Profiling of short RNAs using helicos single-molecule sequencing

Methods in Molecular Biology

Volumn 822, Issue , 2012, Pages 219-232

  Kapranov, Philipp ^a   Ozsolak, Fatih ^a   Milos, Patrice M ^a  

^a Helicos BioSciences Corporation   (United States)

Author keywords

Polyad enylated short RNAs; Promoter associate short RNAs; Short RNAs; Single molecule sequencing

Indexed keywords

COMPLEMENTARY DNA; RNA; SMALL UNTRANSLATED RNA;

ARTICLE; BIOLOGY; DNA SEQUENCE; GENE EXPRESSION PROFILING; HUMAN; INSTRUMENTATION; ISOLATION AND PURIFICATION; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; HUMANS; RNA; RNA, SMALL UNTRANSLATED; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA;

EID: 84855931046     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-427-8_15     Document Type: Article

References (17)

1. Storz, G., Altuvia, S., and Wassarman, K. M. (2005) An abundance of RNA regulators. Annu Rev Biochem 74, 199-217.
2. Ghildiyal, M., and Zamore, P. D. (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10, 94-108.
3. Affymetrix, ENCODE, Transcriptome, Project;, Cold, Spring, et al. (2009) Posttranscriptional processing generates a diversity of 5′ -modifi ed long and short RNAs. Nature 457, 1028-32.
4. Davis, C. A., and Ares, M., Jr. (2006) Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 103, 3262-7.
5. Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive. transcription Science 316, 1484-8.
6. Taft, R. J., Glazov, E. A., Cloonan, N., Simons, C., Stephen, S., Faulkner, G. J., et al. (2009) Tiny RNAs associated with transcription start sites in animals. Nat Genet 41, 572-8.
7. Kapranov, P., Ozsolak, F., Kim, S. W., Foissac, F., Lipson, D., Hart, C., et al. (2010) Novel class of human RNAs associated with gene termini suggests an uncharacterized RNA copying mechanism. Nature 466, 642-6.
8. Rassoulzadegan, M., Grandjean, V., Gounon, P., Vincent, S., Gillot, I., and Cuzin, F. (2006) RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse. Nature 441, 469-74.
9. Kawaji, H., and Hayashizaki, Y. (2008) Exploration of small RNAs. PLoS Genet 4, e22.
10. Mitchell, P. S., Parkin, R. K., Kroh, E. M., Fritz, B. R., Wyman, S. K., Pogosova- Agadjanyan, E. L., et al. (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 105, 10513-8.
11. Chen, X., Ba, Y., Ma, L., Cai, X., Yin, Y., Wang, K., et al. (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18, 997-1006.
12. Sambrook, J., and Russell, D. W. (2001) Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
13. Giladi, E., Healy, J., Myers, G., Hart, C., Kapranov, P., Lipson, D., et al. (2010) Error tolerant indexing and alignment of short reads with covering template families. J. Comput. Biol. 17, 1397-411.
14. Harris, T. D., Buzby, P. R., Babcock, H., Beer, E., Bowers, J., Braslavsky, I., et al. (2008) Single-molecule DNA sequencing of a viral genome. Science 320, 106-9.
15. Lipson, D., Raz, T., Kieu, A., Jones, D. R., Giladi, E., Thayer, E., et al. (2009) Quantifi cation of the yeast transcriptome by single-molecule sequencing. Nat Biotechnol 27, 652-8.
16. Li, H., and Durbin, R. (2009) Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25, 1754-60.
17. Rumble, S. M., Lacroute, P., Dalca, A. V., Fiume, M., Sidow, A., and Brudno, M. (2009) SHRiMP: accurate mapping of short colorspace reads. PLoS Comput Biol 5, e1000386.