Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
10.1038/nbt1144
Crossref journal-article
Springer Science and Business Media LLC
Nature Biotechnology (297)
Bibliography

Washietl, S., Hofacker, I. L., Lukasser, M., Hüttenhofer, A., & Stadler, P. F. (2005). Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nature Biotechnology, 23(11), 1383–1390.

Authors 5
  1. Stefan Washietl (first)
  2. Ivo L Hofacker (additional)
  3. Melanie Lukasser (additional)
  4. Alexander Hüttenhofer (additional)
  5. Peter F Stadler (additional)
References 43 Referenced 307
  1. The Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004). (10.1038/nature03001)
  2. Bertone, P. et al. Global identification of human transcribed sequences with genome tiling arrays. Science 306, 2242–2246 (2004). (10.1126/science.1103388) / Science by P Bertone (2004)
  3. Kampa, D. et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331–342 (2004). (10.1101/gr.2094104) / Genome Res. by D Kampa (2004)
  4. Johnson, J.M., Edwards, S., Shoemaker, D. & Schadt, E.E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21, 93–102 (2005). (10.1016/j.tig.2004.12.009) / Trends Genet. by JM Johnson (2005)
  5. Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149–1154 (2005). (10.1126/science.1108625) / Science by J Cheng (2005)
  6. Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573 (2002). (10.1038/nature01266) / Nature by Y Okazaki (2002)
  7. Imanishi, T. et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology 2, 0856–0875 (2004). (10.1371/journal.pbio.0020162) / PLoS Biology by T Imanishi (2004)
  8. Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499–509 (2004). (10.1016/S0092-8674(04)00127-8) / Cell by S Cawley (2004)
  9. Hüttenhofer, A., Schattner, P. & Polacek, N. Non-coding RNAs: hope or hype? Trends Genet. 21, 289–297 (2005). (10.1016/j.tig.2005.03.007) / Trends Genet. by A Hüttenhofer (2005)
  10. Hofacker, I.L. et al. Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucleic Acids Res. 26, 3825–3836 (1998). (10.1093/nar/26.16.3825) / Nucleic Acids Res. by IL Hofacker (1998)
  11. Rivas, E., Klein, R.J., Jones, T.A. & Eddy, S.R. Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr. Biol. 11, 1369–1373 (2001). (10.1016/S0960-9822(01)00401-8) / Curr. Biol. by E Rivas (2001)
  12. Washietl, S., Hofacker, I.L. & Stadler, P.F. Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. USA 102, 2454–2459 (2005). (10.1073/pnas.0409169102) / Proc. Natl. Acad. Sci. USA by S Washietl (2005)
  13. Moulton, V. Tracking down noncoding RNAs. Proc. Natl. Acad. Sci. USA 102, 2269–2270 (2005). (10.1073/pnas.0500129102) / Proc. Natl. Acad. Sci. USA by V Moulton (2005)
  14. Shabalina, S.A. & Kondrashov, A.S. Pattern of selective constraint in C. elegans and C. briggsae genomes. Genet. Res. 74, 23–30 (1999). (10.1017/S0016672399003821) / Genet. Res. by SA Shabalina (1999)
  15. Shabalina, S.A., Ogurtsov, A.Y., Kondrashov, V.A. & Kondrashov, A.S. Selective constraint in intergenic regions of human and mouse genomes. Trends Genet. 17, 373–376 (2001). (10.1016/S0168-9525(01)02344-7) / Trends Genet. by SA Shabalina (2001)
  16. Margulies, E.H., Blanchette, M., Haussler, D. & Green, E.D. Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507–2518 (2003). (10.1101/gr.1602203) / Genome Res. by EH Margulies (2003)
  17. Dermitzakis, E.T. et al. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science 302, 1033–1035 (2003). (10.1126/science.1087047) / Science by ET Dermitzakis (2003)
  18. Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002). (10.1101/gr.229102) / Genome Res. by WJ Kent (2002)
  19. International Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002). (10.1038/nature01262)
  20. Cooper, G.M. et al. Characterization of evolutionary rates and constraints in three mammalian genomes. Genome Res. 14, 539–548 (2004). (10.1101/gr.2034704) / Genome Res. by GM Cooper (2004)
  21. Le, S.V., Chen, J.H., Currey, K.M. & Maizel, J.V., Jr. A program for predicting significant RNA secondary structures. Comput. Appl. Biosci. 4, 153–159 (1988). / Comput. Appl. Biosci. by SV Le (1988)
  22. Washietl, S. & Hofacker, I.L. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J. Mol. Biol. 342, 19–30 (2004). (10.1016/j.jmb.2004.07.018) / J. Mol. Biol. by S Washietl (2004)
  23. Hofacker, I.L., Fekete, M. & Stadler, P.F. Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319, 1059–1066 (2002). (10.1016/S0022-2836(02)00308-X) / J. Mol. Biol. by IL Hofacker (2002)
  24. Griffiths-Jones, S. et al. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33, D121–D124 (2005). (10.1093/nar/gki081) / Nucleic Acids Res. by S Griffiths-Jones (2005)
  25. Accardo, M.C. et al. A computational search for box C/D snoRNA genes in the D. melanogaster genome. Bioinformatics 20, 3293–3301 (2004). (10.1093/bioinformatics/bth394) / Bioinformatics by MC Accardo (2004)
  26. Childs, J.L., Poole, A.W. & Turner, D.H. Inhibition of Escherichia coli RNase P by oligonucleotide directed misfolding of RNA. RNA 9, 1437–1445 (2003). (10.1261/rna.5780503) / RNA by JL Childs (2003)
  27. Lin, J. et al. A universal telomerase RNA core structure includes structured motifs required for binding the telomerase reverse transcriptase protein. Proc. Natl. Acad. Sci. USA 101, 14713–14718 (2004). (10.1073/pnas.0405879101) / Proc. Natl. Acad. Sci. USA by J Lin (2004)
  28. Avner, P. & Heard, E. X-chromosome inactivation: counting, choice, and initiation. Nat. Rev. Genet. 2, 59–67 (2001). (10.1038/35047580) / Nat. Rev. Genet. by P Avner (2001)
  29. Rougeulle, C. & Heard, E. Antisense RNA in imprinting: spreading silence through Air. Trends Genet. 18, 434–437 (2002). (10.1016/S0168-9525(02)02749-X) / Trends Genet. by C Rougeulle (2002)
  30. Pang, K.C. et al. RNAdb — comprehensive mammalian noncoding RNA database. Nucleic Acids Res. Database issue. 33, D125–D130 (2005). (10.1093/nar/gki089) / Nucleic Acids Res. by KC Pang (2005)
  31. Hüttenhofer, A. et al. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J. 20, 2943–2953 (2001). (10.1093/emboj/20.11.2943) / EMBO J. by A Hüttenhofer (2001)
  32. Bachellerie, J.-P., Cavaillé, J. & Hüttenhofer, A. The expanding snoRNA world. Biochimie 84, 775–790 (2002). (10.1016/S0300-9084(02)01402-5) / Biochimie by J-P Bachellerie (2002)
  33. Berezikov, E. et al. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21–24 (2005). (10.1016/j.cell.2004.12.031) / Cell by E Berezikov (2005)
  34. Bejerano, G. et al. Ultraconserved elements in the human genome. Science 304, 1321–1325 (2004). (10.1126/science.1098119) / Science by G Bejerano (2004)
  35. Mattick, J.S. RNA regulation: a new genetics? Nat. Rev. Genet. 5, 316–323 (2004). (10.1038/nrg1321) / Nat. Rev. Genet. by JS Mattick (2004)
  36. Glazov, E.A., Pheasant, M., McGraw, E.A., Bejerano, G. & Mattick, J.S. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mrna splicing. Genome Res. 15, 800–808 (2005). (10.1101/gr.3545105) / Genome Res. by EA Glazov (2005)
  37. Doudna, J.A. Structural genomics of RNA. Nat. Struct. Biol. 7, 954–956 (2000). (10.1038/80729) / Nat. Struct. Biol. by JA Doudna (2000)
  38. Hartig, J.S., Grüne, I., Najafi-Shoushtari, S.H. & Famulok, M. Sequence-specific detection of microRNAs by signal-amplifying ribozymes. J. Am. Chem. Soc. 126, 722–723 (2004). (10.1021/ja038822u) / J. Am. Chem. Soc. by JS Hartig (2004)
  39. Missal, K., Rose, D. & Stadler, P.F. Non-coding RNAs in Ciona intestinalis. Bioinformatics 21, Suppl 2, ii77–ii78 (2005). (10.1093/bioinformatics/bti1113) / Bioinformatics by K Missal (2005)
  40. Griffiths-Jones, S. The microRNA Registry. Nucleic Acids Res. 32, D109–D111 (2004). (10.1093/nar/gkh023) / Nucleic Acids Res. by S Griffiths-Jones (2004)
  41. Liu, C. et al. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res. Database issue. 33, D112–D115 (2005). (10.1093/nar/gki041) / Nucleic Acids Res. by C Liu (2005)
  42. Pesole, G. et al. UTRdb and UTRSite: specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Res. 30, 335–340 (2002). (10.1093/nar/30.1.335) / Nucleic Acids Res. by G Pesole (2002)
  43. Scherer, S.W. et al. Human chromosome 7: DNA sequence and biology. Science 300, 767–772 (2003). (10.1126/science.1083423) / Science by SW Scherer (2003)
Dates
Type When
Created 19 years, 9 months ago (Nov. 4, 2005, 2:43 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 3:43 p.m.)
Indexed 1 month, 3 weeks ago (July 2, 2025, 2:32 p.m.)
Issued 19 years, 9 months ago (Nov. 1, 2005)
Published 19 years, 9 months ago (Nov. 1, 2005)
Published Online 19 years, 9 months ago (Nov. 4, 2005)
Published Print 19 years, 9 months ago (Nov. 1, 2005)
Funders 0

None

@article{Washietl_2005, title={Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome}, volume={23}, ISSN={1546-1696}, url={http://dx.doi.org/10.1038/nbt1144}, DOI={10.1038/nbt1144}, number={11}, journal={Nature Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Washietl, Stefan and Hofacker, Ivo L and Lukasser, Melanie and Hüttenhofer, Alexander and Stadler, Peter F}, year={2005}, month=nov, pages={1383–1390} }