Genome-wide identification of transcript start and end sites by transcript isoform sequencing

Nature Protocols

Volumn 9, Issue 7, 2014, Pages 1740-1759

  Pelechano, Vicent ^a   Wei, Wu ^a,b   Jakob, Petra ^a   Steinmetz, Lars M ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; ISOPROTEIN; MESSENGER RNA;

ARTICLE; CONTROLLED STUDY; DNA LIBRARY; GENE MAPPING; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC VARIATION; GENOME; HUMAN; NONHUMAN; OVERLAPPING GENE; PRIORITY JOURNAL; TRANSCRIPT ISOFORM SEQUENCING; TRANSCRIPTION END SITE; TRANSCRIPTION INITIATION SITE; CHEMISTRY; GENETICS; GENOMICS; PROCEDURES; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

GENETIC VARIATION; GENOME; GENOMICS; PROTEIN ISOFORMS; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, RNA;

EID: 84988527647     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.121     Document Type: Article

References (33)

1. Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
2. Di Giammartino, D.C., Nishida, K. & Manley, J.L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853-866 (2011).
3. Gupta, I. et al. Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions. Mol. Syst. Biol. 10, 719 (2014).
4. Kelemen, O. et al. Function of alternative splicing. Gene 514, 1-30 (2013).
5. Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033-1037 (2009).
6. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-1349 (2008).
7. Wei, W., Pelechano, V., Jarvelin, A.I. & Steinmetz, L.M. Functional consequences of bidirectional promoters. Trends Genet. 27, 267-276 (2011).
8. Jacquier, A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet. 10, 833-844 (2009).
9. Carninci, P. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38, 626-635 (2006).
10. Zhang, Z. & Dietrich, F.S. Mapping of transcription start sites in Saccharomyces cerevisiae using 5? SAGE. Nucleic Acids Res. 33, 2838-2851 (2005).
11. Ozsolak, F. et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143, 1018-1029 (2010).
12. Moqtaderi, Z., Geisberg, J.V., Jin, Y., Fan, X. & Struhl, K. Species-specific factors mediate extensive heterogeneity of mRNA 3? ends in yeasts. Proc. Natl. Acad. Sci. USA 110, 11073-11078 (2013).
13. Wilkening, S. et al. An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res. 41, e65 (2012).
14. Pelechano, V., Wilkening, S., Jarvelin, A.I., Tekkedil, M.M. & Steinmetz, L.M. Genome-wide polyadenylation site mapping. Methods in Enzymology 513, 271-296 (2012).
15. Pelechano, V., Wei, W. & Steinmetz, L.M. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature 497, 127-131 (2013).
16. Ng, P. et al. Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res. 34, e84 (2006).
17. Ng, P. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat. Methods 2, 105-111 (2005).
18. Fullwood, M.J. et al. An oestrogen receptor-α-bound human chromatin interactome. Nature 462, 58-64 (2009).
19. Ruan, X. & Ruan, Y. Genome wide full-length transcript analysis using 5? and 3? paired-end-tag next generation sequencing (RNA-PET). Methods Mol. Biol. 809, 535-562 (2012).
20. Carninci, P. et al. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37, 327-336 (1996).
21. Zhu, Y.Y., Machleder, E.M., Chenchik, A., Li, R. & Siebert, P.D. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. BioTechniques 30, 892-897 (2001).
22. Maruyama, K. & Sugano, S. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138, 171-174 (1994).
23. Scotto-Lavino, E., Du, G. & Frohman, M.A. Amplification of 5? end cDNA with ?new RACE?. Nat. Protoc. 1, 3056-3061 (2006).
24. Carninci, P. Constructing the landscape of the mammalian transcriptome. J. Exp. Biol. 210, 1497-1506 (2007).
25. Kuai, L., Fang, F., Butler, J.S. & Sherman, F. Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 101, 8581-8586 (2004).
26. Van Nieuwerburgh, F. et al. Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS ONE 6, e26969 (2011).
27. Chen, Y. et al. Systematic evaluation of factors influencing ChIP-seq fidelity. Nat. Methods 9, 609-614 (2012).
28. Miura, F. et al. A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc. Natl. Acad. Sci. USA 103, 17846-17851 (2006).
29. Sharon, D., Tilgner, H., Grubert, F. & Snyder, M. A single-molecule long-read survey of the human transcriptome. Nat. Biotechnol. 31, 1009-1014 (2013).
30. McManus, C.J., Duff, M.O., Eipper-Mains, J. & Graveley, B.R. Global analysis of trans-splicing in Drosophila. Proc. Natl. Acad. Sci. USA 107, 12975-12979 (2010).
31. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
32. Wilkening, S. et al. Genotyping 1000 yeast strains by next-generation sequencing. BMC Genomics 14, 90 (2013).
33. Thorvaldsdottir, H., Robinson, J.T. & Mesirov, J.P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178-192 (2013).