Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes

BMC Genomics

Volumn 5, Issue , 2004, Pages

  Sandelin, Albin ^a   Bailey, Peter ^a   Bruce, Sara ^a   Engström, Pär G ^a   Klos, Joanna M ^a   Wasserman, Wyeth W ^b   Ericson, Johan ^a   Lenhard, Boris ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; DEVELOPMENTAL GENETICS; GENE EXPRESSION; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC CODE; GENETIC CONSERVATION; GENOME ANALYSIS; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; PREDICTION; PUFFER FISH; VERTEBRATE;

VERTEBRATA;

EID: 22144473057     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-5-99     Document Type: Article

References (27)

1. Lenhard B, Sandelin A, Mendoza L, Engstrom P, Jareborg N, Wasserman WW: Identification of conserved regulatory elements by comparative genome analysis. J Biol 2003, 2:13.
2. Ureta-Vidal A, Ettwiller L, Birney E: Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet 2003, 4:251-262.
3. Nobrega MA, Ovcharenko I, Afzal V, Rubin EM: Scanning human gene deserts for long-range enhancers. Science 2003, 302:413.
4. Bagheri-Fam S, Ferraz C, Demaille J, Scherer G, Pfeifer D: Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions. Genomics 2001, 78:73-82.
5. Sumiyama K, Irvine SQ, Ruddle FH: The role of gene duplication in the evolution and function of the vertebrate Dlx/distal-less bigene clusters. J Struct Funct Genomics 2003, 3:151-159.
6. Ghanem N, Jarinova O, Amores A, Long Q, Hatch G, Park BK, Rubenstein JL, Ekker M: Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters. Genome Res 2003, 13:533-543.
7. Spitz F, Gonzalez F, Duboule D: A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 2003, 113:405-417.
8. Santini S, Boore JL, Meyer A: Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Res 2003, 13:1111-1122.
9. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D: Ultraconserved elements in the human genome. Science 2004, 304:1321-1325.
10. Boffelli D, Nobrega MA, Rubin EM: Comparative genomics at the vertebrate extremes. Nat Rev Genet 2004, 5:456-465.
11. Sabarinadh C, Subramanian S, Tripathi A, Mishra RK: Extreme conservation of noncoding DNA near HoxD complex of vertebrates. BMC Genomics 2004, 5:75.
12. Cornell RA, Ohlen TV: Vnd/nkx, ind/gsh, and msh/msx: conserved regulators of dorsoventral neural patterning? Curr Opin Neurobiol 2000, 10:63-71.
13. Briscoe J, Ericson J: Specification of neuronal fates in the ventral neural tube. Curr Opin Neurobiol 2001, 11:43-49.
14. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM: The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 2003, 31:315-318.
15. Westfall PH, Wolfinger RD: Multiple Tests with Discrete Distributions. The American Statistician 1997, 51:3-8.
16. Lettice LA, Horikoshi T, Heaney SJ, van Baren MJ, van der Linde HC, Breedveld GJ, Joosse M, Akarsu N, Oostra BA, Endo N, Shibata M, Suzuki M, Takahashi E, Shinka T, Nakahori Y, Ayusawa D, Nakabayashi K, Scherer SW, Heutink P, Hill RE, Noji S: Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proc Natl Acad Sci U S A 2002, 99:7548-7553.
17. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ: The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31:51-54.
18. de Crombrugghe B, Lefebvre V, Behringer RR, Bi W, Murakami S, Huang W: Transcriptional mechanisms of chondrocyte differentiation. Matrix Biol 2000, 19:389-394.
19. Gomez-Skarmeta JL, Modolell J: Iroquois genes: genomic organization and function in vertebrate neural development. Curr Opin Genet Dev 2002, 12:403-408.
20. Lifanov AP, Makeev VJ, Nazina AG, Papatsenko DA: Homotypic regulatory clusters in Drosophila. Genome Res 2003, 13:579-588.
21. Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
22. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94.
23. Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz H, Iyer V, Kahari A, Jekosch K, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark C, Clamp M, Hubbard T: Ensembl 2004. Nucleic Acids Res 2004, 32 Database issue:D468-70.
24. Mehta CR, Patel NR: FEXACT: A Fortran subroutine for Fisher's exact test on unordered r*c contingency tables ACM Transactions on Mathematical Software, 12, 154-161. ACM Transactions on Mathematical Software 1986, 12:154-161.
25. Conover WJ: Practical nonparametric statistics. New York, John Wiley & Sons; 1971.
26. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
27. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S: The generic genome browser: a building block for a model organism system database. Genome Res 2002, 12:1599-1610.