Identification and classification of conserved RNA secondary structures in the human genome

PLoS Computational Biology

Volumn 2, Issue 4, 2006, Pages 251-262

  Pedersen, Jakob Skou ^a   Bejerano, Gill ^a   Siepel, Adam ^a,e   Rosenbloom, Kate ^a   Lindblad Toh, Kerstin ^b   Lander, Eric S ^b   Kent, Jim ^a   Miller, Webb ^c   Haussler, David ^a,d  

^a University of California Santa Cruz   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTEXT FREE GRAMMARS; FISH; GENES; STOCHASTIC SYSTEMS;

COMPARATIVE GENOMICS; GENOMIC METHODS; HUMAN GENOMES; PHYLOGENETICS; PUFFER FISHES; RIBOSWITCHES; RNA SECONDARY STRUCTURES; RNA STRUCTURES; STOCHASTIC CONTEXT FREE GRAMMAR; ZEBRA FISH;

RNA;

MICRORNA; RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CHICKEN; CHIMPANZEE; COMPARATIVE GENOMIC HYBRIDIZATION; DOG; FISH; GENE IDENTIFICATION; GENE INSERTION SEQUENCE; GENETIC CONSERVATION; GENETIC SCREENING; GENOME ANALYSIS; HUMAN GENOME; HUMAN VERSUS ANIMAL COMPARISON; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; ZEBRA FISH; ANIMAL; BIOLOGY; CHEMISTRY; CONFORMATION; GENOME; HUMAN; METHODOLOGY; MOUSE; RAT; TETRAODONTIFORMES;

ANIMALIA; CANIS FAMILIARIS; DANIO RERIO; PAN TROGLODYTES; TETRAODONTIDAE;

3' UNTRANSLATED REGIONS; ANIMALS; CHICKENS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DOGS; GENOME; GENOME, HUMAN; HUMANS; MICE; MICRORNAS; NUCLEIC ACID CONFORMATION; RATS; SEQUENCE ANALYSIS, RNA; TETRAODONTIFORMES; ZEBRAFISH;

EID: 33646272409     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020033     Document Type: Article

References (68)

1. Eddy SR (2001) Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2: 919-929.
2. Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, et al. (2004) Evolutionary patterns of non-coding RNAs. Theor Biosci 123: 301-369.
3. Mattick JS, Makunin IV (2005) Small regulatory RNAs in mammals. Hum Mol Genet 14 Spec No 1: R121-R132.
4. Brosius J (2003) The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118: 99-116.
5. Rivas E, Eddy SR (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding rnas. Bioinformatics 16: 583-605.
6. Noller HF, Woese CR (1981) Secondary structure of 16S ribosomal RNA. Science 212: 403-411.
7. Rivas E, Eddy SR (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2: 8.
8. di Bernardo D, Down T, Hubbard T (2003) ddbRNA: Detection of conserved secondary structures in multiple alignments. Bioinformatics 19: 1606-1611.
9. Coventry A, Kleitman DJ, Berger B (2004) MSARI: Multiple sequence alignments for statistical detection of rna secondary structure. Proc Natl Acad Sci U S A 101: 12102-12107.
10. Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J (2004) A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res 32: 4925-4936.
11. Washietl S, Hofacker IL (2004) Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 342: 19-30.
12. Washietl S, Hofacker IL, Stadler PF (2005) Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A 102: 2454-2459.
13. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14: 708-715.
14. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, et al. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scalemultiple alignment of genomic DNA. Genome Res 13: 721-731.
15. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
16. Knudsen B, Hein J (1999) RNA Secondary Structure Prediction Using stochastic context-free grammars and evolutionary history. Bioinformatics 15: 446-454.
17. Knudsen B, Hein J (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 31: 3423-3428.
18. Sakakibara Y, Brown M, Underwood R, Mian IS, Haussler D (1994) Stochastic Context-Free Grammars for Modeling RNA. In: Proceedings of the 27th Hawaii International Conference on System Sciences; 1994 4-7 January; Maui, Hawaii, United States. Los Alamitos (California): IEEE Computer Society Press. pp. 284-293.
19. Eddy SR, Durbin R (1994) RNA sequence analysis using covariance models. Nucleic Acids Res 22: 2079-2088.
20. Jukes TH, Cantor CR (1969) Mammalian Protein Metabolism. New York: Academic Press, chapter 24, pp. 21-132.
21. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
22. Felsenstein J (2003) Inferring Phylogenies. Sunderland (Massachusetts): Sinauer Assoc. 664 pp.
23. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
24. Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
25. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
26. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521.
27. Hillier LW, Miller W, Birney E, Warren W, Hardison RC, et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
28. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
29. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, et al. (2003) Human-mouse alignments with BLASTZ. Genome Res 13: 103-107.
30. Green P, Ewing B, Miller W, Thomas PJ, Green ED (2003) Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 33: 514-517.
31. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3′UTRs by comparison of several mammals. Nature 434: 338-345.
32. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, et al. (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37: 766-770.
33. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, et al. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24.
34. Lehmann KA, Bass BL (2000) Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities. Biochemistry 39: 12875-12884.
35. Kallman AM, Sahlin M, Ohman M (2003) ADAR2 A->I editing: Site selectivity and editing efficiency are separate events. Nucleic Acids Res 31: 4874-4881.
36. Dawson TR, Sansam CL, Emeson RB (2004) Structure and sequence determinants required for the RNA editing of ADAR2 substrates. J Biol Chem 279: 4941-4951.
37. Higuchi M, Maas S, Single FN, Hartner J, Rozov A, et al. (2000) Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 406: 78-81.
38. Namy O, Rousset JP, Napthine S, Brierley I (2004) Reprogrammed genetic decoding in cellular gene expression. Mol Cell 13: 157-168.
39. Pedersen JS, Forsberg R, Meyer IM, Hein J (2004) An evolutionary model for protein-coding regions with conserved RNA structure. Mol Biol Evol 21: 1913-1922.
40. Matsufuji S, Matsufuji T, Miyazaki Y, Murakami Y, Atkins JF, et al. (1995) Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme. Cell 80: 51-60.
41. Stefanovic B, Brenner DA (2003) 5′ stem-loop of collagen alpha 1(I) mRNA inhibits translation in vitro but is required for triple helical collagen synthesis in vivo. J Biol Chem 278: 927-933.
42. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, et al. (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12: 735-739.
43. Griffiths-Jones S (2004) The microRNA Registry. Nucleic Acids Res 32: D109-D111.
44. Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, Zehtab O, et al. (2003) Characterization of mammalian selenoproteomes. Science 300: 1439-1443.
45. Berry MJ, Banu L, Chen YY, Mandel SJ, Kieffer JD, et al. (1991) Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untranslated region. Nature 353: 273-276.
46. Zinoni F, Heider J, Bock A (1990) Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. Proc Natl Acad Sci U S A 87: 4660-4664.
47. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, et al. (2005) Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33: D121-D124.
48. Howard MT, Aggarwal G, Anderson CB, Khatri S, Flanigan KM, et al. (2005) Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons. EMBO J 24: 1596-1607.
49. Angrand PO, Apiou F, Stewart AF, Dutrillaux B, Losson R, et al. (2001) NSD3, a new SET domain-containing gene, maps to 8p12 and is amplified in human breast cancer cell lines. Genomics 74: 79-88.
50. Shiohama A, Sasaki T, Noda S, Minoshima S, Shimizu N (2003) Molecular cloning and expression analysis of a novel gene DGCR8 located in the DiGeorge syndrome chromosomal region. Biochem Biophys Res Commun 304: 184-190.
51. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, et al. (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432: 235-240.
52. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ (2004) Processing of primary microRNAs by the microprocessor complex. Nature 432: 231-235.
53. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17: 991-1008.
54. Pahl PM, Hodges YK, Meltesen L, Perryman MB, Horwitz KB, et al. (1998) ZNF207, a ubiquitously expressed zinc finger gene on chromosome 6p21.3. Genomics 53: 410-412.
55. Eddy SR (2005) A model of the statistical power of comparative genome sequence analysis. PLoS Biol 3: e10. DOI: 10.1371/journal.pbio.0030010
56. McCutcheon JP, Eddy SR (2003) Computational identification of noncoding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res 31: 4119-4128.
57. Babak T, Blencowe BJ, Hughes TR (2005) A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics 6: 104.
58. Bejerano G, Haussler D, Blanchette M (2004) Into the heart of darkness: Large-scale clustering of human non-coding dna. Bioinformatics 20 Suppl 1: I40-I48.
59. Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF (2005) Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol 23: 1383-1390.
60. Yang Z (1995) A space-time process model for the evolution of DNA sequences. Genetics 139: 993-1005.
61. Felsenstein J, Churchill GA (1996) A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol 13: 93-104.
62. Thorne JL, Goldman N, Jones DT (1996) Combining protein evolution and secondary structure. Mol Biol Evol 13: 666-673.
63. Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge: Cambridge University Press. 356 p.
64. Kent WJ (2002) BLAT - the BLAST-like alignment tool. Genome Res 12: 656-664.
65. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
66. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
67. Lestrade L, Weber MJ (2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 34: 158-162.
68. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003) Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 100: 11484-11489.