Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies

Nucleic Acids Research

Volumn 38, Issue 16, 2010, Pages

  Hestand, Matthew S ^a   Klingenhoff, Andreas ^b   Scherf, Matthias ^b   Ariyurek, Yavuz ^a   Ramos, Yolande ^a   van Workum, Wilbert ^c   Suzuki, Makoto ^d   Werner, Thomas ^b   van Ommen, Gert Jan B ^a   den Dunnen, Johan T ^a   Harbers, Matthias ^d   't Hoen, Peter A C ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b Genomatix GmbH   (Germany)

^c ServiceXS   (Netherlands)

^d KK DNAFORM   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; CAP ANALYSIS OF GENE EXPRESSION; CELL DIFFERENTIATION; CELL PROLIFERATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC TRANSCRIPTION; MOUSE; MUSCLE DEVELOPMENT; MYOBLAST; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; SERIAL ANALYSIS OF GENE EXPRESSION; TRANSCRIPTION INITIATION SITE; ANIMAL; BIOLOGICAL MODEL; CELL LINE; DNA MICROARRAY; EVALUATION STUDY; GENETICS; METABOLISM; PROCEDURES; REPRODUCIBILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

3' UNTRANSLATED REGIONS; ANIMALS; CELL LINE; GENE EXPRESSION PROFILING; MICE; MODELS, BIOLOGICAL; MUSCLE DEVELOPMENT; MYOBLASTS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION INITIATION SITE;

3' UNTRANSLATED REGION;

EID: 85052549949     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq602     Document Type: Article

References (44)

1. Velculescu, V.E., Zhang, L., Vogelstein, B. and Kinzler, K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
2. Harbers, M. and Carninci, P. (2005) Tag-based approaches for transcriptome research and genome annotation. Nat. Methods, 2, 495-502.
3. Nielsen, K.L., Hogh, A.L. and Emmersen, J. (2006) DeepSAGE-digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucleic Acids Res., 34, e133.
4. Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., Kodzius, R., Watahiki, A., Nakamura, M. and Arakawa, T. (2003) Cap analysis gene expression for highthroughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl Acad. Sci. USA, 100, 15776-15781.
5. Valen, E., Pascarella, G., Chalk, A., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H. and Lazarevic, D. (2009) Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res., 19, 255-265.
6. Morin, R., Bainbridge, M., Fejes, A., Hirst, M., Krzywinski, M., Pugh, T., McDonald, H., Varhol, R., Jones, S. and Marra, M. (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques, 45, 81-94.
7. Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
8. Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., vanBaren, M.J., Salzberg, S.L., Wold, B.J. and Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
9. Sterrenburg, E., Turk, R., 'tHoen, P.A.C., van Deutekom, J.C.T., Boer, J.M., van Ommen, G.-J.B. and den Dunnen, J.T. (2004) Large-scale gene expression analysis of human skeletal myoblast differentiation. Neuromuscul. Disord., 14, 507-518.
10. Turk, R., Sterrenburg, E., van derWees, C.G.C., deMeijer, E.J., deMenezes, R.X., Groh, S., Campbell, K.P., Noguchi, S., vanOmmen, G.J.B., den Dunnen, J.T. et al. (2006) Common pathological mechanisms in mouse models for muscular dystrophies. FASEB J., 20, 127-129.
11. Jelier, R., 'tHoen, P.A.C., Sterrenburg, E., den Dunnen, J.T., van Ommen, G.-J.B., Kors, J.A. and Mons, B. (2008) Literatureaided meta-analysis of microarray data: a compendium study on muscle development and disease. BMC Bioinformatics, 9, 291.
12. Tomczak, K.K., Marinescu, V.D., Ramoni, M.F., Sanoudou, D., Montanaro, F., Han, M., Kunkel, L.M., Kohane, I.S. and Beggs, A.H. (2004) Expression profiling and identification of novel genes involved in myogenic differentiation. FASEB J., 18, 403-405.
13. Pownall, M.E., Gustafsson, M.K. and Emerson, C.P.J. (2002) Myogenic regulatory factors and the specification of muscle progenitors in vertebrate embryos. Annu. Rev. Cell Dev. Biol., 18, 747-783.
14. Sartorelli, V. and Caretti, G. (2005) Mechanisms underlying the transcriptional regulation of skeletal myogenesis. Curr. Opin. Genet. Dev., 15, 528-535.
15. Hestand, M.S., van Galen, M., Villerius, M.P., van Ommen, G.-J.B., den Dunnen, J.T. and 'tHoen, P.A.C. (2008) CORE_TF: a userfriendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. BMC Bioinformatics, 9, 495.
16. Sui, S.J.H., Fulton, D.L., Arenillas, D.J., Kwon, A.T. and Wasserman, W.W. (2007) oPOSSUM: integrated tools for analysis of regulatory motif over-representation. Nucleic Acids Res., 35, W245-W252.
17. Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from highthroughput DNA sequencing. Nucleic Acids Res., 36, e105.
18. Smith, A.D., Xuan, Z. and Zhang, M.Q. (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics, 9, 128.
19. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
20. Faulkner, G.J., Forrest, A.R.R., Chalk, A.M., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D.A. and Grimmond, S.M. (2008) A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics, 91, 281-288.
21. Faulkner, G.J., Kimura, Y., Daub, C.O., Wani, S., Plessy, C., Irvine, K.M., Schroder, K., Cloonan, N., Steptoe, A.L., Lassmann, T. et al. (2009) The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet., 41, 563-571.
22. Vencio, R.Z.N., Brentani, H., Patrao, D.F.C. and Pereira, C.A.B. (2004) Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE). BMC Bioinformatics, 5, 119.
23. 'tHoen, P.A.C., Ariyurek, Y., Thygesen, H.H., Vreugdenhil, E., Vossen, R.H.A.M., de Menezes, R.X., Boer, J.M., van Ommen, G.-J.B. and denDunnen, J.T. (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and interlab portability over five microarray platforms. Nucleic Acids Res., 36, e141.
24. Huber, W., vonHeydebreck, A., Sultmann, H., Poustka, A. and Vingron, M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18(Suppl. 1), S96-104.
25. Smyth, G., Yang, Y. and Speed, T. (2003) Statistical issues in CDNA microarray data analysis. Methods Mol. Biol., 224, 111-136.
26. Gentleman, R., Carey, V., Dudoit, S., Irizarry, R. and Huber, W. (2005) Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York.
27. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J.R. Stat. Soc. B, 57, 289-300.
28. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
29. Camon, E., Barrell, D., Lee, V., Dimmer, E. and Apweiler, R. (2004) The Gene Ontology Annotation (GOA) Database-an integrated resource of GO annotations to the UniProt Knowledgebase. In Silico Biol., 4, 5-6.
30. Jelier, R., Schuemie, M.J., Veldhoven, A., Dorssers, L.C.J., Jenster, G. and Kors, J.A. (2008) Anni 2.0: a multipurpose textmining tool for the life sciences. Genome Biol., 9, R96.
31. Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C.A.M., Taylor, M.S., Engstrom, P.G., Frith, M.C. et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet., 38, 626-635.
32. Hubbard, T.J.P., Aken, B.L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
33. Kel, A.E., Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V. and Wingender, E. (2003) MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.
34. Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
35. Cohen, C.D., Klingenhoff, A., Boucherot, A., Nitsche, A., Henger, A., Brunner, B., Schmid, H., Merkle, M., Saleem, M.A., Koller, K.-P. et al. (2006) Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc. Natl Acad. Sci. USA, 103, 5682-5687.
36. Dohr, S., Klingenhoff, A., Maier, H., deAngelis, M.H., Werner, T. and Schneider, R. (2005) Linking disease-associated genes to regulatory networks via promoter organization. Nucleic Acids Res., 33, 864-872.
37. Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M., Marshall, K.A. et al. (2009) NCBI GEO: archive for highthroughput functional genomic data. Nucleic Acids Res., 37, D885-D890.
38. Velculescu, V.E., Madden, S.L., Zhang, L., Lash, A.E., Yu, J., Rago, C., Lal, A., Wang, C.J., Beaudry, G.A., Ciriello, K.M. et al. (1999) Analysis of human transcriptomes. Nat. Genet., 23, 387-388.
39. Buskin, J.N. and Hauschka, S.D. (1989) Identification of a myocyte nuclear factor that binds to the muscle-specific enhancer of the mouse muscle creatine kinase gene. Mol. Cell Biol., 2627-2640.
40. Olson, E.N. (1990) MyoD family: a paradigm for development? Genes Dev., 4, 1454-1461.
41. Nishida, W., Nakamura, M., Mori, S., Takahashi, M., Ohkawa, Y., Tadokoro, S., Yoshida, K., Hiwada, K., Hayashi, K. and Sobue, K. (2002) A triad of serum response factor and the GATA and NK families governs the transcription of smooth and cardiac muscle genes. J. Biol. Chem., 277, 7308-7317.
42. Suzuki, H., Forrest, A.R.R., vanNimwegen, E., Daub, C.O., Balwierz, P.J., Irvine, K.M., Lassmann, T., Ravasi, T., Hasegawa, Y., deHoon, M.J.L. et al. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet., 41, 553-562.
43. Gustincich, S., Sandelin, A., Plessy, C., Katayama, S., Simone, R., Lazarevic, D., Hayashizaki, Y. and Carninci, P. (2006) The complexity of the mammalian transcriptome. J. Physiol., 575, 321-332.
44. Fejes-Toth, K., Sotirova, V., Sachidanandam, R., Assaf, G., Hannon, G.J., Kapranov, P., Foissac, S., Willingham, A.T., Duttagupta, R., Dumais, E. et al. (2009) Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature, 457, 1028-1032.