single cells suggests the system-level function of a tissue is produced by heterogeneous cell. Single cell genome or transcriptome can be sequenced after amplification based on single cell sequencing. It can reveal the structure and expression of genes and the heterogeneity between cells. Single cell sequencing technology has come into focus for the achievements in cancer, developmental biology, microbiology and neuroscience. The difficulty involves in single cell isolation, whole genome amplification and transcriptome amplification. In this review, we summarize the common single cell isolation technology, whole genome amplification technology and transcriptome amplification technology, and analyze the advantages and disadvantages of current technologies. We also introduce the successful applications in different fields. This review provides references of single cell sequencing study and application.
Blai ney P.C.,2013,The future is now:single-cell genomics ofbacteria and archaea,FEMS Microbiology Reviews,37(3):407-427
Bonner R.F.,Emmert-Buck M.,Cole K.,Pohida T.,Chuaqui R.,Goldstein S.,and Liotta L.A.,1997,Laser capture microdissection:molecular analysis of tissue,Science,278(5342):1481-1483
Cheung V.G.,and Nelson S.F.,1996,Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than onenanogram of genomic DNA,proceedings of the national academy of Sciences,93(25):14676-14679
Chi K.R.,2014,Singled out for sequencing,Nature Methods,11(1):13-17
Choi J.H.,Ogunniyi A.O.,Du M.,Du M.,Kretschmann M.,Eberhardt J.,and Love J.C.,2010,Development and optimization of a process for automated recovery of single cellsidentified by microengraving,Biotechnology Progress,26(3):888-895
Coufal N.G.,Garcia-Perez J.L.,Peng G.E.,Yeo G.W.,Mu Y.,Lovci M.T.,Morell M.,O'Shea K.S.,Moran J.V.,and GageF.H.,2009,L1 retrotransposition in human neural progenitorcells,Nature,460(7259):1127-1131
Dean F.B.,Hosono S.,Fang L.,Wu X.,Faruqi A.F.,Bray-WardP.,Sun Z.,Zong Q.,Du Y.,Du J.,Driscoll M.,Song W.,Kingsmore S.F.,Enholm M.,and Lasken R.S.,2002,Comprehensive human genome amplification using multiple dis-placement amplificatio n,Pproceedings of the national academy of sciences,99(8):5261-5266
DeLorenzo S.,Br?uer S.L.,Edgmont C.A.,Herfort L.,Tebo B.M.,and Zuber P.,2012,Ubiquitous dissolved inorganic carbonassimilation by marine bacteria in the Pacific Northwestcoastal ocean as determined by stable isotope probing,Plo SOne,7:e46695
de Souza N.,2012,Single-cell methods,Nature Methods,9(1):35
Felthaus O.,Ettl T.,Gosau M.,Driemel O.,Brockhoff G.,Reck A.,Zeitler K.,Hautmann M.,Reichert T.E.,Schmalz G.,andMorsczeck C.,2011,Cancer stem cell-like cells from a singlecell of oral squamous carcinoma cell lines,Biochemical andBiophysical Research Communications,407(1):28-33
Frumkin D.,Wasserstrom A.,Itzkovitz S.,Harmelin A.,RechaviG.,and Shapiro E.,2008,Amplification of multiple genomicloci from single cells isolated by laser micro-dissection oftissues,BMC Biotechnology,8(1):17
Gole J.,Gore A.,Richards A.,Chiu Y.J.,Fung H.L.,Bushman D.,Chiang H.I.,Chun J.,Lo Y.H.,and Zhang K.,2013,Massively parallel polymerase cloning and genome sequencingof single cells using nanoliter microwells,Nature Biotechnology,31(12):1126-1132
Hou Y.,Fan W.,Yan L.,Li R.,Lian Y.,Huang J.,Li J.,Xu L.,Tang F.,Xie X.S.,and Qiao J.,2013,Genome analyses ofsingle human oocytes,Cell,155(7):1492-1506
Islam S.,Kj?llquist U.,Moliner A.,Zajac P.,Fan J.B.,L?nnerberg P.,and Linnarsson S.,2011,Characterization of thesingle-cell transcriptional landscape by highly multiplexRNA-seq,Genome Research,21(7):1160-1167
Kantlehner M.,Kirchner R.,Hartmann P.,Ellwart J.W.,Alunni-Fabbroni M.,and Schumacher A.,2011,A high-throughput DNA methylation analysis of a single cell,NucleicAcids Research:39(7):e44
Kvist T.,Ahring B.K.,Lasken R.S.,and Westermann P.,2007,Specific single-cell isolation and genomic amplification ofuncultured microorganisms,Applied Microbiology andBiotechnology,74(4):926-935
Lasken R.S.,2007,Single-cell genomic sequencing using multiple displacement amplification,Current Opinion in Microbiology,10(5):510-516
Li X.,Li L.,and Yan J.,2015,Dissecting meiotic recombinationbased on tetrad analysis by single-microspore sequencing inmaize,Nature Communications,6:6648
Li Y.,Kim H.J.,Zheng C.,Chow W.H.A.,Lim J.,Keenan B.,Pan X.,Lemieux B.,and Kong H.,2008,Primase-basedwhole genome amplification,Nucleic Acids Research,36(13):e79
Lorthongpanich C.,Cheow L.F.,Balu S.,Quake S.R.,KnowlesB.B.,Burkholder W.F.,Solter D.,and Messerschmidt D.M.,2013,Single-cell DNA-methylation analysis reveals epigenetic chimerism in preimplantation embryos,Science,341(6150):1110-1112
Marcy Y.,Ishoey T.,Lasken R.S.,Stockwell T.B.,Walenz B.P.,Halpern A.L.,Beeson K.Y.,Goldberg S.M.,and Quake S.R.,2007,Nanoliter reactors improve multiple displacement amplification of genomes from single cells,PLo S Genetics,3(9):1702-1708
Mardis E.R.,2008,The impact of next-generation sequencingtechnology on genetics,Trends in Genetics,24(3):133-141
Mc Connell M.J.,Lindberg M.R.,Brennand K.J.,Piper J.C.,VoetT.,Cowing-Zitron C.,Shumilina S.,Lasken RS.,VermeeschJ.R.,Hall I.M.,and Gage F.H.,2013,Mosaic copy numbervariation in human neurons,Science,342(6158):632-637
Mussmann M.,Hu F.Z.,Richter M.,de Beer D.,Preisler A.,J?rgensen B.B.,Huntemann M.,Gl?ckner F.O.,Amann R.,Koopman W.J.,Lasken R.S.,Janto B.,Hogg J.,Stoodley P.,Boissy R.,and Ehrlich G.D.,2007,Insights into the genomeof large sulfur bacteria revealed by analysis of single filaments,PLo S Biology,5(9):e230
Navin N.,Kendall J.,Troge J.,Andrews P.,Rodgers L.,Mc IndooJ.,Cook K.,Stepansky A.,Levy D.,Esposito D.,Muthuswamy L.,Krasnitz A.,Mc Combie W.R.,Hicks J.,and Wigler M.,2011,Tumour evolution inferred by single-cell sequencing,Nature,472(7341):90-94
Pan X.,Durrett R.E.,Zhu H.,Tanaka Y.,Li Y.,Zi X.,Marjani S.L.,Euskirchen G.,Ma C.,Lamotte R.H.,Park I.H.,SnyderM.P.,Mason C.E.,and Weissman S.M.,2013,Two methodsfor full-length RNA sequencing for low quantities of cellsand single cells,proceedings of the national academy of sciences,110(2):594-599
Pennisi E.,2012,Single-cell sequencing tackles basic andbiomedical questions,Science,336(6084):976-977
Raghunathan A.,Ferguso n H.R.Jr.,Bornarth C.J.,Song W.,Driscoll M.,and Lasken R.S.,2005,Genomic DNA amplification from a single bacterium,Applied and EnvironmentalMicrobiology,71(6):3342-3347
Ramsk?ld D.,Luo S.,Wang Y.C.,Li R.,Deng Q.,Faridani O.R.,Daniels G.A.,Khrebtukov a I.,Loring J.F.,Laurent L.C.,Schroth G.P.,and Sandberg R.,2012,Full-length mR NASeq from single-cell levels of RNA and individual circulating tumor cells,Nature Biotechnology,30(8):777-782
Reizel Y.,Chapal-Ilani N.,Adar R.,Itzkovitz S.,Elbaz J.,Maruvka Y.E.,Segev E.,Shlush L.I.,Dekel N.,and Shapiro E.,2011,Colon stem cell and crypt dynamics exposed by celllineage reconstruction,PLo S Genetics,7(7):e1002192
Rosenfeld N.,Young J.W.,Alon U.,Swain P.S.,and Elowitz M.B.,2005,Gene regulation at the single-cell level,Science,307(5717):1962-1965
Sato T.,Hongoh Y.,Noda S.,Hattori S.,Ui S.,and Ohkuma M.,2009,Candidatus Desulfovibrio trichonymphae,a novel intracellular symbiont of the flagellate Trichonympha agilis intermite gut,Environmental Microbiology,11(4):1007-1015
Shapiro E.,Biezuner T.,and Linnarsson S.,2013,Single-cell sequencing-based technologies will revolutionize whole-organism science,Nature Reviews Genetics,14(9):618-630
Shendure J.,and Ji H.,2008,Next-generation DNA sequencing,Nature Biotechnology,26(10):1135-1145
Stepanauskas R.,and Sieracki M.E.,2007,Matching phylogenyand metabolism in the uncultured marine bacteria,one cellat a time,proceedings of the national academy of sciences,104(21):9052-9057
Streets A.M.,Zhang X.,Cao C.,Pang Y.,Wu X.,Xiong L.,YangL.,Fu Y.,Zhao L.,Tang F.,and Huang Y.,2014,Microfluidic single-cell whole-transcriptome sequencing,Proc.Natl.Acad.Sci.USA,111(19):7048-7053
Tang F.,Barbacioru C.,Bao S.,Lee C.,Nordman E.,Wang X.,Lao K.,and Surani M.A.,2010,Tracing the derivation ofembryonic stem cells from the inner cell mass by single-cellRNA-Seq analysis,Cell Stem Cell,6(5):468-478
Tang F.,Barbacioru C.,Wang Y.,Nordman E.,Lee C.,Xu N.,Wang X.,Bodeau J.,Tuch B.B.,Siddiqui A.,Lao K.,andSurani M.A.,2009,mR NA-seq whole-transcriptome analysis of a single cell,Nature Methods,6(5):377-382
Tang F.,Hajkova P.,Barton S.C.,O'Carroll D.,Lee C.,Lao K.,and Surani M.A.,2006,220-plex micro RNA expressionprofile of a single cell,Nature Protocols,1(3):1154-1159
Viguera E.,Canceill D.,and Ehrlich S.D.,2001,Replication slippage involves DNA polymerase pausing and dissociation,The EMBO Journal,20(10):2587-2595
Xu X.,Hou Y.,Yin X.,Bao L.,Tang A.,Song L.,Li F.,Tsang S.,Wu K.,Wu H.,He W.,Zeng L.,Xing M.,Wu R.,Jiang H.,Liu X.,Cao D.,Guo G.,Hu X.,Gui Y.,Li Z.,Xie W.,SunX.,Shi M.,Cai Z.,Wang B.,Zhong M.,Li J.,Lu Z.,Gu N.,Zhang X.,Goodman L.,Bolund L.,Wang J.,Yang H.,Kristiansen K.,Dean M.,Li Y.,and Wang J.,2012,Single-cellexome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor,Cell,148(5):886-895
Xue R.D.,Li R.Y.,and Bai F.,2015,Single cell sequencing:technique,application,and future development,ScienceBulletin,60(1):33-42
Xue Z.,Huang K.,Cai C.,Cai L.,Jiang C.Y.,Feng Y.,Liu Z.,Zeng Q.,Cheng L.,Sun Y.E.,Liu J.Y.,Horvath S.,and FanG.,2013,Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing,Nature,500(7464):593-597
Yachida S.,Jones S.,Bozic I.,Antal T.,Leary R.,Fu B.,Kamiyama M.,Hruban R.H.,Eshleman J.R.,Nowak M.A.,Velculescu V.E.,Kinzler K.W.,Vogelstein B.,and Iacobuzio-Donahue C.A.,2010,Distant metastasis occurs lateduring the genetic evolution of pancreatic cancer,Nature,467(7319):1114-1117
Yilmaz S.,and Singh A.K.,2012,Single cell genome sequencing,Current Opinion in Biotechnology,23(3):437-443
Zhang K.,Martiny A.C.,Reppas N.B.,Barry K.W.,Malek J.,Chisholm S.W.,and Church G.M.,2006,Sequencinggenomes from single cells by polymerase cloning,NatureBiotechnology,24(6):680-686
Zong C.,Lu S.,Chapman A.R.,and Xie X.S.,2012,Genome-widedetection of single-nucleotide and copy-number variationsof a single human cell,Science,338(6114):1622-1626
基本信息:
DOI：10.13417/j.gab.034.000902
中图分类号:Q2-33
引用信息:
[1]朱忠旭,陈新.单细胞测序技术及应用进展[J].基因组学与应用生物学,2015,34(05):902-908.DOI:10.13417/j.gab.034.000902.
基金信息:
国家重点基础研究发展计划(2012CB944900);; 国家自然科学基金资助项目(31071161)共同资助