Tissue-specific Imprinting of Bovine (Bos taurus) ATP10A Gene
LIU Xiao-Qian1, DONG Yan-Qiu1, JIN Lan-Jie1, GU Shu-Kai1, LI Dong-Jie2, LI Shi-Jie1,*
1 College of Life Science, Hebei Agricultural University, Baoding 071001, China; 2 College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
Abstract Genomic imprinting is an important epigenetic modification mechanism in mammals, which is closely related to the growth and development of organisms. The ATP10A (ATPase phospholipid transporting 10A) located at one end of the PWS/AS imprinted region, which is related to the development of human (Homo sapiens) PWS (Prader-Willi syndrome) and AS (Angelman syndrome) syndromes. ATP10A is a brain-specific imprinted gene in human, but its imprinting status in cattle (Bos taurus) is still unknown. In this study, genomic DNA from 32 bovine heart tissues and 15 placentas were amplified by PCR first, and the single nucleotide polymorphic sites were found on ATP10A gene by direct sequencing of PCR products, the A/G heterozygous SNP locus (rs136134264) was identified on exon 20 of bovine ATP10A gene. Then total RNA in tissues and placenta of heterozygous cattle were used for RT-PCR to determine the allele expression status of ATP10A gene. The sequencing results of PCR products were compared with above heterozygous SNP locus, it was determined that ATP10A gene was monoallelic expression in bovine brain tissues and biallelic expression in other tissues and placenta. The DNA methylation status of the promoter region of ATP10A gene in bovine placenta and adult bovine tissues was further analyzed by bisulfite sequencing. It was found that the 46 CpG loci in the detected region showed hypomethylation in bovine tissues and placenta, indicating that the DNA methylation modification in the promoter region of ATP10A gene might not be involved in regulating imprinted gene expression of ATP10A. The present study provides a reference for further exploring of bovine ATP10A gene function and imprinting mechanism.
[1] 谷书凯, 李俊良, 陈玮娜, 等. 2019. 牛ANO1基因为胎盘特异的父源印记基因[J]. 农业生物技术学报, 27(11): 1996-2003. (Gu S K, Li J L, Chen W N, et al. 2019. Bovine, 27(11): 1996-2003.) [2] 谷书凯, 刘晓倩, 李俊良, 等. 2020. 牛QPCT基因为母源等位基因表达的印记基因[J]. 农业生物技术学报, 28(09): 1595-1603. (Gu S K, Liu X Q Li J L, et al. 2020. QPCT is an imprinted gene with maternal allele expression in cattle, 8(09): 1595-1603.) [3] Amber H, Katherine A. Patzel, et al.2008. Gender influences monoallelic expression of ATP10A in human brain[J]. Human Genetics, 123(3): 235-242. [4] Babak T, Deveale B, Tsang E K, et al.2015. Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse[J]. Nature Genetics, 47(5): 544-549. [5] Baran Y, Subramaniam M, Biton A, et al.2015. The landscape of genomic imprinting across diverse adult human tissues[J]. Genome Research, 25(7): 927-936. [6] Bartolomei M S, Ferguson-Smith A C.2011. Mammalian genomic imprinting[J]. Cold Spring Harbor Perspectives Biology, 3(7): 839-848 [7] Bjornsson H T, Albert T J., Ladd-Acosta C M., et al.2008. SNP-specific array-based allele-specific expression analysis[J]. Genome Research, 18(5): 771-779. [8] Bourneuf E, Otz P, Pausch H, et al.2017. Rapid discovery of de novo deleterious mutations in cattle enhances the value of livestock as model species[J]. Entific Reports, 7(1): 11466. [9] Chen W, Xu D, Ma C, et al.2019. The molecular structure and imprinting status of the IPW (imprinted gene in the Prader-Willi syndrome region) gene in cattle[J]. Animal Genetics, 50(5): 417-422. [10] DuBose A J, Johnstone K A, Smith E Y, et al.2010. Atp10a, a gene adjacent to the PWS/AS gene cluster, is not imprinted in mouse and is insensitive to the PWS-IC[J]. Neurogenetics, 11(2): 145-151. [11] El-Zein M, Cheishvili D, Gotlieb W, et al.2020. Genome-wide DNA methylation profiling identifies two novel genes in cervical neoplasia[J]. Internation Journal of Cancer, 147(5): 1264-1274. [12] Gillessen-Kaesbach G, Demuth S, Thiele H, et al.1999. A previously unrecognised phenotype characterised by obesity, muscular hypotonia and ability to speak in patients with Angelman syndrome caused by an imprinting defect[J]. European Journal of Human Genetics, 7(6): 638-644. [13] Gregg C, Zhang J, Butler J E, 2010a. Sex specific parent of origin allelic expression in the mouse brain[J]. Science, 329(5992): 682-685. [14] Gregg C, Zhang J, Weissbourd B, et al.2010b. High-resolution analysis of parent-of-origin allelic expression in the mouse brain[J]. Science, 329(5992): 643-648. [15] Hansen P J.2014. Current and future assisted reproductive technologies for mammalian farm animals[J]. Advances in Experimental Medicine and Biology, 752: 1-22 [16] Herzing L, Kim S J, Cook E H, et al.2001. The human aminophospholipid-transporting ATPase gene ATP10C maps adjacent to UBE3A and exhibits similar imprinted expression[J]. The American Journal of Human Genetics, 68(6): 1501-1505. [17] Hogart A, Patzel K A, LaSalle J M.2008. Gender influences monoallelic expression of ATP10A in human brain[J]. Human Genetics, 124(3): 235-242. [18] Kalish J M, Jiang C, Bartolomei M S.2014. Epigenetics and imprinting in human disease[J]. International Journal of Developmental Biology, 58(2-3-4): 291-298. [19] Kayashima T, Ohta T, Niikawa N, et al.2003a. On the conflicting reports of imprinting status of mouse ATP10a in the adult brain: Strain-background-dependent imprinting[J]. Journal Human Genetics, 48(9): 492-493. [20] Kayashima T, Yamasaki K, Joh K, et al.2003b. Atp10a, the mouse ortholog of the human imprinted ATP10A gene, escapes genomic imprinting[J]. Genomics, 81(6): 644-647. [21] Kelsey G, Feil R.2013. New insights into establishment and maintenance of DNA methylation imprints in mammals[J]. Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1609): 20110336. [22] Kim K P, Thurston A, Mummery C, et al.2007. Gene-specific vulnerability to imprinting variability in human embryonic stem cell lines[J]. Genome Research, 17(12): 1731-1742. [23] Kishino T, Lalande M, Wagstaff J.1997. UBE3A/E6-AP mutations cause Angelman syndrome[J]. Nature Genetics, 15(1): 70-73. [24] Landers M, Bancescu D L, Meur E L, et al.2004. Regulation of the large (approximately 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn[J]. Nucleic Acids Research, 32(11): 3480-3492. [25] Li J, Zhang C, Si H, et al.2021. Brain-specific monoallelic expression of bovine UBE3A is associated with genomic position[J]. Animal Genetics, 52(1): 47-54. [26] Li S S, Yu S L, Singh S.2010. Epigenetic states and expression of imprinted genes in human embryonic stem cells[J]. World Journal of Stem Cells, 2(4): 97-102. [27] Lim D H, Maher E R.2010. Genomic imprinting syndromes and cancer[J]. Advances in Genetics, 70: 145-175. [28] Matsuura T, Sutcliffe J S, Fang P, et al.1997. De novo truncating mutations in E6-AP ubiquitin-protein ligase gene (UBE3A) in Angelman syndrome[J]. Nature Genetics, 15(1): 74-77. [29] Meguro M, Kashiwagi A, Mitsuya K, et al.2001. A novel maternally expressed gene, ATP10C, encodes a putative aminophospholipid translocase associated with Angelman syndrome[J]. Nature Genetics, 28(1): 19-20. [30] Nicholls R D, Knepper J L.2001. Genome organization, function, and imprinting in Prader-Willi and Angelman syndromes[J]. Annual Review of Genomics and Human Genetics, 2(1): 153-175. [31] Olivia H S, Catherine D.2019. Influences of genomic imprinting on brain function and behavior[J]. Current Opinion in Behavioral Sciences, 25: 66-76. [32] Peters J.2014. The role of genomic imprinting in biology and disease: An expanding view[J]. Nature Reviews Genetics, 15(8): 517-530. [33] Runte M.2001. The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A[J]. Human Molecular Genetics, 10(23): 2687-2700. [34] Sigurdsson M I, Jamshidi N, Jonsson J J, et al.2009. Genome-scale network analysis of imprinted human metabolic genes[J]. Epigenetics, 4(1): 43-46. [35] Stewart K R, Veselovska L, Kelsey G.2016. Establishment and functions of DNA methylation in the germline[J]. Epigenomics, 8(10): 1399-1413. [36] Tucci V, Isles A R, Kelsey G, et al.2019. Genomic imprinting and physiological processes in mammals[J]. Cell, 176(5): 952-965. [37] Williams C A, Zori R T, Hendrickson J, et al.1995. Angelman syndrome[J]. Current Problems in Pediatrics. 25(7): 216-231 [38] Yamasaki K, Joh K, Ohta T, et al.2003. Neurons but not glial cells show reciprocal imprinting of sense and antisense transcripts of Ube3a[J]. Human Molecular Genetics, 12(8): 837-847. [39] Zhang K, Li J B, Gao Y, et al.2009. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human[J]. Nature Methods, 6(8): 613-618.
