Imprinting Identification and Methylation Analysis of Bovine (Bos taurus) KLF14 and PDE10A Genes
DONG Yan-Qiu1, JIN Lan-Jie1, YANG Xin-Yi1, LI Dong-Jie2, HUO Hao-Nan1, SU Hong3, LI Shi-Jie1*
1 College of Life Sciences, Hebei Agricultural University, Baoding 071000, China; 2 College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; 3 Baoding University of Technology, Baoding 071000, China
Abstract In mammals, imprinted genes play key role in placental development and fetal growth. Changes in the expression of imprinted genes can lead to abnormal growth and development in mammals and cause diseases through various physiological responses and signaling pathways. KLF14 (Kruppel like factor 14) and phosphodiesterase 10a (PDE10A) genes were identified as imprinted genes in human (Homo sapiens) and mouse (Mus musculus). At present, the imprinting studies on KLF14 and PDE10A in cattle (Bos taurus) have not been reported. In this study, the expression of KLF14 and PDE10A genes in bovine heart, liver, spleen, lung, kidney, brain and placenta were firstly analyzed by RT-PCR. The results showed that KLF14 gene was only detected in the placenta; PDE10A gene was expressed in all tested tissues. The allelic expression status of KLF14 and PDE10A genes were further analyzed by direct sequencing of RT-PCR products based on SNP genomic DNA, KLF14 gene was identifiied to be a maternally imprinted gene in bovine placenta. PDE10A gene showed biallelic expression in placenta ant other tissues. PDE10A gene was non-imprinted in bovine. The methylation status of the promoter region of KLF14 gene was analyzed by sulfite sequencing method, hypomethylation were found in both bovine placenta and sperm, and there was no differentially methylated region, which indicated that the methylation modification of the promoter region of KLF14 gene might not be involved in regulating the imprinted expression of KLF14 gene. The above results suggest that bovine KLF14 gene is a placenta-specific maternally imprinted gene and bovine PDE10A gene is non-imprinted gene. This study provides a reference for further study of the function of the bovine KLF14 and PED10A.
[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. Bo-vine (Bos taurus) ANO1 gene is a placental-specific pa-ternal imprinting gene[J]. Journal of Agricultural Bio-technology, 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 expres-sion in cattle (Bos taurus)[J]. Journal of Agricultural Bio-technology, 8(09): 1595-1603. [3] Amin H S, Parikh P K, Ghate M D. 2021. Medicinal chemis-try strategies for the development of phosphodiesterase 10A (PDE10A) inhibitors -an update of recent progress[J]. European Journal of Medicinal Chemistry, 214: 113155. [4] Angiolini E Y, Sandovici I, Coan P M, et al. 2021. Deletion of the imprinted Phlda2 gene increases placental passive permeability in the mouse[J]. Genes, 12(5): 639-639. [5] Bartolomei M S, Oakey R J, Wutz A. 2020. Genomic imprint-ing: An epigenetic regulatory system[J]. PLoS Genetics, 16(8): e1008970. [6] Blunk I, Thomsen H, Reinsch N, et al. 2020. Genomic im-printing analyses identify maternal effects as a cause of phenotypic variability in type 1 diabetes and rheumatoid arthritis[J]. Scientific Reports, 10(1): 11562-11562. [7] Botting R A, Turco M Y, Meyer K B, et al. 2018. Single-cell reconstruction of the early maternal-fetal interface in hu-mans[J]. Nature, 563(7731): 347-353. [8] Boot A, Oosting J, de Miranda N F, et al. 2016. Imprinted sur-vival genes preclude loss of heterozygosity of chromo-some 7 in cancer cells[J]. The Journal of Pathology, 240(1): 72-83. [9] Bjornsson H T, Albert T J, Ladd-Acosta C M, et al. 2008. SNP-specific array-based allele-specific expression anal-ysis[J]. Genome Research, 18(5): 771-779. [10] Bourneuf E, Otz P, Pasuch H, et al. 2017. Rapid discovery of de novo deleterious mutations in cattle enhances the val-ue of livestock as model species[J]. Scientific Reports, 7(1): 11466. [11] Daetwyler H D, Capitan A, Pausch H, et al. 2014. Whole-ge-nome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle[J]. Nature Genet-ics, 46(8): 858-865. [12] Fuke T, Nakamura A, Inoue T, et al. 2021. Role of imprinting disorders in short children born SGA and Silver-Russell syndrome spectrum[J]. Journal of Clinical Endocrinolo-gy & Metabolism, 106(3): 802-813. [13] Gentzel R C, Toolan D, Roberts R, et al. 2015. The PDE10A inhibitor MP-10 and haloperidol produce distinct gene expression profiles in the striatum and influence catalep-tic behavior in rodents[J]. Neuropharmacology, 99: 256-263. [14] Hanna C W. 2020. Placental imprinting: Emerging mecha-nisms and functions[J]. PLoS Genetics, 16(4): e1008709. [15] Inoue A, Jiang L, Lu F, et al. 2017. Maternal H3K27me3 con-trols DNA methylation-independent imprinting[J]. Na-ture, 547(7664): 419-424. [16] Kochmanski J J, Marchlewicz E H, Cavalcante R G, et al. 2018. Longitudinal effects of developmental bisphenol a exposure on epigenome-wide DNA hydroxymethylation at imprinted loci in mouse blood[J]. Environmental Health Perspectives, 126(7): 077006. [17] Li J, Chen W, Li D, et al. 2021. Conservation of imprinting and methylation of MKRN3, MAGEL2 and NDN genes in cattle[J]. Animals (Basel), 11(7): 1185-1197. [18] Livernois A M, Mallard B A, Cartwright S L, et al. 2021. Heat stress and immune response phenotype affect DNA methylation in blood mononuclear cells from Holstein dairy cows[J]. Scientific Reports, 11(1): 11371-11382. [19] Macmullen C M, Fallahi M, Davis R L. 2017. Novel PDE10A transcript diversity in the human striatum: Insights into gene complexity, conservation and regulation[J]. Gene, 606: 17-24. [20] Magee D A, Spillane C, Berkowicz E W, et al. 2014. Imprint-ed loci in domestic livestock species as epigenomic tar-gets for artificial selection of complex traits[J]. Animal Genetics, 45(Suppl 1): 25-39. [21] Magalhase H R, Leite S B P, Paz C C, et al. 2013. Placental hydroxymethylation vs methylation at the imprinting control region 2 on chromosome 11p15. 5[J]. Brazilian Journal of Medical and Biological Research, 46(11): 916-919. [22] Messerschmidt D M, Knowles B B, Solter D. 2014. DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos[J]. Genes & Development, 28(8): 812-828. [23] Mcminn J, Wei M, Sadovsky Y, et al. 2006. Imprinting of PEG1/MEST isoform 2 in human placenta[J]. Placenta, 27(2-3): 119-126. [24] Parker-Katiraee L, Carson A R, Yamada T, et al. 2007. Identi-fication of the imprinted KLF14 transcription factor un-dergoing human-specific accelerated evolution[J]. PLoS Genetics, 3(4): e65. [25] Pignata L, Palumbo O, Cerrato F, et al. 2020. Both epimuta-tions and chromosome aberrations affect multiple im-printed loci in aggressive wilms tumors[J]. Cancers, 12(11): 3411. [26] Ribeiro F I, Azevedo C H, Ferreira B E, et al. 2019. A rapid and accurate methylation-sensitive high-resolution melt-ing analysis assay for the diagnosis of Prader Willi and Angelman patients[J]. Molecular Genetics & Genomic Medicine, 7(6): e637. [27] Wang X, Soloway P D, Clark A G. 2011. A survey for novel imprinted genes in the mouse placenta by mRNA-seq[J]. Genetics, 189(1): 109-122. [28] Scagliotti V, Costa Fernandes E R, Willis T L, et al. 2021. Dy-namic expression of imprinted genes in the developing and postnatal pituitary gland[J]. Genes (Basel), 12(4): 509. [29] Yang Q Y, Civelek M. 2020. Transcription factor KLF14 and metabolic syndrome[J]. Frontiers in Cardiovascular Medicine, 7: 91-94. [30] Zaitoun I, Khatib H. 2006. Assessment of genomic imprinting of SLC38A4, NNAT, NAP1L5, and H19 in cattle[J]. BMC Genetics, 7(1): 49-59. [31] Zaitoun I, Khatib H. 2008. Comparative genomic imprinting and expression analysis of six cattle genes[J]. Journal of Animal Science, 86(1): 25-32.
