香猪CHD3基因3'-侧翼区264 bp结构变异的研究

doi:10.16431/j.cnki.1671-7236.2022.08.018

Abstract

Abstract: 【Objective】 This study was aimed to explore the effect of structural variation of chromodomain-helicase-DNA-binding protein 3 (CHD3) gene on the expression of CHD3 gene in different pig breeds, and preliminarily analyze the relationship between the CHD3 gene structural variation and the formation of wrinkle skin in the Xiang pigs.【Method】 In this study, ordinary Xiang pigs, Xiang pigs with wrinkle skin and Large White pigs were selected as the research subjects. UCSC, miRBase, miRanda and RBPsuite softwares were used to predict the repeated elements, miRNA binding sites and RNA binding protein (RBP) binding sites contained in the CHD3 structural variation interval. PCR method was used for genotyping of structural variation. Excel was used to calculate the population genotype frequency and allele frequency, and χ² test was used to analyze whether the genotype was in Hardy-Weinberg equilibrium. The effect of the variation on CHD3 gene expression was detected by Real-time quantitative PCR and Western blotting.【Result】 Bioinformatics analysis showed that the 3'-flanking region of CHD3 gene was a 254 bp short-scatter element (SINE), belonging to tRNA family, located in Chr12:53 115 742-53 115 995, which contained 35 miRNA binding sites and 10 RBP binding sites. Genotyping results showed that II genotype (insertion), ID genotype (heterozygous) and DD genotype (double deletion) were detected in all three pig groups, indicating that 264 bp structural variation in the 3'-flanking region of CHD3 gene was highly polymorphic in pigs. Genotype population distribution frequency showed that the frequency of D allele in Xiang pigs with wrinkle skin was extremely significantly higher than that in ordinary Xiang pigs and Large White pigs (P<0.01); χ² test showed that the structural variation of CHD3 gene was in Hardy-Weinberg equilibrium state in Xiang pigs with wrinkle skin and ordinary Xiang pigs (P>0.05), but unbalanced in Large White pigs (P<0.05). Real-time quantitative PCR and Western blotting analysis showed that the mRNA and protein expression of DD and ID genotypes of CHD3 in skin of Xiang pigs were extremely significantly higher than that of II genotype (P<0.01).【Conclusion】 The 264 bp structural variation in the 3'-flanking region of CHD3 gene was a SINE element with regulatory effect, which could promote the metabolism of CHD3 gene mRNA and post-transcriptional translation inhibition through the binding of RNA binding protein and miRNAs to the element, thus regulating the expression of CHD3 gene. The structural variation resulted in abnormal expression and accumulation of CHD3 gene, which might be related to the formation of wrinkled skin in Xiang pigs.

Key words: Xiang pigs; CHD3 gene; structural variation; wrinkled skin

CLC Number:

S828

HUANG Yueli, RAN Xueqin, NIU Xi, LI Sheng, HUANG Shihui, WANG Jiafu. Study on 264 bp Structural Variation of 3'-flanking Region of CHD3 Gene in Xiang Pigs[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 3026-3035.

References

[1] 刘培琼,刘若余,申学林,等.中国香猪简介[J].养猪,2011,5:49-51. LIU P Q, LIU R Y, SHEN X L,et al. Introduction to Chinese Xiang pig[J]. Swine Production, 2011,5:49-51.(in Chinese)
[2] 刘晓丽.香猪皱皮性状候选基因筛选鉴定[D].贵阳:贵州大学,2019. LIU X L. Screening and identification of candidate genes for wrinkled skin traits in Xiang pigs[D]. Guiyang:Guizhou University, 2019.(in Chinese)
[3] DABROWSKA A K, SPANO F, DERLER S, et al. The relationship between skin function, barrier properties, and body-dependent factors[J]. Skin Research and Tchnology,2018,24(2):165-174.
[4] FEUK L, CARSON A R, SCHERER S W. Structural variation in the human genome[J]. Nature Reviews, Genetics, 2006, 7(2):85-97.
[5] OLSSON M, MEADOWS J R, TURVE K, et al. A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in chinese Shar-Pei dogs[J]. PLoS Genetics, 2011, 7(3):e1001332.
[6] LUI X L, HU F B, HUANG S H, et al. Detection of genomic structure variants associated with wrinkled skin in Xiang pig by next generation sequencing[J]. Aging, 2021, 13(22):24710-24739.
[7] 胡冯彬.香猪皱皮性状的转录组学研究[D].贵阳:贵州大学,2020. HU F B. Transcriptome study on wrinkled skin traits of Xiang pig[D]. Guiyang:Guizhou University, 2020.(in Chinese)
[8] WOODAGE T, BASRAI M A, BAXEVANIS A D, et al. Characterization of the CHD family of proteins[J]. Proceedings of the National Academy of Sciences of the United States of America, 1997, 94(21):11472-11477.
[9] SEELIG H P, RENZ M, TARGOFF I N, et al. Two forms of the major antigenic protein of the dermatomyositis-specific Mi-2 autoantigen[J]. Arthritis Rheum, 1996, 39(10):1769-1771.
[10] MONSEAU G, LANDON-CARDINAL O, STENZEL W, et al. Systematic retrospective study of 64 patients with anti-Mi2 dermatomyositis:A classic skin rash with a necrotizing myositis and high risk of malignancy[J]. Journal of the American Academy of Dermatology, 2020, 83(6):1759-1763.
[11] GILES K A, GOULD C M, DU Q, et al. Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups[J]. Epigenetics Chromatin, 2019, 12(1):12.
[12] TORCHY M P, HAMICHE A, KLAHOLZ B P. Structure and function insights into the NuRD chromatin remodeling complex[J]. Cellular and Molecular Life Sciences, 2015, 72(13):2491-2507.
[13] LUO M, LING T, XIE W B, et al. NuRD blocks reprogramming of mouse somatic cells into pluripotent stem cells[J]. Stem Cells, 2013, 31(7):1278-1286.
[14] SNIJDERS B L, ROUSSEAU J, TWST J, et al. CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language[J]. Nature Communications, 2018, 9(1):4619.
[15] MIZUKAMI M, ISHIKAWA A, MIYAZAKI S, et al. A de novo CHD3 variant in a child with intellectual disability, autism, joint laxity, and dysmorphisms[J]. Brain&Development, 2021, 43(4):563-565.
[16] PASTORCIC M, DAS H K. The C-terminal region of CHD3/ZFH interacts with the CIDD region of the Ets transcription factor ERM and represses transcription of the human presenilin 1 gene[J]. The FEBS Journal, 2007,274(6):1434-1448.
[17] 边红.基质金属蛋白酶在多发性肌炎/皮肌炎免疫发病机制中的作用研究[D].济南:山东大学,2003. BIAN H. The role of matrix metalloproteinases in immune pathogenesis of polymyositis/dermatomyositis[D]. Jinan:Shandong University, 2003.(in Chinese)
[18] BIRCH H L. Extracellular matrix and ageing[J]. Sub-Cellular Biochemistry, 2018,90:169-190.
[19] INGRAM K G, CURTIS C D, SILASI-MANSAT, et al. The NuRD chromatin-remodeling enzyme CHD4 promotes embryonic vascular integrity by transcriptionally regulating extracellular matrix proteolysis[J]. PLoS Genetics,2013,9(12):e1004031.
[20] OFFMEISTER H, FUCHS A, ERDEL F, et al. CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality[J]. Nucleic Acids Research, 2017, 45(18):10534-10554.
[21] BASTA J, RAUCHMAN M. The nucleosome remodeling and deacetylase complex in development and disease[J]. Translational Research:The Journal of Laboratory and Clinical Medicine, 2015, 165(1):36-47.
[22] LAI A Y, WADE P A. Cancer biology and NuRD:A multifaceted chromatin remodelling complex[J]. Nature Reviews.Cancer, 2011, 11(8):588-596.
[23] PEGORARO G, KUBBEN N, WICKERT U, et al. Ageing-related chromatin defects through loss of the NURD complex[J]. Nature Cell Biology, 2009, 11(10):1261-1267.
[24] VASSETZKY N S, BORODULINA O R, USTYANTSEV I G, et al. Analysis of SINE families B2, Dip, and Ves with special reference to polyadenylation signals and transcription terminators[J]. International Journal of Molecular Sciences, 2021, 22(18):9897.
[25] CHEN C, D'ALESSANDRO E, MURANI E, et al. SINE jumping contributes to large-scale polymorphisms in the pig genomes[J]. Mobile DNA, 2021, 12(1):17.
[26] DANIEL C, BEHM M, ÖHMAN M. The role of Alu elements in the cis-regulation of RNA processing[J]. Cellular and Molecular Life Sciences, 2015, 72(21):4063-76.
[27] LUCAS B A, LAVI E, SHIUE L, et al. Evidence for convergent evolution of SINE-directed staufen-mediated mRNA decay[J]. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(5):968-973.
[28] KIM M Y, PARK J, LEE J J, et al. Staufen1-mediated mRNA decay induces requiem mRNA decay through binding of staufen1 to the requiem 3'-UTR[J]. Nucleic Acids Research, 2014, 42(11):6999-7011.
[29] CORREIA DE SOUSA M, GJORGJIEVA M, DOLICKA D, et al. Deciphering miRNAs'action through miRNA editing[J]. International Journal of Molecular Sciences, 2019, 20(24):6249.
[30] ZIV Y, BIELOPOLSKI D, GALANTY Y, et al. Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM-and KAP-1 dependent pathway[J]. Nature Cell Biology, 2006, 8(8):870-876.
[31] GARVIN A J, MORRIS J R. SUMO, a small, but powerful, regulator of double-strand break repair[J]. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 2017, 372(1731):20160281.
[32] GOODARZI A A, KURKA T, JEGGO P A. KAP-1 phosphorylation regulates CHD3 nucleosome remodeling during the DNA double-strand break response[J]. Nature Structural&Molecular Biology, 2011, 18(7):831-839.
[33] KLEMENT K, LUIJSTERBURG M S, PINDER J B, et al. Opposing ISWI-and CHD-class chromatin remodeling activities orchestrate heterochromatic DNA repair[J]. The Journal of Cell Biology, 2014, 207(6):717-733.
[34] LIU B, WANG Z, GHOSH S, et al. Defective ATM-Kap-1-mediated chromatin remodeling impairs DNA repair and accelerates senescence in progeria mouse model[J]. Aging Cell, 2013;12(2):316-318.
[35] QIAN M, LIU Z, PENG L, et al. Boosting ATM activity alleviates aging and extends lifespan in a mouse model of progeria[J]. eLife, 2018, 7:e34836.

Study on 264 bp Structural Variation of 3'-flanking Region of CHD3 Gene in Xiang Pigs

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 13

Recommended Articles

Metrics

Comments

[1]	ZHANG Quanwei, DU Mengmeng, CHENG Ming, DAI Zhenghao, LIU Kaidong, LIN Xiaokun, GAO Ershang, QIN Zhili, ZHAO Jinshan, LI Hegang. Genotypic Analysis of Polled Intersex Syndrome Reproductive Defect Gene in Laoshan Dairy Goats [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 3054-3061.
[2]	LU Huan, NIU Xi, HUANG Yali, LI Sheng, RAN Xueqin, HUANG Shihui, WANG Jiafu. Screening of Candidate miRNA for Regulating Xiang Pig Reproduction [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(9): 3118-3127.
[3]	CHEN Fang, SUN Manxi, WANG Zhiyong, LIU Chang, HUANG Shihui, WANG Jiafu, RAN Xueqin, NIU Xi. Association Analysis of Structural Variation of ADCY3 and IGF1 Genes with Reproductive Traits in Xiang Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(8): 2920-2927.
[4]	SUN Manxi, CHEN Fang, WANG Zhiyong, LIU Chang, HUANG Shihui, LI Sheng, NIU Xi, WANG Jiafu, RAN Xueqin. Polymorphisms of Two Structural Variant in MAPK Signaling Pathway and Its Association Analysis with Growth Traits in Xiang Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(7): 2448-2456.
[5]	HUANG Yali, NIU Xi, LU Huan, HUANG Shihui, WANG Jiafu, RAN Xueqin, LI Sheng. Identification and Function Prediction Analysis of circ_CSPP1 in Ovarian Tissues of Xiang Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(11): 4055-4066.
[6]	MO Jiayuan, GAO Jiuyu, FENG Lingli, LI Yueyue, TIAN Weilong, LIU Xiaoxiao, CHENG Feng, LIANG Liang, LEI Shuqiao, WEN Wei, LIANG Jing, LAN Ganqiu. Genome-wide Association Study on Alive Litter Size Trait in Bama Xiang Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(12): 3965-3975.
[7]	MA Lina, YANG Jinbo, DING Yifei, LI Yingkang. Research Progress on Three Generations Sequencing Technology and Its Application [J]. , 2019, 46(8): 2246-2256.
[8]	LIU Xiaoli, RAN Xueqin, LIU Chang, NIU Xi, HUANG Shihui, WANG Jiafu. Study on Structural Variation WIF1-I8-sv889 of WIF1 Gene in Xiang Pig with Wrinkled Skin [J]. , 2019, 46(8): 2423-2430.
[9]	WANG Weiyong, GONG Ting, WANG Tingting, XU Yongjian, MENG Lijie. Morphological Analysis of Spermatogenic Epithelial Cycle and Testicular Development in Congjiang Xiang Pigs [J]. , 2019, 46(7): 2012-2020.
[10]	LI Dapeng, RUAN Yiqi, LIU Chang, NIU Xi, HUANG Shihui, RAN Xueqin, WANG Jiafu. Study on the Population Distribution of Two SV Sites in BOLL and STRA8 Genes of Three Indigenous Pig Breeds [J]. , 2018, 45(6): 1599-1607.
[11]	XU Yao, LIU Chang, NIU Xi, RAN Xue-qin, WANG Jia-fu. Polymorphism of FSHR Gene Exon 10 and Its Relationship with the Litter Size of Xiang Pigs [J]. , 2017, 44(3): 799-806.
[12]	GU Li-ju, YAN Zhi-hong, ZHANG Yi-yu, ZHANG Yun, LIU Hua-jun, CHEN Hong-guang. Effects of Partial Substitution of Basal Diet with Wild Buckwheat on Fatty Acids and Amino Acids in Congjiang Xiang Pigs [J]. , 2016, 43(3): 689-694.
[13]	ZHAO Jia-fu;XU Hou-qiang;ZHANG Yong;CHEN Xiang;YU Ding-biao;NIE Yu-li;WU Xuan;DUAN Li-xia;WU Pei-lu. The Comparison of Guizhou Baixiang Pigs with Three Kinds of Hybrid Pigs on Organ Coefficient and Blood Physiological Indexes [J]. , 2011, 38(2): 56-59.