Direct RNA sequencing

Nature

Volumn 461, Issue 7265, 2009, Pages 814-818

  Ozsolak, Fatih ^a   Platt, Adam R ^a   Jones, Dan R ^a   Reifenberger, Jeffrey G ^a   Sass, Lauryn E ^a   McInerney, Peter ^a   Thompson, John F ^a   Bowers, Jayson ^a   Jarosz, Mirna ^a   Milos, Patrice M ^a  

^a Helicos BioSciences Corporation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA POLYMERASE; POLYADENYLIC ACID; POLYTHYMIDYLIC ACID;

BIOCHEMISTRY; BIOLOGICAL CHARACTERISTICS; GENETIC ANALYSIS; GENOMICS; HOMINID; PUBLIC HEALTH; RNA;

ARTICLE; CONTROLLED STUDY; DNA SYNTHESIS; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; RNA SEQUENCE; RNA TRANSCRIPTION; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; OLIGORIBONUCLEOTIDES; POLYMERASE CHAIN REACTION; RNA; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, RNA; TEMPLATES, GENETIC;

SACCHAROMYCES CEREVISIAE;

EID: 70349956497     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature08390     Document Type: Article

References (30)

1. Denoeud, F. et al. Annotating genomes with massive-scale RNA sequencing. Genome Biol. 9, R175 (2008).
2. Kapranov, P., Willingham, A. T. & Gingeras, T. R. Genome-wide transcription and the implications for genomic organization. Nature Rev. Genet. 8, 413-423 (2007).
3. Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M. & Gilad, Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509-1517 (2008).
4. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621-628 (2008).
5. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344-1349 (2008).
6. Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956-960 (2008).
7. Wilhelm, B. T. et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239-1243 (2008).
8. Cocquet, J., Chong, A., Zhang, G. & Veitia, R. A. Reverse transcriptase template switching and false alternative transcripts. Genomics 88, 127-131 (2006).
9. Gubler, U. Second-strand cDNA synthesis: classical method. Methods Enzymol. 152, 325-329 (1987).
10. Gubler, U. Second-strand cDNA synthesis: mRNA fragments as primers. Methods Enzymol. 152, 330-335 (1987).
11. Haddad, F. et al. Regulation of antisense RNA expression during cardiac MHC gene switching in response to pressure overload. Am. J. Physiol. Heart Circ. Physiol. 290, H2351-H2361 (2006).
12. Haddad, F., Qin, A. X., Giger, J. M., Guo, H. & Baldwin, K. M. Potential pitfalls in the accuracy of analysis of natural sense-antisense RNA pairs by reverse transcription-PCR. BMC Biotechnol. 7, 21 (2007).
13. Mader, R. M. et al. Reverse transcriptase template switching during reverse transcriptase-polymerase chain reaction: artificial generation of deletions in ribonucleotide reductase mRNA. J. Lab. Clin. Med. 137, 422-428 (2001).
14. Perocchi, F., Xu, Z., Clauder-Munster, S. & Steinmetz, L. M. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res. 35, e128 (2007).
15. Roberts, J. D. et al. Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro. Mol. Cell. Biol. 9, 469-476 (1989).
16. Roy, S. W. & Irimia, M. When good transcripts go bad: artifactual RT-PCR ?splicing? and genome analysis. Bioessays 30, 601-605 (2008).
17. Roy, S. W. & Irimia, M. Intron mis-splicing: no alternative? Genome Biol. 9, 208 (2008).
18. Spiegelman, S. et al. DNA-directed DNA polymerase activity in oncogenic RNA viruses. Nature 227, 1029-1031 (1970).
19. Varadaraj, K. & Skinner, D. M. Denaturants or cosolvents improve the specificity of PCR amplification of a G 1 C-rich DNA using genetically engineered DNA polymerases. Gene 140, 1-5 (1994).
20. Wu, J. Q. et al. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol. 9, R3 (2008).
21. Braslavsky, I., Hebert, B., Kartalov, E. & Quake, S. R. Sequence information can be obtained from single DNA molecules. Proc. Natl Acad. Sci. USA 100, 3960-3964 (2003).
22. Harris, T. D. et al. Single-molecule DNA sequencing of a viral genome. Science 320, 106-109 (2008).
23. Karkas, J. D., Stavrianopoulos, J. G. & Chargaff, E. Action of DNA polymerase I of Escherichia coli with DNA-RNA hybrids as templates. Proc. Natl Acad. Sci. USA 69, 398-402 (1972).
24. Rüttimann, C., Cotoras, M., Zald́ivar, J. & Vicuna, R. DNA polymerases from the extremely thermophilic bacterium Thermus thermophilus HB-8. Eur. J. Biochem. 149, 41-46 (1985).
25. Stenesh, J., Roe, B. A. & Snyder, T. L. Studies of the deoxyribonucleic acid from mesophilic and thermophilic bacteria. Biochim. Biophys. Acta 161, 442-454 (1968).
26. Kent, W. J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
27. Kim, M. et al. Distinct pathways for snoRNA and mRNA termination. Mol. Cell 24, 723-734 (2006).
28. Grzechnik, P. & Kufel, J. Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast. Mol. Cell 32, 247-258 (2008).
29. Slomovic, S., Laufer, D., Geiger, D. & Schuster, G. Polyadenylation of ribosomal RNA in human cells. Nucleic Acids Res. 34, 2966-2975 (2006).
30. Lipson, D. et al. Quantification of the yeast transcriptome by single-molecule sequencing. Nature Biotechnol. 27, 652-658 (2009).