骨质疏松易感SNP rs4325274通过增强子远程调控SOX6基因的功能机制研究

doi:10.16288/j.yczz.20-098

[an error occurred while processing this directive]

Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (9): 889-897.doi: 10.16288/j.yczz.20-098

• Research Article • Previous Articles Next Articles

The osteoporosis susceptible SNP rs4325274 remotely regulates the SOX6 gene through enhancers

Xiaomei Tuo¹, Dongli Zhu^1,², Xiaofeng Chen¹, Yu Rong¹, Yan Guo¹, Tielin Yang^1,²()

^1. Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049;
^2. Research Institute of Zhejiang Xi'an Jiaotong University, Hangzhou 311215

Received:2020-05-26 Revised:2020-09-04 Online:2020-09-20 Published:2020-09-07
Contact: Yang Tielin E-mail:yangtielin@xjtu.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China No(31771399);Supported by the National Natural Science Foundation of China No(31970569);China PostdoctoralScience Foundation No(2019M650261);Natural Science Basic Research Plan in Shaanxi Province of China No(2020JQ-026);the Zhejiang Provincial Natural Science Foundation of China No(GF18C060003)

Abstract

Abstract:

Osteoporosis is a typical polygenic disease, and its heritability is as high as 85%. The incidence of osteoporosis has jumped to the fifth among the common diseases. Although a large number of osteoporosis-susceptible SNPs have been identified, most of them are in the non-coding regions of the genome and the functional mechanisms are unknown. The purpose of this study was to explore the function of non-coding osteoporosis-susceptible SNP rs4325274 and dissect the molecular regulatory mechanisms through integrating bioinformatics analysis and functional experiments. Firstly, we found the SNP rs4325274 resided in a putative enhancer element through functional annotation. eQTL and Hi-C analysis found that the SOX6 gene might be a potential distal target of rs4325274. We conducted the motif prediction using multiple databases and verified the result using ChIP-seq data from GEO database. The result showed that the transcription factor HNF1A could preferentially bind to SNP rs4325274-G allele. We further demonstrated that SNP rs4325274 acted as an enhancer regulating SOX6 gene expression by using dual-luciferase reporter assays. Knockdown of HNF1A decreased the SOX6 gene expression. Taken together, our results uncovered a new mechanism of a non-coding functional SNP rs4325274 as a distal enhancer to modulate SOX6 expression, which provides new insights into deciphering molecular regulatory mechanisms underlying non-coding susceptibility SNPs on complex diseases.

Key words: SNP rs4325274, SOX6 gene, transcription factor, mechanism of osteoporosis

Xiaomei Tuo, Dongli Zhu, Xiaofeng Chen, Yu Rong, Yan Guo, Tielin Yang. The osteoporosis susceptible SNP rs4325274 remotely regulates the SOX6 gene through enhancers[J]. Hereditas(Beijing), 2020, 42(9): 889-897.

Figures/Tables 8

Table 1

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Fig. 5

Fig. 6

Fig. 7

References 30

[1]	Lamichhane AP . Osteoporosis-an update. JNMA J Nepal Med Assoc, 2005,44(158):60-66. pmid: 16568580
[2]	Reginster JY, Burlet N . Osteoporosis: a still increasing prevalence. Bone, 2006,38(2 Suppl. 1):S4-9. doi: 10.1016/j.bone.2005.11.024 pmid: 16455317
[3]	Morales-Torres J , Gutiérrez-UreñaS.The burden of osteoporosis in latinamerica. OsteoporosInt, 2004,15(8):625-632.
[4]	Nguyen TV, Center JR, Eisman JA . Osteoporosis: underrated, underdiagnosed and undertreated. Med J Aust, 2004,180(S5):S18-22. pmid: 14984358
[5]	Smits P, Li P, Mandel J, Zhang ZP, Deng JM, Behringer RR, de Crombrugghe B, Lefebvre V,. The transcription factors L-Sox5 and Sox6 are essential for cartilage formation. Dev Cell, 2001,1(2):277-290. doi: 10.1016/s1534-5807(01)00003-x pmid: 11702786
[6]	Smits P, Dy P, Mitra S, Lefebvre V . Sox5 and Sox6 are needed to develop and maintain source, columnar, and hypertrophic chondrocytes in the cartilage growth plate. J Cell Biol, 2004,164(5):747-758. doi: 10.1083/jcb.200312045 pmid: 14993235
[7]	Renard E, Porée B, Chadjichristos C, Kypriotou M, Maneix L, Bigot N, Legendre F, Ollitrault D, De Crombrugghe B, Malléin-Gérin F, Moslemi S, Demoor M, Boumediene K, Galéra P . Sox9/Sox6 and Sp1 are involved in the insulin-like growth factor-I-mediated upregulation of human type II collagen gene expression in articular chondrocytes. J Mol Med (Berl), 2012,90(6):649-666. doi: 10.1007/s00109-011-0842-3
[8]	Liu J, Wang HW, Chen Y, Yu HL, Wang Q, Yang HF, Ma JX, Xiang LB . Regulatory effect of SOX6 and SOX9 on the growth and differentiation properties into chondrocytes of MPCs in primary OA articular cartilage. J Reg Anat Oper Surg, 2014, ( 5):477-481.
	刘军, 王洪伟, 陈语, 于海龙, 王琪, 杨会峰, 马骏雄, 项良碧 . SOX6和SOX9基因转染对人原发性骨关节炎关节软骨间充质祖细胞增殖和成软骨分化的调控作用. 局解手术学杂志, 2014, ( 5):477-481.
[9]	Zhang Y, Yang TL, Li X, Guo Y . Functional analyses reveal the essential role of SOX6 and RUNX2 in the communication of chondrocyte and osteoblast. OsteoporosInt, 2015,26(2):553-561.
[10]	Livshits G, Deng HW, Nguyen TV, Yakovenko K, Recker RR, Eisman JA, . Genetics of bone mineral density: evidence for a major pleiotropic effect from an intercontinental study. J Bone Miner Res, 2004,19(6):914-923. doi: 10.1359/JBMR.040132 pmid: 15125790
[11]	Peacock M, Turner CH, Econs MJ, Foroud T . Genetics of osteoporosis. Endocr Rev, 2002,23(3):303-326. doi: 10.1210/edrv.23.3.0464 pmid: 12050122
[12]	Rivadeneira F, Styrkársdottir U, Estrada K, Halldórsson BV, Hsu YH, Richards JB, Zillikens MC, Kavvoura FK, Amin N, Aulchenko YS, Cupples LA, Deloukas P, Demissie S, Grundberg E, Hofman A, Kong A, Karasik D, van Meurs JB, Oostra B, Pastinen T, Pols HA, Sigurdsson G, Soranzo N, Thorleifsson G, Thorsteinsdottir U, Williams FM, Wilson SG, Zhou YH, Ralston SH, van Duijn CM, Spector T, Kiel DP, Stefansson K, Ioannidis JP, Uitterlinden AG. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. Nat Genet, 2009,41(11):1199-1206. doi: 10.1038/ng.446 pmid: 19801982
[13]	Hsu YH, Zillikens MC, Wilson SG, Farber CR, Demissie S, Soranzo N, Bianchi EN, Grundberg E, Liang LM, Richards JB, Estrada K, Zhou YH, van Nas A, Moffatt MF, Zhai GJ, Hofman A, van Meurs JB, Pols HA, Price RI, Nilsson O, Pastinen T, Cupples LA, Lusis AJ, Schadt EE, Ferrari S, Uitterlinden AG, Rivadeneira F, Spector TD, Karasik D, Kiel DP,. An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits. PLoS Genet, 2010,6(6):e1000977. doi: 10.1371/journal.pgen.1000977 pmid: 20548944
[14]	Tan LJ, Liu R, Lei SF, Pan R, Yang TL, Yan H, Pei YF, Yang F, Zhang F, Pan F, Zhang YP, Hu HG, Levy S, Deng HW . A genome-wide association analysis implicates SOX6 as a candidate gene for wrist bone mass. Sci China Life Sci, 2010,53(9):1065-1072. doi: 10.1007/s11427-010-4056-7 pmid: 21104366
[15]	Villalobos-Comparán M, Jiménez-Ortega RF, Estrada K, Parra-Torres AY, González-Mercado A, Patiño N, Castillejos- López M, Quiterio M, Fernandez-López JC, Ibarra B, Romero-Hidalgo S, Salmerón J, Velázquez-Cruz R . A pilot genome-wide association study in postmenopausal mexican- mestizo women implicates the RMND1/CCDC170 locus is associated with bone mineral density. Int J Genomics, 2017,2017:5831020. doi: 10.1155/2017/5831020 pmid: 28840121
[16]	Morris JA, Kemp JP, Youlten SE, Laurent L, Logan JG, Chai RC, Vulpescu NA, Forgetta V, Kleinman A, Mohanty ST, Sergio CM, Quinn J, Nguyen-Yamamoto L, Luco AL, Vijay J, Simon MM, Pramatarova A, Medina-Gomez C, Trajanoska K, Ghirardello EJ, Butterfield NC, Curry KF, Leitch VD, Sparkes PC, Adoum AT, Mannan NS, Komla-Ebri DSK, Pollard AS, Dewhurst HF, Hassall TAD, Beltejar MG, Adams DJ, Vaillancourt SM, Kaptoge S, Baldock P, Cooper C, Reeve J, Ntzani EE, Evangelou E, Ohlsson C, Karasik D, Rivadeneira F, Kiel DP, Tobias JH, Gregson CL, Harvey NC, Grundberg E, Goltzman D, Adams DJ, Lelliott CJ, Hinds DA, Ackert-Bicknell CL, Hsu YH, Maurano MT, Croucher PI, Williams GR, Bassett JHD, Evans DM, Richards JB . An atlas of genetic influences on osteoporosis in humans and mice. Nat Genet, 2019,51(2):258-266. doi: 10.1038/s41588-018-0302-x pmid: 30598549
[17]	Medina-Gomez C, Kemp JP, Trajanoska K, Luan J, Chesi A, Ahluwalia TS, Mook-Kanamori DO, Ham A, Hartwig FP, Evans DS, Joro R, Nedeljkovic I, Zheng HF, Zhu K, Atalay M, Liu CT, Nethander M, Broer L, Porleifsson G, Mullin BH, Handelman SK, Nalls MA, Jessen LE, Heppe DHM, Richards JB, Wang C, Chawes B, Schraut KE, Amin N, Wareham N, Karasik D, Van der Velde N, Ikram MA, Zemel BS, Zhou YH, Carlsson CJ, Liu Y, McGuigan FE, Boer CG, Bønnelykke K, Ralston SH, Robbins JA, Walsh JP, Zillikens MC, Langenberg C, Li-Gao R, Williams FMK, Harris TB, Akesson K, Jackson RD, Sigurdsson G, den Heijer M, van der Eerden BCJ, van de Peppel J, Spector TD, Pennell C, Horta BL, Felix JF, Zhao JH, Wilson SG, de Mutsert R, Bisgaard H, Styrkársdóttir U, Jaddoe VW, Orwoll E, Lakka TA, Scott R, Grant SFA, Lorentzon M, van Duijn CM, Wilson JF, Stefansson K, Psaty BM, Kiel DP, Ohlsson C, Ntzani E, van Wijnen AJ, Forgetta V, Ghanbari M, Logan JG, Williams GR, Bassett JHD, Croucher PI, Evangelou E, Uitterlinden AG, Ackert-Bicknell CL, Tobias JH, Evans DM, Rivadeneira F. Life-Course genome-wide association study meta-analysis of total body BMD and assessment of age-specific effects. Am J Hum Genet, 2018,102(1):88-102. doi: 10.1016/j.ajhg.2017.12.005 pmid: 29304378
[18]	Chau D, Ng K, Chan TS, Cheng YY, Fong B, Tam S, Kwong YL, Tse E . Azacytidine sensitizes acute myeloid leukemia cells to arsenic trioxide by up-regulating the arsenic transporter aquaglyceroporin 9. J Hematol Oncol, 2015,8:46. doi: 10.1186/s13045-015-0143-3 pmid: 25953102
[19]	Pelletier L, Rebouissou S, Paris A, Rathahao-Paris E, Perdu E, Bioulac-Sage P, Imbeaud S, Zucman-Rossi J . Loss of hepatocyte nuclear factor 1alpha function in human hepatocellular adenomas leads to aberrant activationof signaling pathways involved in tumorigenesis. Hepatology, 2010,51(2):557-566. doi: 10.1002/hep.23362 pmid: 20041408
[20]	Krijger PHL, de Laat W . Regulation of disease-associated gene expression in the 3D genome. Nat Rev Mol Cell Biol, 2016,17(12):771-782. doi: 10.1038/nrm.2016.138 pmid: 27826147
[21]	Lane JM, Russell L, Khan SN . Osteoporosis. Clin Orthop Relat Res, 2000, ( 327):139-150.
[22]	Boudin E, Fijalkowski I, Hendrickx G, Van Hul W . Genetic control of bone mass. Mol Cell Endocrinol, 2016,432:3-13. doi: 10.1016/j.mce.2015.12.021 pmid: 26747728
[23]	Huang QY . Genetic study of complex diseases in the post-GWAS era. J Genet Genomics, 2015,42(3):87-98. doi: 10.1016/j.jgg.2015.02.001 pmid: 25819085
[24]	ENCODE Project Consortium . An integrated encyclopedia of DNA elements in the human genome. Nature, 2012,489(7414):57-74. doi: 10.1038/nature11247
[25]	Ding N, Qu HZ, Fang XD . The ENCODE project and functional genomics studies. Hereditas(Beijing), 2014,36(3):237-247.
	丁楠, 渠鸿竹, 方向东 . ENCODE计划和功能基因组研究. 遗传, 2014,36(3):237-247.
[26]	Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA . The NIH roadmap epigenomics mapping consortium. Nat Biotechnol, 2010,28(10):1045-1048. doi: 10.1038/nbt1010-1045 pmid: 20944595
[27]	Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET . Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science, 2013,342(6159):744-747. doi: 10.1126/science.1242463
[28]	Xiao SM, Gao Y, Cheung CL, Bow CH, Lau KS, Sham PC, Tan KC, Kung AW . Association of CDX1 binding site of periostin gene with bone mineral density and vertebral fracture risk. OsteoporosInt, 2012,23(7):1877-1887.
[29]	Xiao SM, Kung AW, Gao Y, Lau KS, Ma A, Zhang ZL, Liu JM, Xia W, He JW, Zhao L, Nie M, Fu WZ, Zhang MJ, Sun J, Kwan JS, Tso GH, Dai ZJ, Cheung CL, Bow CH, Leung AY, Tan KC, Sham PC . Post-genome wide association studies and functional analyses identify association of MPP7 gene variants with site-specific bone mineral density. Hum Mol Genet, 2012,21(7):1648-1657. doi: 10.1093/hmg/ddr586
[30]	Zhu DL, Chen XF, Hu WX, Dong SS, Lu BJ, Rong Y, Chen YX, Chen H, Thynn HN, Wang NN, Guo Y, Yang TL . Multiple functional variants at 13q14 risk locus for osteoporosis regulate RANKL expression through long- range super-enhancer. J Bone Miner Res, 2018,33(7):1335-1346. doi: 10.1002/jbmr.3419 pmid: 29528523

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

引物名称	引物序列(5?→3?)
SOX6启动子扩增引物	上游：CCCAAGCTTATGGTGCCGATAGACTTGCC(Hind III)
SOX6启动子扩增引物	下游：CCGCTCGAGCATCTTATGGGTTCCACGCCT(Xho I)
SNP扩增引物	上游：CGACGCGTAGAAGAGAAACGAGGTGTTGGT(Mlu I)
SNP扩增引物	下游：CCGCTCGAGACAAGTTTAGTGGGACAGGGTT(Xho I)
SNP突变引物	上游：GGGATCCTGCTTACTTACTATCTTTGGTCTTAAACTAGACC
SNP突变引物	下游：TAAGTAAGCAGGATCCCGATATCAAGTACCAGG
SNP分型引物	上游：AAGAGAAACGAGGTGTTGGTGAT
SNP分型引物	下游：GGTATCTTCCGTGCAGTTTTGG
SOX6qRT-PCR引物	上游：AGAACGCGCTTTGAGAATTT
SOX6qRT-PCR引物	下游：GCCCAGTTTTCCATCTTCAT
HNF1AqRT-PCR引物^[18]	上游：CCCCAGATTCAGGATCAGACA
HNF1AqRT-PCR引物^[18]	下游：CCATCATGTTCCATTTTTCGC

The osteoporosis susceptible SNP rs4325274 remotely regulates the SOX6 gene through enhancers

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 8

References 30

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Fengyu Sun, Qianghua Xu. Research progress of microRNAs involved in hematopoiesis [J]. Hereditas(Beijing), 2022, 44(9): 756-771.
[2]	Rongrong Mu, Qingqing Niu, Yuqiang Sun, Jun Mei, Meng Miao. Cloning and characterization of the MYB transcription factor gene GhTT2 in Gossypium hirsutum [J]. Hereditas(Beijing), 2022, 44(8): 720-728.
[3]	Menggang Lv, Aijia Liu, Qingwei Li, Peng Su. Progress on the origin, function and evolutionary mechanism of RHR transcription factor family [J]. Hereditas(Beijing), 2021, 43(3): 215-225.
[4]	Xiaofen Qiu, Dong’e Tang, Haiyan Yu, Qiuyan Liao, Zhiyang Hu, Jun Zhou, Xin Zhao, Huiyan He, Zhuojian Liang, Chengming Xu, Ming Yang, Yong Dai. Analysis of transcription factors in accessible open chromatin in the 18-trisomy syndrome based on single cell ATAC sequencing technique [J]. Hereditas(Beijing), 2021, 43(1): 74-83.
[5]	Jie Wu, Jianping Quan, Yong Ye, ZhenFang Wu, Jie Yang, Ming Yang, Enqin Zheng. Advances in assay for transposase-accessible chromatin with high-throughput sequencing [J]. Hereditas(Beijing), 2020, 42(4): 333-346.
[6]	Taotao Wang, Yong Yang, Wei Wei, Chentao Lin, Liuyin Ma. Identification and expression analyses of the NAC transcription factor family in Spartina alterniflora [J]. Hereditas(Beijing), 2020, 42(2): 194-211.
[7]	Zhaoqing Sun, Bo Yan. The roles and regulation mechanism of transcription factor GATA6 in cardiovascular diseases [J]. Hereditas(Beijing), 2019, 41(5): 375-383.
[8]	Haoqiang Yu,Fuai Sun,Wenqi Feng,Fengzhong Lu,Wanchen Li,Fengling Fu. The BES1/BZR1 transcription factors regulate growth, development and stress resistance in plants [J]. Hereditas(Beijing), 2019, 41(3): 206-214.
[9]	Junyi Ju,Quan Zhao. Regulation of γ-globin gene expression and its clinical applications [J]. Hereditas(Beijing), 2018, 40(6): 429-444.
[10]	Junxia Zou, Ke Chen. Roles and molecular mechanisms of hypoxia-inducible factors in renal cell carcinoma [J]. Hereditas(Beijing), 2018, 40(5): 341-356.
[11]	Qingqian Ding,Xiaoting Wang,Liqin Hu,Xin Qi,Linhao Ge,Weiya XU,Zhaoshi Xu,Yongbin Zhou,Guanqing Jia,Xianmin Diao,Donghong Min,Youzhi Ma,Ming Chen. MYB-like transcription factor SiMYB42 from foxtail millet (Setaria italica L.) enhances Arabidopsis tolerance to low-nitrogen stress [J]. Hereditas(Beijing), 2018, 40(4): 327-338.
[12]	Lan Ren,Rudan Xiao,Qian Zhang,Xiaomin Lou,Zhaojun Zhang,Xiangdong Fang. Synergistic regulation of the erythroid differentiation of K562 cells by KLF1 and KLF9 [J]. Hereditas(Beijing), 2018, 40(11): 998-1006.
[13]	Ling Zhang, Jianbo He. Progress of GATA6 in liver development [J]. Hereditas(Beijing), 2018, 40(1): 22-32.
[14]	Min Yue, Yu Yang, Gaili Guo, Ximing Qin. Genetic and epigeneticregulations of mammalian circadian rhythms [J]. Hereditas(Beijing), 2017, 39(12): 1122-1137.
[15]	Wenya Guo,Yanmei Cui,Tingting Wang,Deyue YU,Fang Huang. Functional analysis of flower development related gene GsLFY from Glycine soja [J]. Hereditas(Beijing), 2017, 39(1): 56-65.