Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Gissi, Carmela ^a   Pesole, Graziano ^a,b   Cattaneo, Elena ^a   Tartari, Marzia ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF BARI   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; HUNTINGTIN; MESSENGER RNA; PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANIMAL TISSUE; ARTICLE; ASCIDIACEA; CHORDATA; CIONA INTESTINALIS; CIONA SAVIGNYI; CONTROLLED STUDY; EXON; EXPRESSED SEQUENCE TAG; FISH; GALLIFORMES; GENE LOSS; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; GENUS; HUMAN; INTRON; INVERTEBRATE; MAMMAL; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PHASE TRANSITION; POLYADENYLATION; PREDICTION; PROTEIN FUNCTION; RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; TRANS SPLICING; VERTEBRATE; XENOPUS;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; AMINO ACID SEQUENCE; ANIMALS; CHICKENS; CHORDATA; CIONA INTESTINALIS; EVOLUTION, MOLECULAR; EXONS; EXPRESSED SEQUENCE TAGS; GENES; HUMANS; MOLECULAR SEQUENCE DATA; NERVE TISSUE PROTEINS; NUCLEAR PROTEINS; PEPTIDES; PHYLOGENY; POLY A; RNA, MESSENGER; RNA, SPLICED LEADER; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC; VERTEBRATES; XENOPUS LAEVIS;

ASCIDIA; CHORDATA; CIONA; CIONA INTESTINALIS; CIONA SAVIGNYI; GALLUS; INVERTEBRATA; MAMMALIA; PISCES; VERTEBRATA;

EID: 33751193268     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-288     Document Type: Article

References (69)

1. Huntington's Disease Collaborative Research Group: A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group. Cell 1993, 72:971-983.
2. Sipione S, Cattaneo E: Modeling Huntington's disease in cells, flies, and mice. Mol Neurobiol 2001, 23:21-51.
3. Cattaneo E, Zuccato C, Tartari M: Normal huntingtin function: an alternative approach to Huntington's disease. Nat Rev Neurosci 2005, 6:919-930.
4. Trottier Y, Devys D, Imbert G, Saudou F, An I, Lutz Y, Weber C, Agid Y, Hirsch EC, Mandel JL: Cellular localization of the Huntington's disease protein and discrimination of the normal and mutated form. Nat Genet 1995, 10:104-110.
5. Zuccato C, Ciammola A, Rigamonti D, Leavitt BR, Goffredo D, Conti L, MacDonald ME, Friedlander RM, Silani V, Hayden MR, Timmusk T, Sipione S, Cattaneo E: Loss of huntingtin-mediated BDNF gene transcription in Huntington's disease. Science 2001, 293:493-498.
6. Zuccato C, Tartari M, Crotti A, Goffredo D, Valenza M, Conti L, Cataudella T, Leavitt BR, Hayden MR, Timmusk T, Rigamonti D, Cattaneo E: Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes. Nat Genet 2003, 35:76-83.
7. Gauthier LR, Charrin BC, Borrell-Pages M, Dompierre JP, Rangone H, Cordelieres FP, De Mey J, MacDonald ME, Lessmann V, Humbert S, Saudou F: Huntingtin controls neurotrophic support and survival of neurons by enhancing BDNF vesicular transport along microtubules. Cell 2004, 118:127-138.
8. Gunawardena S, Her LS, Brusch RG, Laymon RA, Niesman IR, Gordesky-Gold B, Sintasath L, Bonini NM, Goldstein LS: Disruption of axonal transport by loss of huntingtin or expression of pathogenic polyQ proteins in Drosophila. Neuron 2003, 40:25-40.
9. Trushina E, Dyer RB, Badger JD 2nd, Ure D, Eide L, Tran DD, Vrieze BT, Legendre-Guillemin V, McPherson PS, Mandavilli BS, Van Houten B, Zeitlin S, McNiven M, Aebersold R, Hayden M, Parisi JE, Seeberg E, Dragatsis I, Doyle K, Bender A, Chacko C, McMurray CT: Mutant huntingtin impairs axonal trafficking in mammalian neurons in vivo and in vitro. Mol Cell Biol 2004, 24:8195-8209.
10. Lin B, Nasir J, MacDonald H, Hutchinson G, Graham RK, Rommens JM, Hayden MR: Sequence of the murine Huntington disease gene: evidence for conservation, alternate splicing and polymorphism in a triplet (CCG) repeat [corrected]. Hum Mol Genet 1994, 3:85-92.
11. Matsuyama N, Hadano S, Onoe K, Osuga H, Showguchi-Miyata J, Gondo Y, Ikeda JE: Identification and characterization of the miniature pig Huntington's disease gene homolog: evidence for conservation and polymorphism in the CAG triplet repeat. Genomics 2000, 69:72-85.
12. Baxendale S, Abdulla S, Elgar G, Buck D, Berks M, Micklem G, Durbin R, Bates G, Brenner S, Beck S: Comparative sequence analysis of the human and pufferfish Huntington's disease genes. Nat Genet 1995, 10:67-76.
13. Barnes GT, Duyao MP, Ambrose CM, McNeil S, Persichetti F, Srinidhi J, Gusella JF, MacDonald ME: Mouse Huntington's disease gene homolog (Hdh). Somat Cell Mol Genet 1994, 20:87-97.
14. Schmitt I, Bachner D, Megow D, Henklein P, Hameister H, Epplen JT, Riess O: Expression of the Huntington disease gene in rodents: cloning the rat homologue and evidence for down-regulation in non-neuronal tissues during development. Hum Mol Genet 1995, 4:1173-1182.
15. Karlovich CA, John RM, Ramirez L, Stainier DY, Myers RM: Characterization of the Huntington's disease (HD) gene homologue in the zebrafish Danio rerio. Gene 1998, 217:117-125.
16. Li Z, Karlovich CA, Fish MP, Scott MP, Myers RM: A putative Drosophila homolog of the Huntington's disease gene. Hum Mol Genet 1999, 8:1807-1815.
17. Kauffman JS, Zinovyeva A, Yagi K, Makabe KW, Raff RA: Neural expression of the Huntington's disease gene as a chordate evolutionary novelty. J Exp Zoolog B Mol Dev Evol 2003, 297:57-64.
18. Andrade MA, Bork P: HEAT repeats in the Huntington's disease protein. Nat Genet 1995, 11:115-116.
19. Takano H, Gusella JF: The predominantly HEAT-like motif structure of huntingtin and its association and coincident nuclear entry with dorsal, an NF-κB/Rel/dorsal family transcription factor. BMC Neurosci 2002, 3:15.
20. Andrade MA, Petosa C, O'Donoghue SI, Muller CW, Bork P: Comparison of ARM and HEAT protein repeats. J Mol Biol 2001, 309:1-18.
21. Harjes P, Wanker EE: The hunt for huntingtin function: interaction partners tell many different stories. Trends Biochem Sci 2003, 28:425-433.
22. Goehler H, Lalowski M, Stelzl U, Waelter S, Stroedicke M, Worm U, Droege A, Lindenberg KS, Knoblich M, Haenig C, Herbst M, Suopanki J, Scherzinger E, Abraham C, Bauer B, Hasenbank R, Fritzsche A, Ludewig AH, Bussow K, Coleman SH, Gutekunst CA, Landwehrmeyer BG, Lehrach H, Wanker EE: A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell 2004, 15:853-865.
23. Passamaneck YJ, Di Gregorio A: Ciona intestinalis: chordate development made simple. Dev Dyn 2005, 233:1-19.
24. Chen JY, Huang DY, Peng QQ, Chi HM, Wang XQ, Feng M: The first tunicate from the Early Cambrian of South China. Proc Natl Acad Sci U S A 2003, 100:8314-8318.
25. Vandenberghe AE, Meedel TH, Hastings KE: mRNA 5′-leader trans-splicing in the chordates. Genes Dev 2001, 15:294-303.
26. Kozak M: Initiation of translation in prokaryotes and eukaryotes. Gene 1999, 234:187-208.
27. Verrotti AC, Thompson SR, Wreden C, Strickland S, Wickens M: Evolutionary conservation of sequence elements controlling cytoplasmic polyadenylylation. Proc Natl Acad Sci U S A 1996, 93:9027-9032.
28. Lee J, Park EH, Couture G, Harvey I, Garneau P, Pelletier J: An upstream open reading frame impedes translation of the huntingtin gene. Nucleic Acids Res 2002, 30:5110-5119.
29. Lin B, Rommens JM, Graham RK, Kalchman M, MacDonald H, Nasir J, Delaney A, Goldberg YP, Hayden MR: Differential 3′ polyadenylation of the Huntington disease gene results in two mRNA species with variable tissue expression. Hum Mol Genet 1993, 2:1541-1545.
30. Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS: The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 2002, 298:2157-2167.
31. Castrignano T, Canali A, Grillo G, Liuni S, Mignone F, Pesole G: CST-miner: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison. Nucleic Acids Res 2004, 32:W624-7.
32. Satou Y, Hamaguchi M, Takeuchi K, Hastings KE, Satoh N: Genomic overview of mRNA 5′-leader trans-splicing in the ascidian Ciona intestinalis. Nucleic Acids Res 2006, 34:3378-88. Print 2006.
33. Yuasa HJ, Kawamura K, Yamamoto H, Takagi T: The structural organization of ascidian Halocynthia roretzi troponin I genes. J Biochem (Tokyo) 2002, 132:135-141.
34. Hastings KE: SL trans-splicing: easy come or easy go? Trends Genet 2005, 21:240-247.
35. Ganot P, Kallesoe T, Reinhardt R, Chourrout D, Thompson EM: Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome. Mol Cell Biol 2004, 24:7795-7805.
36. Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D: Patterns of variant polyadenylation signal usage in human genes. Genome Res 2000, 10:1001-1010.
37. Venkatesh B, Ning Y, Brenner S: Late changes in spliceosomal introns define clades in vertebrate evolution. Proc Natl Acad Sci U S A 1999, 96:10267-10271.
38. Wada H, Kobayashi M, Sato R, Satoh N, Miyasaka H, Shirayama Y: Dynamic insertion-deletion of introns in deuterostome EF-1 alpha genes. J Mol Evol 2002, 54:118-128.
39. Bates MD, Wells JM, Venkatesh B: Comparative genomics of the Hlx homeobox gene and protein: conservation of structure and expression from fish to mammals. Gene 2005, 352:45-56.
40. Edvardsen RB, Lerat E, Maeland AD, Flat M, Tewari R, Jensen MF, Lehrach H, Reinhardt R, Seo HC, Chourrout D: Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica. J Mol Evol 2004, 59:448-457.
41. Gilbert W: The exon theory of genes. Cold Spring Harb Symp Quant Biol 1987, 52:901-905.
42. Patthy L: Genome evolution and the evolution of exon-shuffling - a review. Gene 1999, 238:103-114.
43. Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J, Hartzell G, Lewis S, Rubin GM: Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput Biol 2006, 2:e15.
44. Gissi C, Iannelli F, Pesole G: Complete mtDNA of Ciona intestinalis reveals extensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians. J Mol Evol 2004, 58:376-389.
45. Johnson DS, Davidson B, Brown CD, Smith WC, Sidow A: Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance. Genome Res 2004, 14:2448-2456.
46. BLAST: Basic Local Alignment Search Tool [http://www.ncbi.nlm.nih.gov/ BLAST/]
47. GENSCAN [http://genes.mit.edu/GENSCAN.html]
48. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94.
49. GenomeScan [http://genes.mit.edu/genomescan.html]
50. Yeh RF, Lim LP, Burge CB: Computational inference of homologous gene structures in the human genome. Genome Res 2001, 11:803-816.
51. SGP2 [http://genome.imim.es/software/sgp2/]
52. Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigo R: Comparative gene prediction in human and mouse. Genome Res 2003, 13:108-117.
53. GMAP: A GEnomic Mapping and Alignment Program [http://www.gene.com/share/ gmap/]
54. Wu TD, Watanabe CK: GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21:1859-1875.
55. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
56. Swofford DL: PAUP*: phylogenetic analysis using parsimony (* and other methods). Edited by: Associated S. Sunderland, Massachussets,; 1998.
57. Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000, 17:540-552.
58. Huelsenbeck JP, Ronquist F: MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
59. Abascal F, Zardoya R, Posada D: ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005, 12:2104-2105.
60. InterProScan [http://www.ebi.ac.uk/InterProScan/]
61. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R: InterProScan: protein domains identifier. Nucleic Acids Res 2005, 33:W116-20.
62. Andrade MA, Ponting CP, Gibson TJ, Bork P: Homology-based method for identification of protein repeats using statistical significance estimates. J Mol Biol 2000, 298:521-537.
63. REP [http://www.embl-heidelberg.de/~andrade/papers/rep/search.html]
64. RepeatMasker [http://www.repeatmasker.org/]
65. 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.
66. CSTminer: a web tool for the identification of coding and non-coding conserved sequence tags [http://www.caspur.it/CSTminer/]
67. UTRscan [http://www.caspur.it/CSTminer/]
68. Pesole G, Liuni S, Grillo G, Licciulli F, Mignone F, Gissi C, Saccone C: UTRdb and UTRsite: specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Res 2002, 30:335-340.
69. Grillo G, Licciulli F, Liuni S, Sbisa E, Pesole G: PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res 2003, 31:3608-3612.