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Genes  2012 

The Human Transcriptome: An Unfinished Story

DOI: 10.3390/genes3030344

Keywords: transcriptome, pervasive transcription, RNA-seq, mRNA, ncRNA

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Despite recent technological advances, the study of the human transcriptome is still in its early stages. Here we provide an overview of the complex human transcriptomic landscape, present the bioinformatics challenges posed by the vast quantities of transcriptomic data, and discuss some of the studies that have tried to determine how much of the human genome is transcribed. Recent evidence has suggested that more than 90% of the human genome is transcribed into RNA. However, this view has been strongly contested by groups of scientists who argued that many of the observed transcripts are simply the result of transcriptional noise. In this review, we conclude that the full extent of transcription remains an open question that will not be fully addressed until we decipher the complete range and biological diversity of the transcribed genomic sequences.


[1]  Ohno, S. So much “junk” DNA in our genome. Brookhaven Symp. Biol. 1972, 23, 366–370.
[2]  The International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001, 409, 860–921, doi:10.1038/35057062.
[3]  Venter, J.C.; Adams, M.D.; Myers, E.W.; Li, P.W.; Mural, R.J.; Sutton, G.G.; Smith, H.O.; Yandell, M.; Evans, C.A.; Holt, R.A.; et al. The sequence of the human genome. Science 2001, 291, 1304–1351.
[4]  Chen, J.; Sun, M.; Lee, S.; Zhou, G.; Rowley, J.D.; Wang, S.M. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc. Natl. Acad. Sci. USA 2002, 99, 12257–12262.
[5]  Kapranov, P.; Cawley, S.E.; Drenkow, J.; Bekiranov, S.; Strausberg, R.L.; Fodor, S.P.; Gingeras, T.R. Large-scale transcriptional activity in chromosomes 21 and 22. Science 2002, 296, 916–919, doi:10.1126/science.1068597.
[6]  Saha, S.; Sparks, A.B.; Rago, C.; Akmaev, V.; Wang, C.J.; Vogelstein, B.; Kinzler, K.W.; Velculescu, V.E. Using the transcriptome to annotate the genome. Nat. Biotechnol. 2002, 20, 508–512, doi:10.1038/nbt0502-508.
[7]  Mattick, J.S. The central role of RNA in human development and cognition. FEBS Lett. 2011, 585, 1600–1616, doi:10.1016/j.febslet.2011.05.001.
[8]  Griffin, H.G.; Griffin, A.M. DNA sequencing. Recent innovations and future trends. Appl. Biochem. Biotechnol. 1993, 38, 147–159, doi:10.1007/BF02916418.
[9]  Adams, M.D.; Kerlavage, A.R.; Fields, C.; Venter, J.C. 3,400 new expressed sequence tags identify diversity of transcripts in human brain. Nat. Genet. 1993, 4, 256–267, doi:10.1038/ng0793-256.
[10]  Adams, M.D.; Kerlavage, A.R.; Fleischmann, R.D.; Fuldner, R.A.; Bult, C.J.; Lee, N.H.; Kirkness, E.F.; Weinstock, K.G.; Gocayne, J.D.; White, O.; et al. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 1995, 377, 3–174.
[11]  Pertea, M.; Salzberg, S.L. Between a chicken and a grape: Estimating the number of human genes. Genome Biol. 2010, 11, 206, doi:10.1186/gb-2010-11-5-206.
[12]  Strausberg, R.L.; Riggins, G.J. Navigating the human transcriptome. Proc. Natl. Acad. Sci. USA 2001, 98, 11837–11838, doi:10.1073/pnas.221463598.
[13]  Velculescu, V.E.; Zhang, L.; Vogelstein, B.; Kinzler, K.W. Serial analysis of gene expression. Science 1995, 270, 484–487.
[14]  Shiraki, T.; Kondo, S.; Katayama, S.; Waki, K.; Kasukawa, T.; Kawaji, H.; Kodzius, R.; Watahiki, A.; Nakamura, M.; Arakawa, T.; et al. 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.
[15]  Brenner, S.; Johnson, M.; Bridgham, J.; Golda, G.; Lloyd, D.H.; Johnson, D.; Luo, S.; McCurdy, S.; Foy, M.; Ewan, M.; et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 2000, 18, 630–634.
[16]  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.
[17]  Schena, M.; Shalon, D.; Davis, R.W.; Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270, 467–470.
[18]  Lashkari, D.A.; DeRisi, J.L.; McCusker, J.H.; Namath, A.F.; Gentile, C.; Hwang, S.Y.; Brown, P.O.; Davis, R.W. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. USA 1997, 94, 13057–13062.
[19]  Bertone, P.; Stolc, V.; Royce, T.E.; Rozowsky, J.S.; Urban, A.E.; Zhu, X.; Rinn, J.L.; Tongprasit, W.; Samanta, M.; Weissman, S.; Gerstein, M.; Snyder, M. Global identification of human transcribed sequences with genome tiling arrays. Science 2004, 306, 2242–2246.
[20]  Cheng, J.; Kapranov, P.; Drenkow, J.; Dike, S.; Brubaker, S.; Patel, S.; Long, J.; Stern, D.; Tammana, H.; Helt, G.; et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005, 308, 1149–1154.
[21]  Castle, J.C.; Zhang, C.; Shah, J.K.; Kulkarni, A.V.; Kalsotra, A.; Cooper, T.A.; Johnson, J.M. Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat. Genet. 2008, 40, 1416–1425.
[22]  Okoniewski, M.J.; Miller, C.J. Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics 2006, 7, 276, doi:10.1186/1471-2105-7-276.
[23]  Pan, Q.; Shai, O.; Misquitta, C.; Zhang, W.; Saltzman, A.L.; Mohammad, N.; Babak, T.; Siu, H.; Hughes, T.R.; Morris, Q.D.; et al. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol. Cell 2004, 16, 929–941, doi:10.1016/j.molcel.2004.12.004.
[24]  Lister, R.; O’Malley, R.C.; Tonti-Filippini, J.; Gregory, B.D.; Berry, C.C.; Millar, A.H.; Ecker, J.R. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133, 523–536, doi:10.1016/j.cell.2008.03.029.
[25]  Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5, 621–628.
[26]  Nagalakshmi, U.; Wang, Z.; Waern, K.; Shou, C.; Raha, D.; Gerstein, M.; Snyder, M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320, 1344–1349.
[27]  Salzberg, S.L. Recent advances in RNA sequence analysis. F1000 Biol. Rep. 2010, 2, 64.
[28]  Cloonan, N.; Forrest, A.R.; Kolle, G.; Gardiner, B.B.; Faulkner, G.J.; Brown, M.K.; Taylor, D.F.; Steptoe, A.L.; Wani, S.; Bethel, G.; et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods 2008, 5, 613–619.
[29]  Wang, Z.; Gerstein, M.; Snyder, M. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57–63, doi:10.1038/nrg2484.
[30]  Ponting, C.P.; Oliver, P.L.; Reik, W. Evolution and functions of long noncoding RNAs. Cell 2009, 136, 629–641.
[31]  Dinger, M.E. lncRNAs: Finding the forest among the trees? Mol. Ther. 2011, 19, 2109–2111, doi:10.1038/mt.2011.251.
[32]  Fire, A.; Xu, S.; Montgomery, M.K.; Kostas, S.A.; Driver, S.E.; Mello, C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391, 806–811.
[33]  Lee, R.C.; Feinbaum, R.L.; Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75, 843–854, doi:10.1016/0092-8674(93)90529-Y.
[34]  Jacquier, A. The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet. 2009, 10, 833–844, doi:10.1038/nrg2683.
[35]  Taft, R.J.; Pang, K.C.; Mercer, T.R.; Dinger, M.; Mattick, J.S. Non-coding RNAs: Regulators of disease. J. Pathol. 2010, 220, 126–139, doi:10.1002/path.2638.
[36]  Derrien, T.; Guigo, R.; Johnson, R. The long non-coding RNAs: A New (P)layer in the “Dark Matter”. Front Genet. 2011, 2, 107.
[37]  Cabili, M.N.; Trapnell, C.; Goff, L.; Koziol, M.; Tazon-Vega, B.; Regev, A.; Rinn, J.L. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011, 25, 1915–1927.
[38]  Iafrate, A.; Feuk, L.; Rivera, M.; Listewnik, M.; Donahoe, P.; Qi, Y.; Scherer, S.; Lee, C. Detection of large-scale variation in the human genome. Nat Genet. 2004, 36, 949–951.
[39]  Sebat, J.; Lakshmi, B.; Troge, J.; Alexander, J.; Young, J.; Lundin, P.; Maner, S.; Massa, H.; Walker, M.; Chi, M.; Navin, N.; Lucito, R.; Healy, J.; Hicks, J.; Ye, K.; Reiner, A.; Gilliam, T.C.; Trask, B.; Patterson, N.; Zetterberg, A.; Wigler, M. Large-scale copy number polymorphism in the human genome. Science 2004, 305, 525–528.
[40]  Li, R.; Li, Y.; Zheng, H.; Luo, R.; Zhu, H.; Li, Q.; Qian, W.; Ren, Y.; Tian, G.; Li, J.; et al. Building the sequence map of the human pan-genome. Nat. Biotechnol. 2009, 28, 57–63.
[41]  Trapnell, C.; Williams, B.A.; Pertea, G.; Mortazavi, A.; Kwan, G.; van Baren, M.J.; Salzberg, S.L.; Wold, B.J.; Pachter, L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28, 511–515.
[42]  Pan, Q.; Shai, O.; Lee, L.J.; Frey, B.J.; Blencowe, B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 2008, 40, 1413–1415.
[43]  Kampa, D.; Cheng, J.; Kapranov, P.; Yamanaka, M.; Brubaker, S.; Cawley, S.; Drenkow, J.; Piccolboni, A.; Bekiranov, S.; Helt, G.; et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 2004, 14, 331–342, doi:10.1101/gr.2094104.
[44]  Wang, E.T.; Sandberg, R.; Luo, S.; Khrebtukova, I.; Zhang, L.; Mayr, C.; Kingsmore, S.F.; Schroth, G.P.; Burge, C.B. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456, 470–476.
[45]  Blencowe, B.J. Alternative splicing: New insights from global analyses. Cell 2006, 126, 37–47, doi:10.1016/j.cell.2006.06.023.
[46]  Mudge, J.M.; Frankish, A.; Fernandez-Banet, J.; Alioto, T.; Derrien, T.; Howald, C.; Reymond, A.; Guigo, R.; Hubbard, T.; Harrow, J. The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol. Biol. Evol. 2011, 28, 2949–2959, doi:10.1093/molbev/msr127.
[47]  Ravasi, T.; Suzuki, H.; Pang, K.C.; Katayama, S.; Furuno, M.; Okunishi, R.; Fukuda, S.; Ru, K.; Frith, M.C.; Gongora, M.M.; et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res. 2006, 16, 11–19.
[48]  Seok, J.; Xu, W.; Jiang, H.; Davis, R.W.; Xiao, W. Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research. PLoS One 2012, 7, e31440.
[49]  Carninci, P.; Kasukawa, T.; Katayama, S.; Gough, J.; Frith, M.C.; Maeda, N.; Oyama, R.; Ravasi, T.; Lenhard, B.; Wells, C.; Kodzius, R.; et al. The transcriptional landscape of the mammalian genome. Science 2005, 309, 1559–1563.
[50]  Ensembl Genome Browser. Available online: http://useast.ensembl.org/Homo_sapiens/Info/Index (accessed on 5 September 2011).
[51]  NCBI’s RefSeq Database. Available online: http://www.ncbi.nlm.nih.gov/RefSeq/ (accessed on 5 September 2011).
[52]  UCSC Genome Table Browser. Available online: http://genome.ucsc.edu/cgi-bin/hgTables (accessed on 5 September 2011).
[53]  Kapranov, P.; Drenkow, J.; Cheng, J.; Long, J.; Helt, G.; Dike, S.; Gingeras, T.R. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 2005, 15, 987–997, doi:10.1101/gr.3455305.
[54]  Zheng, D.; Frankish, A.; Baertsch, R.; Kapranov, P.; Reymond, A.; Choo, S.W.; Lu, Y.; Denoeud, F.; Antonarakis, S.E.; Snyder, M.; et al. Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution. Genome Res. 2007, 17, 839–851, doi:10.1101/gr.5586307.
[55]  Sasidharan, R.; Gerstein, M. Genomics: Protein fossils live on as RNA. Nature 2008, 453, 729–731, doi:10.1038/453729a.
[56]  Sie, C.P.; Kuchka, M. RNA editing adds flavor to complexity. Biochemistry (Mosc) 2011, 76, 869–881, doi:10.1134/S0006297911080025.
[57]  Bass, B.L.; Weintraub, H. An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell 1988, 55, 1089–1098, doi:10.1016/0092-8674(88)90253-X.
[58]  Wagner, R.W.; Smith, J.E.; Cooperman, B.S.; Nishikura, K. A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. Proc. Natl. Acad. Sci. USA 1989, 86, 2647–2651.
[59]  Powell, L.M.; Wallis, S.C.; Pease, R.J.; Edwards, Y.H.; Knott, T.J.; Scott, J. A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 1987, 50, 831–840, doi:10.1016/0092-8674(87)90510-1.
[60]  Chen, S.H.; Habib, G.; Yang, C.Y.; Gu, Z.W.; Lee, B.R.; Weng, S.A.; Silberman, S.R.; Cai, S.J.; Deslypere, J.P.; Rosseneu, M.; et al. Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. Science 1987, 238, 363–366.
[61]  Teng, B.; Burant, C.F.; Davidson, N.O. Molecular cloning of an apolipoprotein B messenger RNA editing protein. Science 1993, 260, 1816–1819.
[62]  Athanasiadis, A.; Rich, A.; Maas, S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2004, 2, e391, doi:10.1371/journal.pbio.0020391.
[63]  Levanon, E.Y.; Eisenberg, E.; Yelin, R.; Nemzer, S.; Hallegger, M.; Shemesh, R.; Fligelman, Z.Y.; Shoshan, A.; Pollock, S.R.; Sztybel, D.; et al. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 2004, 22, 1001–1005.
[64]  Li, M.; Wang, I.X.; Li, Y.; Bruzel, A.; Richards, A.L.; Toung, J.M.; Cheung, V.G. Widespread RNA and DNA sequence differences in the human transcriptome. Science 2011, 333, 53–58.
[65]  Kleinman, C.L.; Majewski, J. Comment on “Widespread RNA and DNA sequence differences in the human transcriptome”. Science 2012, 335, 1302, doi:10.1126/science.1209658.
[66]  Lin, W.; Piskol, R.; Tan, M.H.; Li, J.B. Comment on “Widespread RNA and DNA sequence differences in the human transcriptome”. Science 2012, 335, 1302-e.
[67]  Pickrell, J.K.; Gilad, Y.; Pritchard, J.K. Comment on “Widespread RNA and DNA sequence differences in the human transcriptome”. Science 2012, 335, doi:10.1126/science.1210484.
[68]  Schrider, D.R.; Gout, J.F.; Hahn, M.W. Very few RNA and DNA sequence differences in the human transcriptome. PLoS One 2011, 6, e25842.
[69]  Barak, M.; Levanon, E.Y.; Eisenberg, E.; Paz, N.; Rechavi, G.; Church, G.M.; Mehr, R. Evidence for large diversity in the human transcriptome created by Alu RNA editing. Nucleic Acids Res. 2009, 37, 6905–6915, doi:10.1093/nar/gkp729.
[70]  Martin, J.A.; Wang, Z. Next-generation transcriptome assembly. Nat. Rev. Genet. 2011, 12, 671–682, doi:10.1038/nrg3068.
[71]  Costa, V.; Angelini, C.; de Feis, I.; Ciccodicola, A. Uncovering the complexity of transcriptomes with RNA-Seq. J. Biomed. Biotechnol. 2010, 853916.
[72]  Garber, M.; Grabherr, M.G.; Guttman, M.; Trapnell, C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods 2011, 8, 469–477.
[73]  Zerbino, D.R.; Birney, E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18, 821–829, doi:10.1101/gr.074492.107.
[74]  Simpson, J.T.; Wong, K.; Jackman, S.D.; Schein, J.E.; Jones, S.J.; Birol, I. ABySS: A parallel assembler for short read sequence data. Genome Res. 2009, 19, 1117–1123, doi:10.1101/gr.089532.108.
[75]  Butler, J.; MacCallum, I.; Kleber, M.; Shlyakhter, I.A.; Belmonte, M.K.; Lander, E.S.; Nusbaum, C.; Jaffe, D.B. ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res. 2008, 18, 810–820, doi:10.1101/gr.7337908.
[76]  Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10, R25, doi:10.1186/gb-2009-10-3-r25.
[77]  Li, H.; Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25, 1754–1760, doi:10.1093/bioinformatics/btp324.
[78]  Trapnell, C.; Pachter, L.; Salzberg, S.L. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25, 1105–1111, doi:10.1093/bioinformatics/btp120.
[79]  Au, K.F.; Jiang, H.; Lin, L.; Xing, Y.; Wong, W.H. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res. 2010, 38, 4570–4578, doi:10.1093/nar/gkq211.
[80]  Wang, K.; Singh, D.; Zeng, Z.; Coleman, S.J.; Huang, Y.; Savich, G.L.; He, X.; Mieczkowski, P.; Grimm, S.A.; Perou, C.M.; et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010, 38, e178.
[81]  Wu, T.D.; Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 2010, 26, 873–881, doi:10.1093/bioinformatics/btq057.
[82]  Kent, W.J. BLAT--the BLAST-like alignment tool. Genome Res. 2002, 12, 656–664.
[83]  Guttman, M.; Garber, M.; Levin, J.Z.; Donaghey, J.; Robinson, J.; Adiconis, X.; Fan, L.; Koziol, M.J.; Gnirke, A.; Nusbaum, C.; Rinn, J.L.; et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 2010, 28, 503–510.
[84]  Feng, J.; Li, W.; Jiang, T. Inference of isoforms from short sequence reads. J. Comput. Biol. 2011, 18, 305–321, doi:10.1089/cmb.2010.0243.
[85]  Li, W.; Feng, J.; Jiang, T. IsoLasso: A LASSO regression approach to RNA-Seq based transcriptome assembly. J. Comput. Biol. 2011, 18, 1693–1707, doi:10.1089/cmb.2011.0171.
[86]  Grabherr, M.G.; Haas, B.J.; Yassour, M.; Levin, J.Z.; Thompson, D.A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q.; et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29, 644–652.
[87]  Oases: De novo transcriptome assembler for very short reads. Available online: http://www.ebi.ac.uk/~zerbino/oases/ (accessed on 12 April 2012).
[88]  Li, R.; Yu, C.; Li, Y.; Lam, T.W.; Yiu, S.M.; Kristiansen, K.; Wang, J. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics 2009, 25, 1966–1967.
[89]  Birol, I.; Jackman, S.D.; Nielsen, C.B.; Qian, J.Q.; Varhol, R.; Stazyk, G.; Morin, R.D.; Zhao, Y.; Hirst, M.; Schein, J.E.; et al. De novo transcriptome assembly with ABySS. Bioinformatics 2009, 25, 2872–2877.
[90]  Zhao, Q.Y.; Wang, Y.; Kong, Y.M.; Luo, D.; Li, X.; Hao, P. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: A comparative study. BMC Bioinformatics 2011, 12, S2.
[91]  International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 2004, 431, 931–945, doi:10.1038/nature03001.
[92]  Kapranov, P.; Cheng, J.; Dike, S.; Nix, D.A.; Duttagupta, R.; Willingham, A.T.; Stadler, P.F.; Hertel, J.; Hackermuller, J.; Hofacker, I.L.; et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316, 1484–1488.
[93]  Okazaki, Y.; Furuno, M.; Kasukawa, T.; Adachi, J.; Bono, H.; Kondo, S.; Nikaido, I.; Osato, N.; Saito, R.; Suzuki, H.; et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420, 563–573, doi:10.1038/nature01266.
[94]  Katayama, S.; Tomaru, Y.; Kasukawa, T.; Waki, K.; Nakanishi, M.; Nakamura, M.; Nishida, H.; Yap, C.C.; Suzuki, M.; Kawai, J.; et al. Antisense transcription in the mammalian transcriptome. Science 2005, 309, 1564–1566.
[95]  Rinn, J.L.; Euskirchen, G.; Bertone, P.; Martone, R.; Luscombe, N.M.; Hartman, S.; Harrison, P.M.; Nelson, F.K.; Miller, P.; Gerstein, M.; et al. The transcriptional activity of human Chromosome 22. Genes Dev. 2003, 17, 529–540.
[96]  Birney, E.; Stamatoyannopoulos, J.A.; Dutta, A.; Guigo, R.; Gingeras, T.R.; Margulies, E.H.; Weng, Z.; Snyder, M.; Dermitzakis, E.T.; Thurman, R.E.; et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447, 799–816.
[97]  Van Bakel, H.; Nislow, C.; Blencowe, B.J.; Hughes, T.R. Most “dark matter” transcripts are associated with known genes. PLoS Biol. 2010, 8, e1000371, doi:10.1371/journal.pbio.1000371.
[98]  Asmann, Y.W.; Necela, B.M.; Kalari, K.R.; Hossain, A.; Baker, T.R.; Carr, J.M.; Davis, C.; Getz, J.E.; Hostetter, G.; Li, X.; et al. Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer. Cancer Res. 2012, 72, 1921–1928, doi:10.1158/0008-5472.CAN-11-3142.
[99]  Clark, M.B.; Amaral, P.P.; Schlesinger, F.J.; Dinger, M.E.; Taft, R.J.; Rinn, J.L.; Ponting, C.P.; Stadler, P.F.; Morris, K.V.; Morillon, A.; et al. The reality of pervasive transcription. PLoS Biol. 2011, 9, e1000625, doi:10.1371/journal.pbio.1000625.
[100]  Amaral, P.P.; Mattick, J.S. Noncoding RNA in development. Mamm. Genome 2008, 19, 454–492, doi:10.1007/s00335-008-9136-7.
[101]  Berretta, J.; Morillon, A. Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep. 2009, 10, 973–982, doi:10.1038/embor.2009.181.
[102]  Kapranov, P.; St Laurent, G.; Raz, T.; Ozsolak, F.; Reynolds, C.P.; Sorensen, P.H.; Reaman, G.; Milos, P.; Arceci, R.J.; Thompson, J.F.; et al. The majority of total nuclear-encoded non-ribosomal RNA in a human cell is ‘dark matter’ un-annotated RNA. BMC Biol. 2010, 8, 149, doi:10.1186/1741-7007-8-149.
[103]  Agarwal, A.; Koppstein, D.; Rozowsky, J.; Sboner, A.; Habegger, L.; Hillier, L.W.; Sasidharan, R.; Reinke, V.; Waterston, R.H.; Gerstein, M. Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics 2010, 11, 383.
[104]  Malone, J.H.; Oliver, B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol. 2011, 9, 34, doi:10.1186/1741-7007-9-34.
[105]  Van Bakel, H.; Nislow, C.; Blencowe, B.J.; Hughes, T.R. Response to “The reality of pervasive transcription”. PLoS Biol. 2011, 9, e1001102, doi:10.1371/journal.pbio.1001102.
[106]  Ameur, A.; Zaghlool, A.; Halvardson, J.; Wetterbom, A.; Gyllensten, U.; Cavelier, L.; Feuk, L. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat. Struct. Mol. Biol. 2011, 18, 1435–1440, doi:10.1038/nsmb.2143.
[107]  Mercer, T.R.; Gerhardt, D.J.; Dinger, M.E.; Crawford, J.; Trapnell, C.; Jeddeloh, J.A.; Mattick, J.S.; Rinn, J.L. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat. Biotechnol. 2011, 30, 99–104, doi:10.1038/nbt.2024.
[108]  Jarvis, K.; Robertson, M. The noncoding universe. BMC Biol. 2011, 9, 52, doi:10.1186/1741-7007-9-52.
[109]  Louro, R.; Smirnova, A.S.; Verjovski-Almeida, S. Long intronic noncoding RNA transcription: Expression noise or expression choice? Genomics 2009, 93, 291–298.
[110]  Mercer, T.R.; Dinger, M.E.; Mattick, J.S. Long non-coding RNAs: Insights into functions. Nat. Rev. Genet. 2009, 10, 155–159, doi:10.1038/nrg2521.
[111]  Dinger, M.E.; Amaral, P.P.; Mercer, T.R.; Pang, K.C.; Bruce, S.J.; Gardiner, B.B.; Askarian-Amiri, M.E.; Ru, K.; Solda, G.; Simons, C.; et al. S. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 2008, 18, 1433–1445, doi:10.1101/gr.078378.108.
[112]  Ahituv, N.; Zhu, Y.; Visel, A.; Holt, A.; Afzal, V.; Pennacchio, L.A.; Rubin, E.M. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 2007, 5, e234, doi:10.1371/journal.pbio.0050234.
[113]  Monroe, D. Genetics. Genomic clues to DNA treasure sometimes lead nowhere. Science 2009, 325, 142–143, doi:10.1126/science.325_142.
[114]  Knowles, D.G.; McLysaght, A. Recent de novo origin of human protein-coding genes. Genome Res. 2009, 19, 1752–1759, doi:10.1101/gr.095026.109.
[115]  Kaplan, C.D. The architecture of RNA polymerase fidelity. BMC Biol. 2010, 8, 85, doi:10.1186/1741-7007-8-85.
[116]  Ponting, C.P.; Hardison, R. What fraction of the human genome is functional? Genome Res. 2011, 21, 1769–1776, doi:10.1101/gr.116814.110.
[117]  Cawley, S.; Bekiranov, S.; Ng, H.H.; Kapranov, P.; Sekinger, E.A.; Kampa, D.; Piccolboni, A.; Sementchenko, V.; Cheng, J.; Williams, A.J.; et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 2004, 116, 499–509, doi:10.1016/S0092-8674(04)00127-8.
[118]  Wang, J.; Zhang, J.; Zheng, H.; Li, J.; Liu, D.; Li, H.; Samudrala, R.; Yu, J.; Wong, G.K. Mouse transcriptome: Neutral evolution of ‘non-coding’ complementary DNAs. Nature 2004, 431, doi:10.1038/nature03016.
[119]  Pang, K.C.; Frith, M.C.; Mattick, J.S. Rapid evolution of noncoding RNAs: Lack of conservation does not mean lack of function. Trends Genet. 2006, 22, 1–5, doi:10.1016/j.tig.2005.10.003.
[120]  Ebisuya, M.; Yamamoto, T.; Nakajima, M.; Nishida, E. Ripples from neighbouring transcription. Nat. Cell Biol. 2008, 10, 1106–1113, doi:10.1038/ncb1771.
[121]  Johnson, J.M.; Edwards, S.; Shoemaker, D.; Schadt, E.E. Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 2005, 21, 93–102, doi:10.1016/j.tig.2004.12.009.


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