Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses

Nature Genetics

Volumn 48, Issue 2, 2016, Pages 152-158

  Imsland, Freyja ^a   McGowan, Kelly ^b,c   Rubin, Carl Johan ^a   Henegar, Corneliu ^c   Sundström, Elisabeth ^a   Berglund, Jonas ^a   Schwochow, Doreen ^d,e   Gustafson, Ulla ^d   Imsland, Páll ^f   Lindblad Toh, Kerstin ^a,g   Lindgren, Gabriella ^d   Mikko, Sofia ^d   Millon, Lee ^h   Wade, Claire ^g   Schubert, Mikkel ⁱ   Orlando, Ludovic ⁱ   Penedo, Maria Cecilia T ^h   Barsh, Gregory S ^b,c   Andersson, Leif ^a,d,j  

^a UPPSALA UNIVERSITY   (Sweden)

^b HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^e UMR1313 GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE   (France)

^f Menntaskólinn vio Hamrahlío   (Iceland)

^g BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

ⁱ UNIVERSITY OF COPENHAGEN   (Denmark)

^j TEXAS A AND M UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PIGMENT; T BOX TRANSCRIPTION FACTOR; TRANSCRIPITON FACTOR TBX3; UNCLASSIFIED DRUG;

ALLELE; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; COLOR; DILUTION; DOMESTIC HORSE; GENE MUTATION; GENETIC IDENTIFICATION; GENETIC POLYMORPHISM; HAIR; HAIR FOLLICLE; HAIR PIGMENTATION; MELANOCYTE; NONHUMAN; PHENOTYPE; PIGMENTATION; PRIORITY JOURNAL; ANIMAL; GENE EXPRESSION PROFILING; GENETICS; HAIR COLOR; HORSE; METABOLISM; MUTATION; SKIN;

ANIMALS; GENE EXPRESSION PROFILING; HAIR COLOR; HAIR FOLLICLE; HORSES; MUTATION; SKIN; T-BOX DOMAIN PROTEINS;

EID: 84956609192     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3475     Document Type: Article

References (32)

1. Wade, C.M., et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326, 865-867 (2009
2. Orlando L., et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499, 74-78 (2013
3. Bowling, A.T., & Ryder, O.A. Genetic studies of blood markers in Przewalski?s horses. J. Hered. 78, 75-80 (1987
4. Adalsteinsson, S. Inheritance of yellow dun and blue dun in the Icelandic toelter horse. J. Hered. 69, 146-148 (1978
5. Bamshad, M., et al. Mutations in human TBX3 alter limb, apocrine and genital development in ulnar-mammary syndrome. Nat. Genet. 16, 311-315 (1997
6. Frank, D.U., Emechebe, U., Thomas, K.R., & Moon, A.M. Mouse TBX3 mutants suggest novel molecular mechanisms for Ulnar-mammary syndrome. PLoS One 8, e67841 (2013
7. Kumar P.P., et al. TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome. PLoS Genet. 10, e1004247 (2014
8. Gremmel, F. Coat colors in horses. J. Hered. 30, 437-445 (1939
9. Andersson L.S., et al. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature 488, 642-646 (2012
10. Schubert M., et al. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc. Natl. Acad. Sci. USA 111, E5661-E5669 (2014
11. Thomas-Chollier M., et al. Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nat. Protoc. 6, 1860-1869 (2011
12. Ma L., et al. Cyclic alopecia? in Msx2 mutants: defects in hair cycling and hair shaft differentiation. Development 130, 379-389 (2003
13. Kayserili H., et al. ALX4 dysfunction disrupts craniofacial and epidermal development. Hum. Mol. Genet. 18, 4357-4366 (2009
14. Reginelli, A.D., Wang, Y.Q., Sassoon, D., & Muneoka, K. Digit tip regeneration correlates with regions of Msx1 (Hox 7) expression in fetal and newborn mice. Development 121, 1065-1076 (1995
15. Satokata I., et al. Msx2 deficiency in mice causes pleiotropic defects in bone growth and ectodermal organ formation. Nat. Genet. 24, 391-395 (2000
16. Steingrímsson, E., Copeland, N.G., & Jenkins, N.A. Melanocytes and the microphthalmia transcription factor network. Annu. Rev. Genet. 38, 365-411 (2004
17. Kunisada, T., et al. Transgene expression of steel factor in the basal layer of epidermis promotes survival, proliferation, differentiation and migration of melanocyte precursors. Development 125, 2915-2923 (1998
18. Yoshida H., et al. Review: melanocyte migration and survival controlled by SCF/c-kit expression. J. Investig. Dermatol. Symp. Proc. 6, 1-5 (2001
19. St-Jacques B., et al. Sonic hedgehog signaling is essential for hair development. Curr. Biol. 8, 1058-1068 (1998
20. van den Boogaard M., et al. Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer. J. Clin. Invest. 122, 2519-2530 (2012
21. Fang, M., Larson, G., Ribeiro, H.S., Li, N., & Andersson, L. Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet. 5, e1000341 (2009
22. Pruvost M., et al. Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art. Proc. Natl. Acad. Sci. USA 108, 18626-18630 (2011
23. Gabriel S.B., et al. The structure of haplotype blocks in the human genome. Science 296, 2225-2229 (2002
24. Barrett, J.C., Fry, B., Maller, J., & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265 (2005
25. Sundström E., et al. Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses. BMC Genomics 13, 365 (2012
26. Li, H., & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009
27. DePristo M.A., et al A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011
28. Schubert M., et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat. Protoc. 9, 1056-1082 (2014
29. Lindgreen, S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337 (2012
30. Wang, K., Li, M., & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-Throughput sequencing data. Nucleic Acids Res. 38, e164 (2010
31. Purcell S., et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007
32. Delaneau, O., Marchini, J., & Zagury, J.-F A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179-181 (2012