Browse > Article
http://dx.doi.org/10.5713/ajas.14.0860

Novel Nucleotide Variations, Haplotypes Structure and Associations with Growth Related Traits of Goat AT Motif-Binding Factor (ATBF1) Gene  

Zhang, Xiaoyan (College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture)
Wu, Xianfeng (College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture)
Jia, Wenchao (College of Life Sciences, Northwest A&F University)
Pan, Chuanying (College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture)
Li, Xiangcheng (Institute of Beijing Animal Science and Veterinary, Chinese Academy of Agricultural Science)
Lei, Chuzhao (College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture)
Chen, Hong (College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture)
Lan, Xianyong (College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.28, no.10, 2015 , pp. 1394-1406 More about this Journal
Abstract
The AT motif-binding factor (ATBF1) not only interacts with protein inhibitor of activated signal transducer and activator of transcription 3 (STAT3) (PIAS3) to suppress STAT3 signaling regulating embryo early development and cell differentiation, but is required for early activation of the pituitary specific transcription factor 1 (Pit1) gene (also known as POU1F1) critically affecting mammalian growth and development. The goal of this study was to detect novel nucleotide variations and haplotypes structure of the ATBF1 gene, as well as to test their associations with growth-related traits in goats. Herein, a total of seven novel single nucleotide polymorphisms (SNPs) (SNP 1-7) within this gene were found in two well-known Chinese native goat breeds. Haplotypes structure analysis demonstrated that there were four haplotypes in Hainan black goat while seventeen haplotypes in Xinong Saanen dairy goat, and both breeds only shared one haplotype (hap1). Association testing revealed that the SNP2, SNP5, SNP6, and SNP7 loci were also found to significantly associate with growth-related traits in goats, respectively. Moreover, one diplotype in Xinong Saanen dairy goats significantly linked to growth related traits. These preliminary findings not only would extend the spectrum of genetic variations of the goat ATBF1 gene, but also would contribute to implementing marker-assisted selection in genetics and breeding in goats.
Keywords
ATBF1 Gene; Single Nucleotide Polymorphisms; Haplotypes; Growth-related Traits; Association;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
1 Akcay, A., K. Ulucan, N. Taskin, M. Boyraz, T. Akcay, O. Zurita, A. Gomez, K. E. Heath, and A. Campos-Barros. 2013. Suprasellar mass mimicking a hypothalamic glioma in a patient with a complete PROP1 deletion. Eur. J. Med. Genet. 56:445-451.   DOI   ScienceOn
2 Araujo, R. V., C. V. Chang, V. A. S. Cescato, M. C. B. V. Fragoso, M. D. Bronstein, B. B. Mendonca, I. J. P. Arnhold, and L. R. S. Carvalho. 2013. PROP1 overexpression in corticotrophinomas: evidence for the role of PROP1 in the maintenance of cells committed to corticotrophic differentiation. Clinics 68:887-891.   DOI
3 Bastos, E., S. Avila, A. Cravador, R. Renaville, P. H Guedes, and C. J Luis. 2006. Identification and characterization of four splicing variants of ovine POU1F1 gene. Gene 382:12-19.   DOI   ScienceOn
4 Benjamin, E. J., K. M. Rice, D. E. Arking, A. Pfeufer, C. van Noord, A. V. Smith, R. B. Schnabel, J. C. Bis, E. Boerwinkle, and M. F. Sinner et al. 2009. Variants in ZFHX3 are associated with atrial fibrillation in individuals of European ancestry. Nat. Genet. 41:879-881.   DOI   ScienceOn
5 Carvalho, L., R. D. Ward, M. L. Brinkmeier, M. A. Potok, A. H. Vesper, and S. A. Camper. 2006. Molecular basis for pituitary dysfunction: Comparison of Prop1 and Pit1 mutant mice. Dev. Biol. 295:340.
6 Chamary, J. V. and L. D. Hurst. 2005. Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol. 6:R75.   DOI
7 Choudhary, V., P. Kumar, T. K. Bhattacharya, B. Bhushan, A. Sharma, and A. Shukla. 2007. DNA polymorphism of insulin-like growth factor-binding protein-3 gene and its association with birth weight and body weight in cattle. J. Anim. Breed. Genet. 124:29-34.   DOI   ScienceOn
8 Cleton-Jansen, A. M., R. van Eijk, M. Lombaerts, M. K. Schmidt, L. J. Van't Veer, K. Philippo, R. M. E. Zimmerman, J. L. Peterse, V. T. B. H. M. Smit, T. van Wezel, C. J. Cornelisse, A. M. Cleton-Jansen, R. Van Eijk, and M. Lombaerts. 2008. ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: Absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism. BMC Cancer 8:105.   DOI   ScienceOn
9 Darnell, J. E. 1997. STATs and gene regulation. Science 277(5332):1630-1635.   DOI   ScienceOn
10 Davis, S. W., F. Castinetti, L. R. Carvalho, B. S. Ellsworth, M. A. Potok, R. H. Lyons, M. L. Brinkmeier, L. T. Raetzman, P. Carninci, A. H. Mortensen, Y. Hayashizaki, I. J. P. Arnhold, B. B. Mendonca, T. Brue, and S. A. Camper. 2010. Molecular mechanisms of pituitary organogenesis: In search of novel regulatory genes. Mol. Cell. Endocrinol. 323:4-19.   DOI   ScienceOn
11 Fang, Q., A. M. Giordimaina, D. F. Dolan, S. A. Camper, and M. Mustapha. 2012. Genetic Background of Prop1(df) mutants provides remarkable protection against hypothyroidism-induced hearing impairment. J. Assoc. Res. Otolaryngol. 13:173-184.   DOI   ScienceOn
12 Fang, X. T., H. X Xu, C. L. Zhang, J. M. Zhang, X. Y. Lan, C. W. Gu, and H. Chen. 2010. Polymorphisms in BMP-2 gene and their associations with growth traits in goats. Genes Genomics 32:29-35.   DOI   ScienceOn
13 Gilbert, R. P., D. R. Bailey, and N. H. Shannon. 1993 Linear body measurements of cattle before and after twenty years of selection for post weaning gain when fed two different diets. J. Anim. Sci. 71:1712-1720.   DOI
14 Godi, M., S. Mellone, L. Tiradani, R. Marabese, C. Bardelli, M. Salerno, F. Prodam, S. Bellone, A. Petri, P. Momigliano-Richiardi, G. Bona, and M. Giordano. 2012. Functional SNPs within the intron 1 of the PROP1 gene contribute to combined growth hormone deficiency (CPHD). J. Clin. Endocrinol. Metab. 97:E1791-E1797.   DOI
15 Green, M. R. and J. Sambrook. 2012. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York, USA. 65-73.
16 Gudbjartsson, D. F., H. Holm, S. Gretarsdottir, and G. Thorleifsson, G. B. Walters, G. Thorgeirsson, J. Gulcher, E. B. Mathiesen, I. Njolstad, and A. Nyrnes et al. 2009. A sequence variant in ZFHX3 on 16q22 associates with atrial fibrillation and ischemic stroke. Nat. Genet. 41:876-878.   DOI   ScienceOn
17 Ishii, Y., M. Kawaguchi, K. Takagawa, T. Oya, S. Nogami, A. Tamura, Y. Miura, A. Ido, N. Sakata, T. Hashimoto-Tamaoki, T. Kimura, T. Saito, T. Tamaoki, and M. Sasahara. 2003. ATBF1­A protein, but not ATBF1-B, is preferentially expressed in developing rat brain. J. Comp. Neurol. 465:57-71.   DOI   ScienceOn
18 Guy, J. C., C. S. Hunter, A. D. Showalter, T. P. L. Smith, K. Charoonpatrapong, K. W. Sloop, J. P. Bidwell, and S. J. Rhodes. 2004. Conserved amino acid sequences confer nuclear localization upon the Prophet of Pit-1 pituitary transcription factor protein. Gene 336:263-273.   DOI   ScienceOn
19 He, H., H. L. Zhang, Z. X. Li, Y. Liu, and X. L. Liu. 2014. Expression, SNV identification, linkage disequilibrium, and combined genotype association analysis of the muscle-specific gene CSRP3 in Chinese cattle. Gene 535:17-23.   DOI   ScienceOn
20 Heinrich, P. C., I. Behrmann, G. Muller-Newen, F. Schaper, and L. Graeve. 1998. Interleukin-6-type cytokine signalling through the gp130/Jak/STAT pathway. Biochem. J. 334:297-314.   DOI
21 Jiang, Q., B. Ni, J. Shi, Z. L. Han, R. D. Qi, W. H. Xu, D. Wang, D. W. Wang, and M. L. Chen. 2014. Down-regulation of ATBF1 activates STAT3 signaling via PIAS3 in pacing-induced HL-1 atrial myocytes. Biochem. Biophys. Res. Commun. 449:278-283.   DOI   ScienceOn
22 Jung, C. G., H. J. Kim, M. Kawaguchi, K. K. Khanna, H. Hida, K. Asai, H. Nishino, and Y. Miura. 2005. Homeotic factor ATBF1 induces the cell cycle arrest associated with neuronal differentiation. Development 132:5137-5145.   DOI   ScienceOn
23 Jung, C. G., K. O. Uhm, Y. Miura, T. Hosono, H. Horike, K. K. Khanna, M. J. Kim, and M. Michikawa. 2011. Beta-amyloid increases the expression level of ATBF1 responsible for death in cultured cortical neurons. Mol. Neurodegener. 6:47.   DOI   ScienceOn
24 Lan, X. Y., H. Y. Zhao, Z. J. Li, R. Zhou, C. Y. Pan, C. Z. Lei, and H. Chen. 2013. Exploring the novel genetic variant of PITX1 gene and its effect on milk performance in dairy goats. J. Integr. Agric. 12:118-126.   DOI
25 Kai, K., Z. Zhang, H. Yamashita, Y. Yamamoto, Y. Miura, and H. Iwase. 2008. Loss of heterozygosity at the ATBF1-A locus located in the 16q22 minimal region in breast cancer. BMC Cancer 8:262.   DOI   ScienceOn
26 Kamohara, Y., N. Sugiyama, T. Mizuguchi, D. Inderbitzin, H. Lilja, Y. Middleton, T. Neuman, A. A. Demetriou, and J. Rozga. 2000. Inhibition of signal transducer and activator transcription factor 3 in rats with acute hepatic failure. Biochem. Biophys. Res. Commun. 273:129-135.   DOI   ScienceOn
27 Lan, X. Y., C. Y. Pan, H. Chen, C. L. Zhang, J. Y. Li, M. Zhao, C. Z. Lei, A. L. Zhang, and L. Zhang. 2007. An AluI PCR-RFLP detecting a silent allele at the goat POU1F1 locus and its association with production traits. Small Rumin. Res. 73:8-12.   DOI   ScienceOn
28 Li, M., X. Fu, G. Ma, X. D. Sun, X. Y. Dong, T. Nagy, C. S. Xing, J. Li, and J. T. Dong. 2012. Atbf1 regulates pubertal mammary gland development likely by inhibiting the pro-proliferative function of estrogen-ER signaling. PLoS One 7(12):e51283.   DOI   ScienceOn
29 Li, M., D. Zhao, G. Ma, B. Zhang, X. Fu, Z. Zhu, L. Fu, X. Sun, and J. T. Dong. 2013. Upregulation of ATBF1 by progesterone-PR signaling and its functional implication in mammary epithelial cells. Biochem. Biophys. Res. Commun. 430:358-363.   DOI   ScienceOn
30 Li, F., H. Chen, C. Z. Lei, G. Ren, J. Wang, Z. J. Li, and J. Q. Wang. 2010. Novel SNPs of the bovine NUCB2 gene and their association with growth traits in three native Chinese cattle breeds. Mol. Biol. Rep. 37:541-546.   DOI   ScienceOn
31 Morinaga, T., H. Yasuda, T. Hashimoto, K. Higashio, and T. Tamaoki. 1991. A human alpha-fetoprotein enhancer-binding protein, ATBF1, contains four homeodomains and seventeen zinc fingers. Mol. Cell. Biol. 11:6041-6049.   DOI
32 Li, Z. Q., Z. Zhang, Z. He, W. Tang, T. Li, Z. Zeng, L. He, and Y. Y. Shi. 2009. A partition-ligation-combination-subdivision EM algorithm for haplotype inference with multiallelic markers: update of the SHEsis. Cell Res. 19:519-523.   DOI   ScienceOn
33 Massague, J. 2012. TGF-$\beta$ signalling in context. Nat. Rev. Mol. Cell Biol. 13:616-630.   DOI   ScienceOn
34 Massague, J., J. Seoane, and D. Wotton. 2005. Smad transcription factors. Genes Dev. 19:2783-2810.   DOI   ScienceOn
35 Moustakas, A. and C. H. Heldin. 2009. The regulation of TGF-$\beta$ signal transduction. Development 136:3699-3714.   DOI   ScienceOn
36 Navardauskaite, R., P. Dusatkova, B. Obermannova, R. W. Pfaeffle, W. F. Blum, D. Adukauskiene, N. Smetanina, O. Cinek, R. Verkauskiene, and J. Lebl. 2014. High prevalence of PROP1 defects in Lithuania: Phenotypic findings in an ethnically homogenous cohort of patients with multiple pituitary hormone deficiency. J. Clin. Endocrinol. Metab. 99:299-306.   DOI   ScienceOn
37 Ninomiya, T., K. Mihara, K. Fushimi, Y. Hayashi, T. Hashimoto-Tamaoki, and T. Tamaoki. 2002. Regulation of the alpha­fetoprotein gene by the isoforms of ATBF1 transcription factor in human hepatoma. Hepatology 35:82-87.   DOI   ScienceOn
38 Nishio, E., Y. Miura, M. Kawaguchi, and A. Morita. 2012. Nuclear translocation of ATBF1 is a potential prognostic marker for skin cancer. Acta Dermatovenerol. Croat. 20:239-245.
39 Pan, C. Y., C. Y. Wu, W. C. Jia, Y. Xu, C. Z. Lei, S. R. Hu, X. Y. Lan, and H. Chen. 2013. A critical functional missense mutation (H173R) in the bovine PROP1 gene significantly affects growth traits in cattle. Gene 531:398-402.   DOI   ScienceOn
40 Nojiri, S., T. Joh, Y. Miura, N. Sakata, T. Nomura, H. Nakao, S. Sobue, H. Oharra, K. Asai, and M. Ito. 2004. ATBF1 enhances the suppression of STAT3 signaling by interaction with PIAS3. Biochem. Biophys. Res. Commun. 314:97-103.   DOI   ScienceOn
41 Perea, D., K. Molohon, K. Edwards, and F. J. Diaz-Benjumea. 2013. Multiple roles of the gene zinc finger homeodomain-2 in the development of the Drosophila wing. Mech. Dev. 130: 467-481.   DOI   ScienceOn
42 Qi, Y. C., J. A. Ranish, X. Y. Zhu, A. Krones, J. Zhang, R. Aebersold, D. W. Rose, M. G. Rosenfeld, and C. Carriere. 2008. Atbf1 is required for the Pit1 gene early activation. Proc. Natl. Acad. Sci. USA 105:2481-2486.   DOI   ScienceOn
43 Sakata, N., S. Kaneko, S. Ikeno, Y. Miura, H. Nakabayashi, X. Y. Dong, J. T. Dong, T. Tamaoki, N. Nakano, and S. Itoh. 2014. TGF-$\beta$ Signaling Cooperates with AT Motif-Binding Factor-1 for Repression of the $\alpha$-Fetoprotein Promoter. J. Signal Transduct. Article ID 970346.
44 Sambrock, J. and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, NY, USA.
45 Schindler, C. and J. E. Darnell. 1995. Transcriptional responses to polypeptide ligands: The JAK-STAT pathway. Annu. Rev. Biochem. 64:621-652.   DOI   ScienceOn
46 Shuai, K. 1999. The STAT family of proteins in cytokine signaling. Prog. Biophys. Mol. Biol. 71:405-422.   DOI   ScienceOn
47 Van Laere, A. S., M. Nguyen, M. Braunschweig, C. Nezer, C. Collette, L. Moreau, A. L. Archibald, C. S. Haley, N. Buys, and M. Tally et al. 2003. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425: 832-836.   DOI   ScienceOn
48 Sun, X., X. Fu, J. Li, C. S. Xing, D. W. Martin, H. H. Zhang, Z. J. Chen, and J. T. Dong. 2012. Heterozygous deletion of Atbf1 by the Cre-loxP system in mice causes preweaning mortality. Genesis 50:819-827.   DOI   ScienceOn
49 Sun, X. D., X. Y. Fu, J. Li, C. S. Xing, H. F. Frierson, H. Wu, X. K. Ding, T. Z. Ju, R. D. Cummings, and J. T. Dong. 2014. Deletion of Atbf1/Zfhx3 in mouse prostate causes neoplastic lesions, likely by attenuation of membrane and secretory proteins and multiple signaling pathways. Neoplasia 16:377-389.   DOI   ScienceOn
50 Sun, X. D., Y. F. Zhou, K. B. Otto, M. R. Wang, C. S. Chen, W. Zhou, K. Subramanian, P. M. Vertino, and J. T. Dong. 2007. Infrequent mutation of ATBF1 in human breast cancer. J. Cancer Res. Clin. 133:103-105.
51 Wang, A. L., Y. Zhang, M. J. Li, X. Y. Lan, J. Q. Wang, and H. Chen. 2013. SNP identi.cation in FBXO32 gene and their associations with growth traits in cattle. Gene 515:181-186.   DOI   ScienceOn
52 Wang, G., S. Zhang, S. Wei, Y. Zhang, Y. Li, C. Fu, C. Zhao, and L. Zan. 2014. Novel polymorphisms of SIX4 gene and their association with body measurement traits in Qinchuan cattle. Gene 539:107-110.   DOI   ScienceOn
53 Yasuda, H., A. Mizuno, T. Tamaoki, and T. Morinaga. 1994. ATBF1, a multiple-homeodomain zinc finger protein, selectively down-regulates AT-rich elements of the human $\alpha$-fetoprotein gene. Mol. Cell. Biol. 14:1395-1401.   DOI
54 Zhong, Z., Z. L. Wen, and J. E. Darnell. 1994. Stat3: A STAT family member activated by tyrosine phosphorylation in response to epidermal growth factor and interleukin-6. Science 264(5155):95-98.   DOI
55 Yeh, F. C., R. Yang, T. J. Boyle, Z. Ye, and J. M. Xiyan. 2000. PopGene32, Microsoft Windows-based freeware for population genetic analysis, version 1.32. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, AB, Canada.
56 Zhao, H. Y., X. F. Wu, H. F. Cai, C. Y. Pan, C. Z. Lei, H. Chen, X. Y. Lan. 2013. Genetic variants and effects on milk traits of the caprine paired-like homeodomain transcription factor 2 (PITX2) gene in dairy goats. Gene 532:203-210.   DOI   ScienceOn