Abstract
Transcriptomics is one of the most developed fields in the post-genomic era. Transcriptome is the complete set of RNA transcripts in a specific cell type or tissue at a certain developmental stage and/or under a specific physiological condition, including messenger RNA, transfer RNA, ribosomal RNA, and other non-coding RNAs. Transcriptomics focuses on the gene expression at the RNA level and offers the genome-wide information of gene structure and gene function in order to reveal the molecular mechanisms involved in specific biological processes. With the development of next-generation high-throughput sequencing technology, transcriptome analysis has been progressively improving our understanding of RNA-based gene regulatory network. Here, we discuss the concept, history, and especially the recent advances in this inspiring field of study.
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Venter J C, Adams M D, Myers E W, et al. The Sequence of the human genome. Science, 2001, 291: 1304–1351
Hamilton J P, Buell C R. Advances in plant genome sequencing. Plant J, 2012, 70: 177–190
Lockhart D J, Winzeler E A. Genomics, gene expression and DNA arrays. Nature, 2000, 405: 827–836
Carthew R W, Sontheimer E J. Origins and mechanisms of miRNAs and siRNAs. Cell, 2009, 136: 642–655
Eddy S R. Non-coding RNA genes and the modern RNA world. Nat Rev Genet, 2001, 2: 919–929
Mattick J S. The functional genomics of noncoding RNA. Science, 2005, 309: 1527–1528
Taft R J, Pheasant M, Mattick J S. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays, 2007, 29: 288–299
Willingham A T, Gingeras T R. TUF love for “junk” DNA. Cell, 2006, 125: 1215–1220
Carninci P, Yasuda J, Hayashizaki Y. Multifaceted mammalian transcriptome. Curr Opin Cell Biol, 2008, 20: 274–280
Carninci P, Kasukawa T, Katayama S, et al. The transcriptional landscape of the mammalian genome. Science, 2005, 309: 1559–1563
Shabalina S A, Spiridonov N A. The mammalian transcriptome and the function of non-coding DNA sequences. Genome Biol, 2004, 5: 105
Green E D, Chakravarti A. The human genome sequence expedition: Views from the “base camp”. Genome Res, 2001, 11: 645–651
Mardis E R. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet, 2008, 9: 387–402
Wang Z, Gerstein M, Snyder M. RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet, 2009, 10: 57–63
Kohler R E. The eighth day of creation: Makers of the revolution in biology. Isis, 1997, 88: 730–731
Gesteland R F, Cech T R, Atkins J F. The RNA World, 2nd Ed: The Nature of Modern RNA Suggests a Prebiotic RNA World. New York: Cold Spring Harbor Laboratory Press, 1999
Crick F H. On protein synthesis. Symp Soc Exp Biol, 1958, 12: 138–163
Jacob F, Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol, 1961, 3: 318–356
Crick F H. The origin of the genetic code. J Mol Biol, 1968, 38: 367–379
Hoagland M B, Stephenson M L, Scott J F, et al. A soluble ribonucleic acid intermediate in protein synthesis. J Biol Chem, 1958, 231: 241–257
Berget S M, Moore C, Sharp P A. Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci USA, 1977, 74: 3171–3175
Chow L T, Gelinas R E, Broker T R, et al. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell, 1977, 12: 1–8
Stark B C, Kole R, Bowman E J, et al. Ribonuclease P: An enzyme with an essential RNA component. Proc Natl Acad Sci USA, 1978, 75: 3717–3721
Cech T R. The generality of self-splicing RNA: Relationship to nuclear mRNA splicing. Cell, 1986, 44: 207–210
Guerrier-Takada C, Gardiner K, Marsh T, et al. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 1983, 35(3 Pt 2): 849–857
Kruger K, Grabowski P J, Zaug A J, et al. Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 1982, 31: 147–157
Ecker J R, Davis R W. Inhibition of gene expression in plant cells by expression of antisense RNA. Proc Natl Acad Sci USA, 1986, 83: 5372–5376
Napoli C, Lemieux C, Jorgensen R. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell, 1990, 2: 279–289
Romano N, Macino G. Quelling—transient inactivation of geneexpression in neurospora-crassa by transformation with homologous sequences. Mol Microbiol, 1992, 6: 3343–3353
Fire A, Xu S, Montgomery M K, et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 1998, 391: 806–811
Montgomery M K, Xu S Q, Fire A. RNA as a target of doublestranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc Natl Acad Sci USA, 1998, 95: 15502–15507
Elbashir S M, Harborth J, Lendeckel W, et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 2001, 411: 494–498
Hamilton A J, Baulcombe D C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 1999, 286: 950–952
Zamore P D, Tuschl T, Sharp P A, et al. RNAi: Double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 2000, 101: 25–33
Kim V N. microRNA biogenesis: Coordinated cropping and dicing. Nat Rev Mol Cell Biol, 2005, 6: 376–385
Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet, 2010, 11: 597–610
Brodersen P, Voinnet O. Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol, 2009, 10: 141–148
Lippman Z, Martienssen R. The role of RNA interference in heterochromatic silencing. Nature, 2004, 431: 364–370
Mello C C, Conte D Jr. Revealing the world of RNA interference. Nature, 2004, 431: 338–342
Peng J C, Lin H. Beyond transposons: The epigenetic and somatic functions of the Piwi-piRNA mechanism. Curr Opin Cell Biol, 2013, 25: 190–194
Saxe J P, Lin H. Small noncoding RNAs in the germline. Cold Spring Harb Perspect Biol, 2011, 3: a002717
Zhang H, Chen Z, Wang X, et al. Long non-coding RNA: A new player in cancer. J Hematol Oncol, 2013, 6: 37
Wilusz J E, Sunwoo H, Spector D L. Long noncoding RNAs: Functional surprises from the RNA world. Genes Dev, 2009, 23: 1494–1504
Jacquier A. The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs. Nat Rev Genet, 2009, 10: 833–844
Nagalakshmi U, Wang Z, Waern K, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 2008, 320: 1344–1349
Wilhelm B T, Marguerat S, Watt S, et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature, 2008, 453: 1239–1243
Mortazavi A, Williams B A, Mccue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods, 2008, 5: 621–628
Boguski M S, Tolstoshev C M, Bassett D E. Gene discovery in dbEST. Science, 1994, 265: 1993–1994
Schena M, Shalon D, Davis R W, et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 1995, 270: 467–470
Velculescu V E, Zhang L, Vogelstein B, et al. Serial analysis of gene expression. Science, 1995, 270: 484–487
Lashkari D A, DeRisi J L, McCusker J H, et al. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA, 1997, 94: 13057–13062
Lewin B, Krebs J E, Goldstein E S, et al. Lewin’s genes X. Sudbury: Jones and Bartlett, 2011
Ozsolak F, Milos P M. RNA sequencing: Advances, challenges and opportunities. Nat Rev Genet, 2011, 12: 87–98
Shiraki T. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci USA, 2003, 100: 15776–15781
Carninci P. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet, 2006, 38: 626–635
Lu C, Tej S S, Luo S, et al. Elucidation of the small RNA component of the transcriptome. Science, 2005, 309: 1567–1569
Lu C, Meyers B C, Green P J. Construction of small RNA cDNA libraries for deep sequencing. Methods, 2007, 43: 110–117
Valen E. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res, 2009, 19: 255–265
Plessy C. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods, 2010, 7: 528–534
Ni T. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods, 2010, 7: 521–527
Kwak H, Fuda N J, Core L J, et al. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science, 2013, 339: 950–953
Core L J, Waterfall J J, Lis J T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 2008, 322: 1845–1848
Jan C H, Friedman R C, Ruby J G, et al. Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs. Nature, 2011, 469: 97–101
Shepard P J, Choi E A, Lu J, et al. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA, 2011, 17: 761–772
Tani H, Mizutani R, Salam K A, et al. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res, 2012, 22: 947–956
Imamachi N, Tani H, Mizutani R, et al. BRIC-seq: A genome-wide approach for determining RNA stability in mammalian cells. Methods, 2013, doi: 10.1016/j.ymeth.2013.07.014
Hafner M, Landthaler M, Burger L, et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 2010, 141: 129–141
Chi S W, Zang J B, Mele A, et al. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature, 2009, 460: 479–486
Zisoulis D G, Lovci M T, Wilbert M L, et al. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol, 2010, 17: 173–179
German M A, Pillay M, Jeong D H, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol, 2008, 26: 941–946
Addo-Quaye C, Eshoo T W, Bartel D P, et al. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol, 2008, 18: 758–762
Zhou M, Gu L, Li P, et al. Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica). Front Biol, 2010, 5: 67–90
Wu L, Zhang Q, Zhou H, et al. Rice microRNA effector complexes and targets. Plant Cell, 2009, 21: 3421–3435
Islam S, Kjallquist U, Moliner A, et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res, 2011, 21: 1160–1167
Ramskold D, Luo S, Wang Y C, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol, 2012, 30: 777–782
Hashimshony T, Wagner F, Sher N, et al. CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification. Cell Rep, 2012, 2: 666–673
Sultan M. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 2008, 321: 956–960
Carninci P. Is sequencing enlightenment ending the dark age of the transcriptome? Nat Methods, 2009, 6: 711–713
Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem, 2010, 79: 321–349
Li J B. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science, 2009, 324: 1210–1213
Park E, Williams B, Wold B J, et al. RNA editing in the human ENCODE RNA-seq data. Genome Res, 2012, 22: 1626–1633
Shi Y. Alternative polyadenylation: New insights from global analyses. RNA, 2012, 18: 2105–2117
Kozomara A, Griffiths-Jones S. miRBase: Integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res, 2011, 39: D152–D157
Hammell C M. The microRNA-argonaute complex: A platform for mRNA modulation. RNA Biol, 2008, 5: 123–127
Yang J H, Li J H, Shao P, et al. starBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res, 2011, 39: D202–D209
Mamanova L. FRT-seq: Amplification-free, strand-specific transcriptome sequencing. Nat Methods, 2010, 7: 130–132
Lipson D. Quantification of the yeast transcriptome by singlemolecule sequencing. Nat Biotechnol, 2009, 27: 652–658
Parkhomchuk D. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res, 2009, 37: e123
Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res, 2012, 22: 1775–1789
Cloonan N. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods, 2008, 5: 613–619
Maher C A. Transcriptome sequencing to detect gene fusions in cancer. Nature, 2009, 458: 97–101
Korbel J O. Paired-end mapping reveals extensive structural variation in the human genome. Science, 2007, 318: 420–426
Grabherr M G, Haas B J, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol, 2011, 29: 644–652
Clark T A, Sugnet C W, Ares M Jr. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science, 2002, 296: 907–910
Stolc V, Samanta M P, Tongprasit W, et al. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci USA, 2005, 102: 4453–4458
Bertone P, Stolc V, Royce T E, et al. Global identification of human transcribed sequences with genome tiling arrays. Science, 2004, 306: 2242–2246
Cheng J, Kapranov P, Drenkow J, et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 2005, 308: 1149–1154
Draghici S, Khatri P, Eklund A C, et al. Reliability and reproducibility issues in DNA microarray measurements. Trends Genet, 2006, 22: 101–109
Brenner S, Johnson M, Bridgham J, et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol, 2000, 18: 630–634
Dafforn A. Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis. Biotechniques, 2004, 37: 854–857
Lo Y M. Plasma placental RNA allelic ratio permits noninvasive prenatal chromosomal aneuploidy detection. Nature Med, 2007, 13: 218–223
Amit I. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science, 2009, 326: 257–263
Ozsolak F, Platt A R, Jones D R, et al. Direct RNA sequencing. Nature, 2009, 461: 814–818
Tang F, Barbacioru C, Wang Y, et al. mRNA-Seq wholetranscriptome analysis of a single cell. Nat Methods, 2009, 6: 377–382
Shiroguchi K, Jia T Z, Sims P A, et al. Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc Natl Acad Sci USA, 2012, 109: 1347–1352
Kivioja T, Vaharautio A, Karlsson K, et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods, 2012, 9: 72–74
Langmead B, Trapnell C, Pop M, et al. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol, 2009, 10: R25
Trapnell C, Pachter L, Salzberg S L. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics, 2009, 25: 1105–1111
Trapnell C, Williams B A, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 2010, 28: 511–515
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Dong, Z., Chen, Y. Transcriptomics: Advances and approaches. Sci. China Life Sci. 56, 960–967 (2013). https://doi.org/10.1007/s11427-013-4557-2
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DOI: https://doi.org/10.1007/s11427-013-4557-2