Sequencing of first-strand cDNA library reveals full-length transcriptomes

Nature Communications

Volumn 6, Issue , 2015, Pages

  Agarwal, Saurabh ^a   Macfarlan, Todd S ^b   Sartor, Maureen A ^a   Iwase, Shigeki ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; SINGLE STRANDED RNA; TRANSCRIPTOME; DNA DIRECTED DNA POLYMERASE BETA; OLIGONUCLEOTIDE; RNA;

DNA; ENZYME ACTIVITY; GENE EXPRESSION; GENOMICS; REACTION KINETICS;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DNA LIBRARY; DNA SEQUENCE; DNA STRAND; DNA SYNTHESIS; EMBRYO; ENZYME MECHANISM; GENE CONTROL; GENOMICS; MALE; MOUSE; NONHUMAN; POLYADENYLATION; TRANSCRIPTION INITIATION SITE; ANIMAL; BIOLOGY; BRAIN CORTEX; EMBRYOLOGY; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; PROCEDURES; SEQUENCE ANALYSIS;

ANIMALS; CEREBRAL CORTEX; COMPUTATIONAL BIOLOGY; DNA POLYMERASE I; DNA, COMPLEMENTARY; GENE LIBRARY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MALE; MICE; OLIGONUCLEOTIDES; POLYADENYLATION; RNA; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84948567835     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7002     Document Type: Article

References (57)

1. Brenner, S. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnol. 18, 630-634 (2000).
2. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008).
3. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
4. 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).
5. Armour, C. D. et al. Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat. Methods 6, 647-649 (2009).
6. He, Y., Vogelstein, B., Velculescu, V. E., Papadopoulos, N. & Kinzler, K. W. The antisense transcriptomes of human cells. Science 322, 1855-1857 (2008).
7. Schaefer, M., Pollex, T., Hanna, K. & Lyko, F. RNA cytosine methylation analysis by bisulfite sequencing. Nucleic Acids Res. 37, e12 (2009).
8. Parkhomchuk, D. et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 37, e123 (2009).
9. Okayama, H. & Berg, P. High-efficiency cloning of full-length cDNA. Mol. Cell. Biol. 2, 161-170 (1982).
10. Lehman, I. R. DNA polymerase I of Escherichia coli. in Enzymes Vol. 14 (ed. Paul, D. B.) 15-37 (Academic, 1981).
11. D'Alessio, J. M. & Gerard, G. F. Second-strand cDNA synthesis with E. coli DNA polymerase I and RNase H: the fate of information at the mRNA 50 terminus and the effect of E. coli DNA ligase. Nucleic Acids Res. 16, 1999-2014 (1988).
12. Carninci, P. et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genet. 38, 626-635 (2006).
13. Valen, E. et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res. 19, 255-265 (2009).
14. Arribere, J. A. & Gilbert, W. V. Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing. Genome Res. 23, 977-987 (2013).
15. Plessy, C. et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat. Methods 7, 528-534 (2010).
16. Salimullah, M., Sakai, M., Plessy, C. & Carninci, P. NanoCAGE: a highresolution technique to discover and interrogate cell transcriptomes. Cold Spring Harbor Protoc. 2011, pdb prot5559 (2011).
17. Yoon, O. K. & Brem, R. B. Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA 16, 1256-1267 (2010).
18. Fox-Walsh, K., Davis-Turak, J., Zhou, Y., Li, H. & Fu, X. D. A multiplex RNAseq strategy to profile poly(A) RNA: application to analysis of transcription response and 30 end formation. Genomics 98, 266-271 (2011).
19. Ozsolak, F. et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143, 1018-1029 (2010).
20. Beck, A. H. et al. 30-End sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One 5, e8768 (2010).
21. Shepard, P. J. et al. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA 17, 761-772 (2011).
22. Jan, C. H., Friedman, R. C., Ruby, J. G. & Bartel, D. P. Formation, regulation and evolution of Caenorhabditis elegans 30UTRs. Nature 469, 97-101 (2011).
23. Derti, A. et al. A quantitative atlas of polyadenylation in five mammals. Genome Res. 22, 1173-1183 (2012).
24. Elkon, R. et al. E2F mediates enhanced alternative polyadenylation in proliferation. Genome Biol. 13, R59 (2012).
25. Wilkening, S. et al. An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res. 41, e65 (2013).
26. Pease Jim, R. S. Novel methods for rRNA removal and directional, ligation-free RNA-seq library preparation. Nat. Methods 7 (2010).
27. Pease Jim, R. S. A rapid, directional RNA-seq library preparation workflow for Illumina sequencing. Nat. Methods 9 (2012).
28. Levin, J. Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709-715 (2010).
29. Lindahl, T., Ljungquist, S., Siegert, W., Nyberg, B. & Sperens, B. DNA N-glycosidases: properties of uracil-DNA glycosidase from Escherichia coli. J. Biol. Chem. 252, 3286-3294 (1977).
30. DeAngelis, M. M., Wang, D. G. & Hawkins, T. L. Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res. 23, 4742-4743 (1995).
31. Miller, D. F. et al. A new method for stranded whole transcriptome RNA-seq. Methods 63, 126-134 (2013).
32. Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218-223 (2009).
33. Macfarlan, T. S. et al. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev. 25, 594-607 (2011).
34. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
35. DeLuca, D. S. et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28, 1530-1532 (2012).
36. Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008).
37. Seila, A. C. et al. Divergent transcription from active promoters. Science 322, 1849-1851 (2008).
38. Seila, A. C., Core, L. J., Lis, J. T. & Sharp, P. A. Divergent transcription: a new feature of active promoters. Cell Cycle 8, 2557-2564 (2009).
39. Preker, P. et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322, 1851-1854 (2008).
40. Preker, P. et al. PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters. Nucleic Acids Res. 39, 7179-7193 (2011).
41. Kruesi, W. S., Core, L. J., Waters, C. T., Lis, J. T. & Meyer, B. J. Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. eLife 2, e00808 (2013).
42. Kwak, H., Fuda, N. J., Core, L. J. & Lis, J. T. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 950-953 (2013).
43. Core, L. J. et al. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nature Genet. 46, 1311-1320 (2014).
44. Lee, Y., Jeon, K., Lee, J. T., Kim, S. & Kim, V. N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663-4670 (2002).
45. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415-419 (2003).
46. Chen, D. & Patton, J. T. Reverse transcriptase adds nontemplated nucleotides to cDNAs during 50-RACE and primer extension. BioTechniques 30, 582 (2001).
47. Mayr, C. & Bartel, D. P. Widespread shortening of 30UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673-684 (2009).
48. Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Prot. 7, 562-578 (2012).
49. Klenow, H. & Henningsen, I. Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis. Proc. Natl Acad. Sci. USA 65, 168-175 (1970).
50. Elkon, R., Ugalde, A. P. & Agami, R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet. 14, 496-506 (2013).
51. Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377-382 (2009).
52. Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160-1167 (2011).
53. Picelli, S. et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature Methods 10, 1096-1098 (2013).
54. Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Prot 9, 171-181 (2014).
55. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
56. Bushnell, B. BBMap short read aligner, and other bioinformatic tools http:// sourceforge. net/projects/bbmap (2014).
57. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).