Gene expression regulation in the context of mouse interspecific mosaic genomes

Genome Biology

Volumn 9, Issue 8, 2008, Pages

  L'Hôte, David ^a,b,c,d   Serres, Catherine ^c   Veitia, Reiner A ^a,b,c   Montagutelli, Xavier ^e   Oulmouden, Ahmad ^d   Vaiman, Daniel ^a,b,c,f  

^a INSTITUT COCHIN   (France)

^b CNRS   (France)

^c Institut Cochin   (France)

^d UNIVERSITY OF LIMOGES   (France)

^e INSTITUT PASTEUR   (France)

^f Institut National de la Recherche Agronomique   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; TRANSCRIPTION FACTOR; TRANSCRIPTOME; MESSENGER RNA;

ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; FEMALE; GENE EXPRESSION REGULATION; GENETIC SCREENING; GENETIC SIMILARITY; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; HOMOZYGOSITY; MALE; MOLECULAR GENETICS; MOSAICISM; MOUSE; MOUSE STRAIN; NONHUMAN; PROMOTER REGION; RECOMBINANT CONGENIC STRAIN; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; TESTIS; ANIMAL; CHROMOSOME MAP; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETIC MARKER; GENOME; METABOLISM; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

MUS; MUS MUSCULUS; MUS SPRETUS;

ANIMALS; CHROMOSOME MAPPING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC MARKERS; GENOME; LINEAR MODELS; MALE; MICE; MICE, INBRED STRAINS; MOSAICISM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; TESTIS;

EID: 52649111137     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-8-r133     Document Type: Article

References (37)

1. Wade CM Kulbokas EJ 3rd Kirby AW Zody MC Mullikin JC Lander ES Lindblad-Toh K Daly MJ The mosaic structure of variation in the laboratory mouse genome. Nature 2002, 420:574-578. 10.1038/nature01252 12466852
2. Frazer KA Eskin E Kang HM Bogue MA Hinds DA Beilharz EJ Gupta RV Montgomery J Morenzoni MM Nilsen GB Pethiyagoda CL Stuve LL Johnson FM Daly MJ Wade CM Cox DR A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 2007, 448:1050-1053. 10.1038/ nature06067 17660834
3. Yang H Bell TA Churchill GA Pardo-Manuel de Villena F On the subspecific origin of the laboratory mouse. Nat Genet 2007, 39:1100-1107. 10.1038/ ng2087 17660819
4. Voolstra C Tautz D Farbrother P Eichinger L Harr B Contrasting evolution of expression differences in the testis between species and subspecies of the house mouse. Genome Res 2007, 17:42-49. 1716265 17038563 10.1101/ gr.5683806
5. Rottscheidt R Harr B Extensive additivity of gene expression differentiates subspecies of the house mouse. Genetics 2007, 177:1553-1567. 2147974 17947435 10.1534/genetics.107.076190
6. Cui X Affourtit J Shockley KR Woo Y Churchill GA Inheritance patterns of transcript levels in F1 hybrid mice. Genetics 2006, 174:627-637. 1602077 16888332 10.1534/genetics.106.060251
7. Gibson G Riley-Berger R Harshman L Kopp A Vacha S Nuzhdin S Wayne M Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster. Genetics 2004, 167:1791-1799. 1471026 15342517 10.1534/ genetics.104.026583
8. Vuylsteke M van Eeuwijk F Van Hummelen P Kuiper M Zabeau M Genetic analysis of variation in gene expression in Arabidopsis thaliana. Genetics 2005, 171:1267-1275. 1456830 16020790 10.1534/ genetics.105.041509
9. Landry CR Wittkopp PJ Taubes CH Ranz JM Clark AG Hartl DL Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 2005, 171:1813-1822. 1456106 16143608 10.1534/genetics.105.047449
10. Hegarty MJ Barker GL Wilson ID Abbott RJ Edwards KJ Hiscock SJ Transcriptome shock after interspecific hybridization in senecio is ameliorated by genome duplication. Curr Biol 2006, 16:1652-1659. 10.1016/ j.cub.2006.06.071 16920628
11. McClintock B The significance of responses of the genome to challenge. Science 1984, 226:792-801. 10.1126/science.15739260 15739260
12. Wittkopp PJ Haerum BK Clark AG Evolutionary changes in cis and trans gene regulation. Nature 2004, 430:85-88. 10.1038/nature02698 15229602
13. Veitia RA Exploring the molecular etiology of dominant-negative mutations. Plant Cell 2007, 19:3843-3851. 10.1105/tpc.107.055053 18083908
14. Burgio G Szatanik M Guenet JL Arnau MR Panthier JJ Montagutelli X Interspecific recombinant congenic strains between C57BL/6 and mice of the Mus spretus species: A powerful tool to dissect genetic control of complex traits. Genetics 2007, 177:2321-2333. 2219498 17947429 10.1534/ genetics.107.078006
15. Orth A Adama T Din W Bonhomme F [Natural hybridization between two subspecies of the house mouse, Mus musculus domesticus and Mus musculus castaneus, near Lake Casitas, California]. Genome 1998, 41:104-110. 10.1139/gen-41-1-104 9549063
16. Guenet JL Bonhomme F Wild mice: An ever-increasing contribution to a popular mammalian model. Trends Genet 2003, 19:24-31. 10.1016/ S0168-9525(02)00007-0 12493245
17. DAVID http://david.abcc.ncifcrf.gov/
18. Khaitovich P Weiss G Lachmann M Hellmann I Enard W Muetzel B Wirkner U Ansorge W Pääbo S A neutral model of transcriptome evolution. PLoS Biol 2004, 2:E132. 406393 15138501 10.1371/journal.pbio.0020132
19. Cosseddu GM Perez-Enciso M Fellous M Vaiman D Interspecific chromosome-wide transcription profiles reveal the existence of mammalian-specific and species-specific chromosome domains. J Mol Evol 2004, 59:317-328. 10.1007/s00239-004-2627-6 15553087
20. Veitia RA Paralogs in polyploids: One for all and all for one? Plant Cell 2005, 17:4-11. 544485 15632052 10.1105/tpc.104.170130
21. Genomatix http://www.genomatix.de
22. Ranz JM Namgyal K Gibson G Hartl DL Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Res 2004, 14:373-379. 353219 14962989 10.1101/gr.2019804
23. Adams KL Cronn R Percifield R Wendel JF Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 2003, 100:4649-4654. 153610 12665616 10.1073/pnas.0630618100
24. Adams KL Evolution of duplicate gene expression in polyploid and hybrid plants. J Hered 2007, 98:136-141. 10.1093/jhered/esl061 17208934
25. Chimpanzee Sequencing and Analysis Consortium Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005, 437:69-87. 10.1038/nature03958 16136131
26. Dobzhansky T Studies on hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics 1936, 21:113-135. 1208664 17246786
27. Madlung A Tyagi AP Watson B Jiang H Kagochi T Doerge RW Martienssen R Comai L Genomic changes in synthetic Arabidopsis polyploids. Plant J 2005, 41:221-230. 10.1111/j.1365-313X.2004.02297.x 15634199
28. Shaked: H Kashkush K Ozkan H Feldman M Levy AA Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 2001, 13:1749-1759. 139131 11487690 10.1105/tpc.13.8.1749
29. L'Hôte D Serres C Laissue P Oulmouden A Rogel-Gaillard C Montagutelli X Vaiman D Centimorgan-range one-step mapping of fertility traits using interspecific recombinant congenic mice. Genetics 2007, 176:1907-1921. 1931527 17483418 10.1534/genetics.107.072157
30. Good JM Handel MA Nachman MW Asymmetry and polymorphism of hybrid male sterility during the early stages of speciation in house mice. Evolution 2008, 62:50-65. 18005156
31. Oka A Mita A Sakurai-Yamatani N Yamamoto H Takagi N Takano-Shimizu T Toshimori K Moriwaki K Shiroishi T Hybrid breakdown caused by substitution of the X chromosome between two mouse subspecies. Genetics 2004, 166:913-924. 1470736 15020476 10.1534/genetics.166.2.913
32. Teeter KC Payseur BA Harris LW Bakewell MA Thibodeau LM O'Brien JE Krenz JG Sans-Fuentes MA Nachman MW Tucker PK Genome-wide patterns of gene flow across a house mouse hybrid zone. Genome Res 2008, 18:67-76. 2134771 18025268 10.1101/gr.6757907
33. Gregorová S Divina P Storchova R Trachtulec Z Fotopulosova V Svenson KL Donahue LR Paigen B Forejt J Mouse consomic strains: exploiting genetic divergence between Mus m. musculus and Mus m. domesticus subspecies. Genome Res 2008, 18:509-515. 2259115 18256238 10.1101/gr.7160508
34. Takada T Mita A Maeno A Sakai T Shitara H Kikkawa Y Moriwaki K Yonekawa H Shiroishi T Mouse inter-subspecific consomic strains for genetic dissection of quantitative complex traits. Genome Res 2008, 18:500-508. 2259114 18256237 10.1101/gr.7175308
35. Su AI Cooke MP Ching KA Hakak Y Walker JR Wiltshire T Orth AP Vega RG Sapinoso LM Moqrich A Patapoutian A Hampton GM Schultz PG Hogenesch JB Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 2002, 99:4465-4470. 123671 11904358 10.1073/pnas.012025199
36. SymAtlas http://symatlas.gnf.org/SymAtlas/
37. VassarStats http://faculty.vassar.edu/lowry/VassarStats.html