Unexpectedly large number of conserved noncoding regions within the ancestral chordate Hox cluster

Development Genes and Evolution

Volumn 218, Issue 11-12, 2008, Pages 591-597

  Pascual Anaya, Juan ^a   D'Aniello, Salvatore ^a   Garcia Fernàndez, Jordi ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Amphioxus; Conserved noncoding regions; Hox genes; Phylogenetic footprinting

Indexed keywords

HOX PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR HOXA; TRANSCRIPTION FACTOR HOXB; TRANSCRIPTION FACTOR HOXC; TRANSCRIPTION FACTOR HOXD; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ARTICLE; BRANCHIOSTOMA FLORIDAE; BRANCHIOSTOMA LANCEOLATUM; CONTROLLED STUDY; DNA FOOTPRINTING; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; GENOME ANALYSIS; INTRON; INVERTEBRATE CHORDATA; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; CHORDATA, NONVERTEBRATE; CONSERVED SEQUENCE; GENES, HOMEOBOX; MOLECULAR SEQUENCE DATA;

BRANCHIOSTOMA FLORIDAE; BRANCHIOSTOMA LANCEOLATUM; CHORDATA; VERTEBRATA;

EID: 57649237971     PISSN: 0949944X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00427-008-0246-8     Document Type: Article

References (37)

1. Amemiya CT, Prohaska SJ, Hill-Force A, Cook A, Wasserscheid J, Ferrier DEK, Pascual-Anaya J, Garcia-Fernàndez J, Dewar K, Stadler PF (2008) The amphioxus Hox cluster: Characterization, comparative genomics, and evolution. J Exp Zoolog (Mol Dev Evol) 310B:n/a
2. Bray N, Dubchak I, Pachter L (2003) AVID: A global alignment program. Genome Res 13:97-102
3. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Program NCS, Green ED, Sidow A, Batzoglou S (2003) LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13:721-731
4. Cañestro C, Hjelmqvist L, Albalat R, Garcia-Fernàndez J, González-Duarte R, Jornvall H (2000) Amphioxus alcohol dehydrogenase is a class 3 form of single type and of structural conservation but with unique developmental expression. Eur J Biochem 267:6511-6518
5. Chiu C-H, Amemiya C, Dewar K, Kim C-B, Ruddle FH, Wagner GP (2002) Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc Natl Acad Sci USA 99:5492-5497
6. Duboule D (1994) Temporal colinearity and the phylotypic progression: A basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony. Dev Suppl 1994:135-142
7. Duboule D (2007) The rise and fall of Hox gene clusters. Development 134:2549-2560
8. Duboule D, Dollé P (1989) The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. EMBO J 8:1497-1505
9. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error Probabilities. Genome Res 8:186-194
10. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8:175-185
11. Ferrier DEK, Minguillón C, Holland PWH, Garcia-Fernàndez J (2000) The amphioxus Hox cluster: Deuterostome posterior flexibility and Hox14. Evol Dev 2:284-293
12. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545
13. Garcia-Fernàndez J, Holland PWH (1994) Archetypal organization of the amphioxus Hox gene cluster. Nature 370:563-566
14. Gómez-Skarmeta JL, Lenhard B, Becker TS (2006) New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences. Dev Dyn 235:870-885
15. Gordon D, Abajian C, Green P (1998) Consed: A graphical tool for sequence finishing. Genome Res 8:195-202
16. Haerry TE, Gehring WJ (1996) Intron of the mouse Hoxa-7 gene contains conserved homeodomain binding sites that can function as an enhancer element in Drosophila. Proc Natl Acad Sci USA 93:13884-13889
17. Haerry TE, Gehring WJ (1997) A conserved cluster of homeodomain binding sites in the mouse Hoxa-4 intron functions in Drosophila embryos as an enhancer that is directly regulated by Ultrabithorax. Dev Biol 186:1-15
18. Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez È, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DEK, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu J-K, Zhang Q, Zmasek CM, Putnam NH, Rokhsar DS, Satoh N, Holland PWH (2008) The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res 18:1100-1111
19. International Human Genome Sequence Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945
20. Kessel M, Gruss P (1991) Homeotic transformations of murine vertebrae and concomitant alteration of Hox codes induced by retinoic acid. Cell 67:89-104
21. Kim CB, Amemiya C, Bailey W, Kawasaki K, Mezey J, Miller W, Minoshima S, Shimizu N, Wagner G, Ruddle F (2000) Hox cluster genomics in the horn shark, Heterodontus francisci. Proc Natl Acad Sci USA 97:1655-1660
22. Kon T, Nohara M, Yamanoue Y, Fujiwara Y, Nishida M, Nishikawa T (2007) Phylogenetic position of a whale-fall lancelet (Cephalochordata) inferred from whole mitochondrial genome sequences. BMC Evolutionary Biology 7:127
23. Lewis EB (1978) A gene complex controlling segmentation in Drosophila. Nature 276:565-570
24. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I (2000) VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16:1046-1047
25. Nohara M, Nishida M, Nishikawa T (2005) New complete mitochondrial DNA sequence of the lancelet Branchiostoma lanceolatum (Cephalochordata) and the Identity of this Species' Sequences. Zoological Science 22:671-674
26. Packer AI, Crotty DA, Elwell VA, Wolgemuth DJ (1998) Expression of the murine Hoxa4 gene requires both autoregulation and a conserved retinoic acid response element. Development 125:1991-1998
27. Podlasek C, Houston J, McKenna KE, McVary KT (2002) Posterior Hox gene expression in developing genitalia. Evol Dev 4:142-163
28. Prohaska SJ, Fried C, Flamm C, Wagner GP, Stadler PF (2004) Surveying phylogenetic footprints in large gene clusters: Applications to Hox cluster duplications. Mol Phylogenet Evol 31:581-604
29. Richardson MK, Crooijmans RP, Groenen MA (2007) Sequencing and genomic annotation of the chicken (Gallus gallus) Hox clusters, and mapping of evolutionarily conserved regions. Cytogenet Genome Res 117:110-119
30. Santini S, Boore JL, Meyer A (2003) Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Res 13:1111-1122
31. Schubert M, Holland ND, Laudet V, Holland LZ (2006) A retinoic acid-Hox hierarchy controls both anterior/posterior patterning and neuronal specification in the developing central nervous system of the cephalochordate amphioxus. Developmental Biology 296:190-202
32. Tanzer A, Amemiya CT, Kim CB, Stadler PF (2005) Evolution of microRNAs located within Hox gene clusters. J Exp Zoolog B Mol Dev Evol 304:75-85
33. Wada H, Garcia-Fernàndez J, Holland PWH (1999) Colinear and segmental expression of amphioxus Hox genes. Dev Biol 213:131-141
34. Wagner GP, Lynch VJ (2005) Molecular evolution of evolutionary novelties: The vagina and uterus of therian mammals. J Exp Zoolog B Mol Dev Evol 304B:580-592
35. Wasserman WW, Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5:276-287
36. Yamamoto KR, Alberts BM, Benzinger R, Lawhorne L, Treiber G (1970) Rapid bacteriophage sedimentation in the presence of polyethylene glycol and its application to large-scale virus purification. Virology 40:734-744
37. Zakany J, Duboule D (2007) The role of Hox genes during vertebrate limb development. Curr Opin Genet Dev 17:359-366