Genetic variation in the MITF promoter affects skin colour and transcriptional activity in black-boned chickens

References

• Bauer, G. L., C. Praetorius, K. Bergsteinsd Ttir, J. H. Hallsson, B. K. G Slad Ttir, A. Schepsky, D. A. Swing, T. N. O’sullivan, H. Arnheiter, and K. Bismuth. 2009. “The Role of MITF Phosphorylation Sites during Coat Color and Eye Development in Mice Analyzed by Bacterial Artificial Chromosome Transgene Rescue.” Genetics 183: 581–594. doi:10.1534/genetics.109.103945.
   PubMed Web of Science ®Google Scholar
• Beckmann, H., L. K. Su, and T. Kadesch. 1990. “TFE3: A Helix-Loop-Helix Protein that Activates Transcription through the Immunoglobulin Enhancer muE3 Motif.” Genes & Development 4: 167–179. doi:10.1101/gad.4.2.167.
   PubMed Web of Science ®Google Scholar
• Borg, J., P. Papadopoulos, M. Georgitsi, L. Guti Rrez, G. Grech, P. Fanis, M. Phylactides, A. J. M. H. Verkerk, P. J. V. D. Spek, and C. A. Scerri. 2010. “Haploinsufficiency for the Erythroid Transcription Factor KLF1 Causes Hereditary Persistence of Fetal Hemoglobin.” Nature Genetics 42: 801–805. doi:10.1038/ng.630.
   PubMed Web of Science ®Google Scholar
• Chorley, B. N., X. Wang, M. R. Campbell, G. S. Pittman, M. A. Noureddine, and D. A. Bell. 2008. “Discovery and Verification of Functional Single Nucleotide Polymorphisms in Regulatory Genomic Regions: Current and Developing Technologies.” Mutation Research/Reviews in Mutation Research 659: 147–157. doi:10.1016/j.mrrev.2008.05.001.
   PubMed Web of Science ®Google Scholar
• Corre, S., and M. D. Galibert. 2005. “Upstream Stimulating Factors: Highly Versatile Stress-Responsive Transcription Factors.” Pigment Cell Research 18: 337–348. doi:10.1111/j.1600-0749.2005.00262.x.
   PubMedGoogle Scholar
• Coulson, J. M., J. L. Edgson, Z. V. Marshalljones, R. Mulgrew, J. P. Quinn, and P. J. Woll. 2003. “Upstream Stimulatory Factor Activates the Vasopressin Promoter via Multiple Motifs, Including a Non-Canonical E-Box.” Biochemical Journal 369: 549–561. doi:10.1042/bj20021176.
   PubMed Web of Science ®Google Scholar
• Dang, X. Y., W. W. Chu, H. C. Shi, S. G. Yu, H. Y. Han, S. H. Gu, and J. Chen. 2015. “Genetic Variants in ABCA1 Promoter Affect Transcription Activity and Plasma HDL Level in Pigs.” Gene 555: 414–420. doi:10.1016/j.gene.2014.11.041.
   PubMed Web of Science ®Google Scholar
• Das, S. K., N. K. Sharma, W. S. Chu, W. Hua, and S. C. Elbein. 2008. “Aryl Hydrocarbon Receptor Nuclear Translocator (ARNT) Gene as a Positional and Functional Candidate for Type 2 Diabetes and Prediabetic Intermediate Traits: Mutation Detection, Case-Control Studies, and Gene Expression Analysis.” BMC Medical Genetics 9: 16. doi:10.1186/1471-2350-9-16.
   PubMed Web of Science ®Google Scholar
• Denecker, G., N. Vandamme, Ö. Akay, D. Koludrovic, J. Taminau, K. Lemeire, A. Gheldof, B. D. Craene, M. V. Gele, and L. Brochez. 2014. “Identification of a ZEB2-MITF-ZEB1 Transcriptional Network that Controls Melanogenesis and Melanoma Progression.” Cell Death & Differentiation 21: 1250–1261. doi:10.1038/cdd.2014.44.
   PubMed Web of Science ®Google Scholar
• Hauswirth, R., B. Haase, M. Blatter, S. A. Brooks, D. Burger, C. Gem Ller, V. Gerber, D. Henke, J. Janda, and R. Jude. 2011. “Mutations in MITF and PAX3 Cause “Splashed White” and Other White Spotting Phenotypes in Horses.” PLoS Genetics 8: e1002653. doi:10.1371/journal.pgen.1002653.
   Web of Science ®Google Scholar
• Hobert, O. 2008. “Gene Regulation by Transcription Factors and microRNAs.” Science 319: 1785–1786. doi:10.1126/science.1151651.
   PubMed Web of Science ®Google Scholar
• Horton, J. D., J. L. Goldstein, and M. S. Brown. 2002. “SREBPs: Activators of the Complete Program of Cholesterol and Fatty Acid Synthesis in the Liver.” Journal of Clinical Investigation 109: 1125–1131. doi:10.1172/JCI0215593.
   PubMed Web of Science ®Google Scholar
• Jackson, I. J. 1994. “Evolution and Expression of Tyrosinase-Related Proteins.” Pigment Cell Research 7: 241. doi:10.1111/j.1600-0749.1994.tb00056.x.
   PubMedGoogle Scholar
• Jin, S., H. B. Park, D. W. Seo, M. Cahyadi, N. R. Choi, K. N. Heo, C. Jo, and J. H. Lee. 2014. “Association of MC1R Genotypes with Shank Color Traits in Korean Native Chicken.” Livestock Science 170: 1–7. doi:10.1016/j.livsci.2014.10.001.
   Web of Science ®Google Scholar
• Karlsson, E. K., I. Baranowska, C. M. Wade, N. H. Salmon Hillbertz, M. C. Zody, N. Anderson, T. M. Biagi, N. Patterson, and G. R. Pielberg. 2007. “Efficient Mapping of Mendelian Traits in Dogs through Genome-Wide Association.” Nature Genetics 39: 1321–1328. doi:10.1038/ng.2007.10.
   PubMed Web of Science ®Google Scholar
• Kwasnieski, J. C., I. Mogno, C. A. Myers, J. C. Corbo, and B. A. Cohen. 2012. “Complex Effects of Nucleotide Variants in a Mammalian Cis-Regulatory Element.” Proceedings of the National Academy of Sciences of the United States of America 109: 19498–19503. doi:10.1073/pnas.1210678109.
   PubMed Web of Science ®Google Scholar
• Levy, C., M. Khaled, and D. E. Fisher. 2006. “MITF: Master Regulator of Melanocyte Development and Melanoma Oncogene.” Trends in Molecular Medicine 12: 406–414. doi:10.1016/j.molmed.2006.07.008.
   PubMed Web of Science ®Google Scholar
• Li, Y., X. Zhu, L. Yang, J. Li, Z. Lian, N. Li, and X. Deng. 2011. “Expression and Network Analysis of Genes Related to Melanocyte Development in the Silky Fowl and White Leghorn Embryos.” Molecular Biology Reports 38: 1433–1441. doi:10.1007/s11033-010-0248-2.
   PubMed Web of Science ®Google Scholar
• Maston, G. A., S. K. Evans, and M. R. Green. 2006. “Transcriptional Regulatory Elements in the Human Genome.” Annual Review of Genomics & Human Genetics 7: 29–59. doi:10.1146/annurev.genom.7.080505.115623.
   PubMed Web of Science ®Google Scholar
• Mathelier, A., X. Zhao, A. W. Zhang, F. Parcy, R. Worsleyhunt, D. J. Arenillas, S. Buchman, C. Chen, A. Chou, and H. Ienasescu. 2014. “JASPAR 2014: An Extensively Expanded and Updated Open-Access Database of Transcription Factor Binding Profiles.” Nucleic Acids Research 42: 142–147. doi:10.1093/nar/gkt997.
   PubMed Web of Science ®Google Scholar
• Minvielle, F., B. Bed’hom, J. L. Coville, S. Ito, M. Inouemurayama, and D. Gourichon. 2010. “The “Silver” Japanese Quail and the MITF Gene: Causal Mutation, Associated Traits and Homology with the “Blue” Chicken Plumage.” BMC Genetics 11: 15. doi:10.1186/1471-2156-11-15.
   PubMed Web of Science ®Google Scholar
• Miyazono, K. 2000. “Positive and Negative Regulation of TGF-beta Signaling.” Journal of Cell Science 113: 1101.
   PubMed Web of Science ®Google Scholar
• Nagore, L. I., R. J. Nadeau, Q. Guo, Y. L. Jadhav, H. W. Jarrett, and W. E. Haskins. 2013. “Purification and Characterization of Transcription Factors.” Mass Spectrometry Reviews 32: 386–398. doi:10.1002/mas.v32.5.
   PubMed Web of Science ®Google Scholar
• Pingault, V., D. Ente, F. Dastot-Le Moal, M. Goossens, S. Marlin, and N. Bondurand. 2010. “Review and Update of Mutations Causing Waardenburg Syndrome.” Human Mutation 31: 391–406. doi:10.1002/humu.21211.
   PubMed Web of Science ®Google Scholar
• Riechmann, J. L., J. Heard, G. Martin, L. Reuber, C. Z. Jiang, J. Keddie, L. Adam, O. Pineda, O. J. Ratcliffe, and R. R. Samaha. 2001. “Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis among Eukaryotes.” Science 290: 2105–2110. doi:10.1126/science.290.5499.2105.
   Web of Science ®Google Scholar
• Shah, M., A. Bhoumik, V. Goel, A. Dewing, W. Breitwieser, H. Kluger, S. Krajewski, M. Krajewska, J. Dehart, and E. Lau. 2010. “A Role for ATF2 in Regulating MITF and Melanoma Development.” PLoS Genetics 6: 1071–1074. doi:10.1371/journal.pgen.1001258.
   Web of Science ®Google Scholar
• Shen, Q., and P. Singh. 2004. “Identification of a Novel SP3 Binding Site in the Promoter of Human IGFBP4 Gene: Role of SP3 and AP-1 in Regulating Promoter Activity in CaCo2 Cells.” Oncogene 23: 2454–2464. doi:10.1038/sj.onc.1207354.
   PubMed Web of Science ®Google Scholar
• Singh, K. B., R. C. Foley, and L. O Ate-S Nchez. 2002. “Transcription Factors in Plant Defense and Stress Responses.” Current Opinion in Plant Biology 5: 430–436. doi:10.1016/S1369-5266(02)00289-3.
   PubMed Web of Science ®Google Scholar
• Tsunoda, T., and T. Takagi. 1999. “Estimating Transcription Factor Bindability on DNA.” Bioinformatics 15: 622–630. doi:10.1093/bioinformatics/15.7.622.
   PubMed Web of Science ®Google Scholar
• Wang, Y., S.-M. Li, J. Huang, S.-Y. Chen, and Y.-P. Liu. 2014. “Mutations of TYR and MITF Genes are Associated with Plumage Colour Phenotypes in Geese.” Asian-Australasian Journal of Animal Sciences 27: 778–783. doi:10.5713/ajas.2013.13350.
   PubMed Web of Science ®Google Scholar
• Zhou, D., K. Liu, C. W. Sun, K. M. Pawlik, and T. M. Townes. 2010. “KLF1 Regulates BCL11A Expression and Gamma- to Beta-Globin Gene Switching.” Nature Genetics 42: 742–744. doi:10.1038/ng.637.
   PubMed Web of Science ®Google Scholar
• Zhu, W., I. Shiojima, Y. Ito, Z. Li, H. Ikeda, M. Yoshida, A. T. Naito, J. I. Nishi, H. Ueno, and A. Umezawa. 2008. “IGFBP-4 Is an Inhibitor of Canonical Wnt Signaling Required for Cardiogenesis.” Nature 454: 345–349. doi:10.1038/nature07027.
   PubMed Web of Science ®Google Scholar
• Zhu, Z., J. He, X. Jia, J. Jiang, R. Bai, X. Yu, L. Lv, R. Fan, X. He, and J. Geng. 2010. “MicroRNA-25 Functions in Regulation of Pigmentation by Targeting the Transcription Factor MITF in Alpaca (Lama Pacos) Skin Melanocytes.” Domestic Animal Endocrinology 38: 200–209. doi:10.1016/j.domaniend.2009.10.004.
   PubMed Web of Science ®Google Scholar