Interspecific chromosome-wide transcription profiles reveal the existence of mammalian-specific and species-specific chromosome domains

Journal of Molecular Evolution

Volumn 59, Issue 3, 2004, Pages 317-328

  Cosseddu, Gian Mario ^a   Perez Enciso, Miguel ^b   Fellous, Marc ^c   Vaiman, Daniel ^a,c  

^a CEMAGREF   (France)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c Dept Ciencia Animal Y Alimentos ^*  (France)

Author keywords

Comparative genomics; Mammals; Transcription

Indexed keywords

ARTICLE; CATTLE; CHICKEN; CHROMOSOME; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION; GENE MAPPING; GENE OVEREXPRESSION; GENETIC TRANSCRIPTION; HOUSEKEEPING GENE; HUMAN GENOME; MAMMAL; NONHUMAN; SWINE;

ANIMALS; CHROMOSOMES; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE ORDER; GENOME, HUMAN; HUMANS; LOD SCORE; MAMMALS; SPECIES SPECIFICITY; SYNTENY;

BOS TAURUS; EUKARYOTA; GALLUS GALLUS; MAMMALIA; SUS SCROFA;

EID: 4344701766     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-2627-6     Document Type: Article

References (36)

1. Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW, Donovan J, Windish R, Steining C, Mahyuddin P, Womack JE, Lewin HA (2000) An ordered comparative map of the cattle and human genomes. Genome Res 10(9):1359-1368
2. Bishop CE, Whitworth DJ, Qin Y, Agoulnik AI, Agoulnik IU, Harrison WR, Behringer RR, Overbeek PA (2000) A transgenic insertion upstream of Sox9 is associated with dominant XX sex reversal in the mouse. Nat Genet 26(4):490-494
3. Boss JM, Jensen PE (2003) Transcriptional regulation of the MHC class II antigen presentation pathway. Curr Opin Immunol 15(1):105-111
4. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI (2002) Large clusters of co-expressed genes in the Drosophila genome. Nature 420(6916):666-669
5. Caron H, Van Schaik B, Van Der Mee M, Baas F, Riggins G, Van Sluis P, Hermus MC, Van Asperen R, Boon K, Voute PA, Heisterkamp S, VanKampen A, Versteeg R. (2001) The human transcriptome map: Clustering of highly expressed genes in chromosomal domains. Science 291(5507):1289-1292
6. Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P. (2002) Long-range chromatin regulatory interactions in vivo. Nat Genet 32(4):623-626
7. Charlier C, Segers K, Karim L, Shay T, Gyapay G, Cockett N, Georges M (2001) The callipyge mutation enhances the expression of coregulated imprinted genesin eis without affecting their imprinting status. Nat Genet 27(4):367-369
8. Cocquet J, Pailhoux E, Jaubert F, Servel N, Xia X, Pannetier M, De Baere E, Messiaen L, Cotinot C, Fellous M, Veitia RA (2002) Evolution and expression of FOXL2. J Med Genet 39(12):916-921
9. Cremer T, Cremer C. (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2(4):292-301
10. Cremer T, Kurz A, Zirbel R, Dietzel S, Rinke B, Schrock E, Speicher Mr, Mathieu U, Jauch A, Emmerich P et al. (1993) Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harb Symp Quant Biol 58:777-792
11. Ferdinandusse S, Denis S, Clayton PT, Graham A, Rees JE, Alien JT, McLean BN, Brown AY, Vreken P, Waterham HR, Wanders RJ (2000) Mutations in the gene encoding peroxisomal alpha-methylacyl-CoA racemase cause adult-onset sensory motor neuropathy. Nat Genet 24(2):188-191
12. Fujishima-Kanaya N, Toki D, Suzuki K, Sawazaki T, Hiraiwa H, Iida M, Hayashi T, Uenishi H, Wada Y, Ito Y, Awata (2003) Development of 50 gene-associated microsatellite markers using BAC clones and the construction of a linkage map of swine chromosome 4. Anim Genet 34(2):135-141
13. Jennen DG, Crooijmans RP, Kamps B, Acar R, van der Poel JJ, Groenen MA (2003) Comparative map between chicken chromosome 15 and human chromosomal region 12q24 and 22q11-q12. Mamm Genome 14(9):629-639
14. Kurz A, Lampel S, Nickolenko Je, Bradl J, Benner A, Zirbel RM, Cremer T, Lichter P (1996) Active and inactive genes localize preferentially in the periphery of chromosome territories. J Cell Biol 135(5):1195-1205
15. Larkin DM, Everts-van der Wind A, Rebeiz M, Schweitzer PA, Bachman S, Green C, Wright CL, Campos EJ, Benson LD, Edwards J, Liu L, Osoegawa K, Womack JE, de Jong PJ, Lewin HA (2003) A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res 13(8):1966-1972
16. Lawrence JG (2002) Shared strategies in gene organization among prokaryotes and eukaryotes. Cell 23(110(4):407-413
17. Lercher MJ, Urrutia AO, Hurst LD (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 131(2):180-183
18. Liu L, Gong G, Liu Y, Natarajan S, Larkin DM, Everts-van der Wind A, Rebeiz M, Beever JE (2004) Multi-species comparative mapping in silico using the COMPASS strategy. Bioinformatics 22(20(2):148-154
19. Loffler KA, Zarkower D, Koopman P (2003) Etiology of ovarian failure in blepharophimosis ptosis epicanthus in versus syndrome: FOXL2 is a conserved, early-acting gene in vertebrate ovarian development. Endocrinology 144(7):3237-3243
20. Mahy NL, Perry PE, Bickmore WA (2002a) Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 159(5):753-763
21. Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA (2002b) Spatial organization of active and inactive genes and non-coding DNA within chromosome territories. J Cell Biol 157(4):579-589
22. Pailhoux E, Vigier B, Chaffaux S, Servel N, Taourit S, Furet Jp, Fellous M, Grosclaude F, Cribiu Ep, Cotinot C, Vaiman D (2001) A 11.7-kb deletion triggers intersexuality and polledness in goats. Nat Genet 29(4):453-458
23. Parada L, Misteli T (2002) Chromosome positioning in the interphase nucleus. Trends Cell Biol 12(9):425-432
24. Raymond CS, Shamu CE, Shen MM, Seifert KJ, Hirsch B, Hodgkin J, Zarkower D (1998) Evidence for evolutionary conservation of sex-determining genes. Nature 391(6668):691-695
25. Rebeiz M, Lewin HA (2000) Compass of 47,787 cattle ESTs. Anim Biotechnol 11(2):75-241
26. Reymond A, Marigo V, Yaylaoglu MB, Leoni A, Ucla C, Scamuffa N, Caccioppoli C, Dermitzakis ET, Lyle R, Banfi S, Eichele G, Antonarakis SE, Ballabio A (2002) Human chromosome 21 gene expression atlas in the mouse. Nature 420(6915):582-586
27. Schibler L, Vaiman D, Oustry A, Giraud-Delville C, Cribiu EP (1998) Comparative gene mapping: A fine-scale survey of chromosome rearrangements between ruminants and humans. Genome Res 8(9):901-915
28. Smith EJ, Shi L, Prevost L, Drummond P, Ramlal S, Smith G, Pierce K, Foster J (2001) Expressed sequence tags for the chicken genome from a normalized, ten-day-oldwhite leghorn whole embryo cDNA library. Poult ScL 80(9):1263-1272
29. Smith TP, Fahrenkrug SC, Rohrer GA, Simmen FA, Rexroad CE, Keele JW (2001a) Mapping of expressed sequence tags from a porcine early embryonic cDNA library. Anim Genet 32(2):66-72
30. Smith TP, Grosse WM, Freking BA, Roberts AJ, Stone RT, Casas E, Wray JE, White J, Cho J, Fahrenkrug SC, Bennett GL, Heaton MP, Laegreid WW, Rohrer GA, Chitko-Mckown CG, Pertea G, Holt I, Karamycheva S, Liang F, Quackenbush J, Keele JW (2001b) Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res. 1(1(4):626-630
31. Spellman PT, Rubin GM (2002) Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol. 1(1):5
32. Takasuga A, Hirotsune S, Itoh R, Jitohzono A, Suzuki H, Aso H, Sugimoto Y (2001) Establishment of a high throughput EST sequencing system using poly (A) tail-removed cDNA libraries and determination of 36,000 bovine ESTs. Nucleic Acids Res 29(22):E108
33. Tanabe H, Muller S, Neusser M, Von Hase J, Calcagno E, Cremer M, Solovei I, Cremer C, Cremer T (2002) Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci USA 99(7):4424-4429
34. Thomas JW, Prasad AB, Summers TJ, Lee-Lin SQ, Maduro VV, Idol JR, Ryan JF, Thomas PJ, McDowell JC, Green ED (2002) Parallel construction of orthologous sequence-ready clone contig maps in multiple species. Genome Res 12(8):1277-1285
35. Vaiman D, Schibler L, Oustry-Vaiman A, Pailhoux E, Goldammer T, Stevanovic M, Furet JP, Schwerin M, Cotinot C, Fellous M, Cribiu EP (1999) High-resolution human/goat comparative map of the goat polled/intersex syndrome (PIS): The human homologue is contained in a human YAC from HSA3q23. Genomics 15(56(1):31-39
36. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al. (2001) The sequence of the human genome. Science 291(5507):1304-1351