Comparative genomics using fugu: A tool for the identification of conserved vertebrate cis-regulatory elements

BioEssays

Volumn 27, Issue 1, 2005, Pages 100-107

  Venkatesh, Byrappa ^a   Yap, Wai Ho ^a  

^a INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; COMPARATIVE GENOMIC HYBRIDIZATION; EVOLUTIONARY ADAPTATION; FISH; GENE CONTROL; GENE DUPLICATION; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CONSERVATION; GENOME ANALYSIS; HUMAN GENOME; NONHUMAN; REVIEW; VALIDATION PROCESS; VERTEBRATE;

ANIMALS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DNA; EVOLUTION, MOLECULAR; GENOME; GENOMICS; HUMANS; MICE; MODELS, BIOLOGICAL; PHYLOGENY; REGULATORY SEQUENCES, NUCLEIC ACID; TAKIFUGU;

DANIO RERIO; MAMMALIA; RODENTIA; TAKIFUGU; TAKIFUGU RUBRIPES; TETRAODONTIDAE; VERTEBRATA;

EID: 12344296750     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20134     Document Type: Review

References (62)

1. 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.
2. 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.
3. Rat Genome Sequencing Project Consortium, 2004.
4. Hardison RC. 2000. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 16:369-372.
5. Nobrega MA, Pennacchio LA. 2004. Comparative genomic analysis as a tool for biological discovery. J Physiol 554:31-39.
6. Arnone MI, Davidson EH. 1997. The hardwiring of development: organization and function of genomic regulatory systems. Development 124:1851-1864
7. Pennacchio LA, Rubin EM. 2001. Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet 2:100-109.
8. Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, et al. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299:1391-1394.
9. Loots GG, Locksley RM, Blankespoor CM, Wang ZE, Miller W, et al. 2000. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288:136-140.
10. Lee DU, Avni O, Chen L, Rao A, 2004. A distal enhancer in the interferon-gamma (IFN-gamma) locus revealed by genome sequence comparison. J Biol Chem 279:4802-4810.
11. Lien CL, McAnally J, Richardson JA, Olson EN. 2002. Cardiac-specific activity of an Nkx2-5 enhancer requires an evolutionary conserved Smad binding site. Dev Biol 244:257-266.
12. Dodou E, Xu SM, Black BL. 2003. mef2c is activated directly by myogenic basic helix-loop-helix proteins during skeletal muscle development in vivo. Mech Dev 120:1021-1032.
13. Bagheri-Fam S, Ferraz C, Demaille J, Scherer G, Pfeifer D. 2001. Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions. Genomics 78:73-82.
14. Santagati F, Abe K, Schmidt V, Schmitt-John T, Suzuki M, et al. 2003. Identification of Cis-regulatory elements in the mouse Pax9/Nkx2-9 genomic region: implication for evolutionary conserved synteny. Genetics 165:235-242.
15. Brenner S, Elgar G, Sandford R, Macrae A, Venkatesh B, Aparicio S. 1993. Characterization of the pufferfish (fugu) genome as a compact model vertebrate genome. Nature 366:265-268.
16. Marshall H, Studer M, Popperl H, Aparicio S, Kuroiwa A, et al. 1994 A conserved retinoic acid response element required for early expression of the homeobox gene Hoxb-1. Nature 370:567-571.
17. Popperl H, Bienz M, Studer M, Chan SK, Aparicio S, et al. 1995. Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx. Cell 81:1031-1042.
18. Aparicio S, Morrison A, Gould A, Gilthorpe J, Chaudhuri C, et al. 1995. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc Natl Acad Sci USA 92:1684-1688.
19. Kimura C, Takeda N, Suzuki M, Oshimura M, Aizawa S, Matsuo I. 1997. Cis-acting elements conserved between mouse and pufferfish Otx2 genes govern the expression in mesencephalic neural crest cells. Development 124:3929-3941.
20. Venkatesh B, Si-Hoe SL, Murphy D, Brenner S. 1997. Transgenic rats reveal functional conservation of regulatory controls between the fugu isotocin and rat oxytocin genes. Proc Natl Acad Sci USA 94:12462-12466.
21. Kumar S, Hedges SB. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
22. Rowitch DH, Echelard Y, Danielian PS, Gellner K, Brenner S, McMahon AP. 1998. Identification of an evolutionarily conserved 110 base-pair cis-acting regulatory sequence that governs Wnt-1 expression in the murine neural plate. Development 125:2735-2746.
23. Kammandel B, Chowdhury K, Stoykova A, Aparicio S, Brenner S, Gruss P. 1999. Distinct cis-essential modules direct the time-space pattern of the Pax6 gene activity. Dev Biol 205:79-97.
24. Griffin C, Kleinjan DA, Doe B, van Heyningen V. 2002. New 3′ elements control Pax6 expression in the developing pretectum, neural retina and olfactory region. Mech Dev 112:89-100.
25. Gilligan P, Brenner S, Venkatesh B. 2003. Neurone-specific expression and regulation of the pufferfish isotocin and vasotocin genes in transgenic mice. J Neuroendocrinol 15:1027-1036.
26. Lettice LA, Heaney SJ, Purdie LA, Li L, de Beer P, et al. 2003. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet 12:1725-1735.
27. Kimura-Yoshida C, Kitajima K. Oda-Ishii I, Tian E, Suzuki M, et al. 2004. Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification. Development 13:57-71.
28. Miles C, Elgar G, Coles E, Kleinjan DJ, van Heyningen V, Hastie N. 1998. Complete sequencing of the fugu WAGR region from WT1 to PAX6: dramatic compaction and conservation of synteny with human chromosome 11p13. Proc Natl Acad Sci USA 95:13068-13072.
29. Eggers JH, Stock M, Fliegauf M, Vonderstrass B, Otto F. 2002. Genomic characterization of the RUNX2 gene of Fugu rubripes. Gene 291:159-167.
30. Goode DK, Snell PK, Elgar GK. 2003. Comparative analysis of vertebrate Shh genes identifies novel conserved non-coding sequence. Mamm Genome 14:192-201.
31. Dubchak I, Brudno M, Loots GG, Pachter L, Mayor C, et al. 2000. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 10:1304-1306.
32. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, et al. 2000. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16:1046-1047.
33. Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, et al. 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res 13:13-26.
34. Nobrega MA, Ovcharenko I, Afzal V, Rubin EM. 2003. Scanning human gene deserts for long-range enhancers. Science 302:413.
35. Barton LM, Gottgens B, Gering M, Gilbert JG, Grafham D, et al. 2001. Regulation of the stem cell leukemia (SCL) gene: a tale of two fishes. Proc Natl Acad Sci USA 98:6747-6752.
36. Sanchez M, Gottgens B, Sinclair AM, Stanley M, Begley CG, et al. 1999. An SCL 3′ enhancer targets developing endothelium together with embryonic and adult haematopoietic progenitors. Development 126: 3891-3904.
37. Sinclair AM, Gottgens B, Barton LM, Stanley ML, Pardanaud L, et al. 1999. Distinct 5′ SCL enhancers direct transcription to developing brain, spinal cord, and endothelium: neural expression is mediated by GATA factor binding sites. Dev Biol 209:128-142.
38. Gottgens B, Barton LM, Gilbert JG, Bench AJ, Sanchez MJ, et al. 2000. Analysis of vertebrate SCL loci identifies conserved enhancers. Nat Biotechnol 18:181-186.
39. Gottgens B, Barton LM, Chapman MA, Sinclair AM, Knudsen B, et al. 2002. Transcriptional regulation of the stem cell leukemia gene (SCL)-comparative analysis of five vertebrate SCL loci. Genome Res 12:749-759.
40. Gilligan P, Venkatesh B. 2004. Application of comparative genomics to the analysis of vertebrate regulatory elements. Briefings in Functional Genomics and Proteomics 3:7-11.
41. Ghanem N, Jarinova O, Amores A, Long Q, Hatch G, et al. 2003. Regulatory roles of conserved intergenic domains in vertebrate Dlx bigene clusters. Genome Res 13:533-543.
42. Kleinjan DA, Seawright A, Childs AJ, van Heyningen V. 2004. Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription. Dev Biol 265:462-477.
43. Brenner S, Venkatesh B, Yap WH, Chou CF, Tay A, et al. 2002. Conserved regulation of the lymphocyte-specific expression of lck in the fugu and mammals. Proc Natl Acad Sci USA 99:2936-2941.
44. Zhang T, Tan YH, Fu J, Lui D, Ning Y, et al. 2003. The regulation of retina specific expression of rhodopsin gene in vertebrates. Gene 313:189-200.
45. Zhang T, Haws P, Wu Q. 2004. Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. Genome Res 14:79-89.
46. Amores A, Force A, Van YL, Joly L, Amemiya C, et al. 1998. Zebrafish hox clusters and vertebrate genome evolution. Science 282:1711-1714.
47. Christoffels A, Koh EG, Chia JM, Brenner S, Aparicio S, Venkatesh B. 2004. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol 21:1146-1151.
48. Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y. 2003. Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res 13:382-390.
49. Robinson-Rechavi M, Marchand O, Escriva H, Laudet V. 2001. An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes. Curr Biol 11:R458-R459.
50. Robinson-Rechavi M, Marchand O, Escriva H, Bardet PL, Zelus D, et al. 2001. Euteleost fish genomes are characterized by expansion of gene families. Genome Res 11:781-788.
51. Chiang EF, Pai CI, Wyatt M, Yan YL, Postlethwait J, Chung B. 2001. Two sox9 genes on duplicated zebrafish chromosomes: expression of similar transcription activators in distinct sites. Dev Biol 231:149-163.
52. Lister JA, Close J, Raible DW. 2001. Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential. Dev Biol 237:333-344.
53. McClintock JM, Kheirbek MA, Prince VE. 2001. Knockdown of duplicated zebrafish hoxb1 genes reveals disntinct roles in hindbrain patterning and a novel mechanism of duplicate gene retention. Development 129:2339-2354.
54. Elgar G, Clark MS, Meek S, Smith S, Warner S, et al. 1999. Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res 9:960-971.
55. Koopman P, Schepers G, Brenner S, Venkatesh B. 2004. Origin and diversity of the Sox transcription factor gene family: genome-wide analysis in Fugu rubripes. Gene 328:177-186.
56. Christoffels A, Venkatesh B. Unpublished data.
57. Venkatesh B. 2003. Evolution and diversity of fish genomes. Curr Opin Genet Dev 13:588-592.
58. Dickmeis T, Plessy C, Rastegar S, Aanstad P, Herwig R, et al. 2004. Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo. Genome Res 14:228-238.
59. Beck CW, Slack JM. 2001. An amphibian with ambition: a new role for Xenopus in the 21st century. Genome Biol 2:1029.1-1029.5.
60. Muller F, Blader P, Strahle U. 2002. Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elements. Bioessays 24:564-572.
61. Wittbrodt J, Shima A, Schartl M. 2002. Medaka - a model organim from the far East. Nat Rev Genet 3:53-64.
62. Stapleton T, Luchman A, Johnston J, Browder L, Brenner S, et al. 2003. Compact intergenic regions of the pufferfish genome facilitate isolation of gene promoters: characterization of fugu 3′-phosphoadenosine 5′-phosphosulfate synthase 2 (fPapss2) gene promoter function in transgenic Xenopus. FEBS Lett 556:59-63.