西南矮马矮小性状基因SHOX的克隆测序和多态性研究
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摘要
本研究以不同类型西南矮马为研究对象,参考着GenBank中已发表物种的矮小性状基因SHOX的序列,利用PCR技术,首次克隆了7个类型西南马矮小性状基因SHOX的部分序列。其中,德保马的序列提交到了GenBank中,登录号为:EU556739。此外,对7个类型西南马的矮小性状基因序列及核苷酸组成进行了初步研究,同时采用PCR-SSCP技术和PCR产物直接测序等方法,采用纯种设特兰矮马(ST,3只)作为对照组,对各类型西南马SHOX基因序列进行了多态性分析。研究结果表明:
1、克隆所得的序列长度为520bp,包含着CDS的部分序列。
2、通过GenBank中的Blast软件对此序列进行同源性比较以后发现,与人的矮小性状基因SHOX有95%的相似性。并通过DNAman等软件比较发现此片段主要是马矮小性状基因SHOX的第2外显子部分。
3、将序列提交到了GenBank,登陆号为EU556739。
4、西南马SHOX基因序列核苷酸组成富含GC,且马与其它物种的SHOX基因密码子在第2外显子上核苷酸均偏向使用G和C。
5、PCR-SSCP分析结果表明,在克隆所得序列上选择的两个位点中P2位点出现了多态性,经测序得知在第268处有一个G→A的突变,在431处有一个T→G的突变,由此导致等位基因B变为等位基因A。该位点除云南文山马的优势基因型和优势等位基因为BB型和B外,其余类群马均为AB型,且X2检验结果表明:云南丘北马、云南文山马、云南大理马、建昌马和设特兰马在P2位点上处于Hardy-Weinberg平衡状态。
6、不同类型马SHOX基因P2位点的纯合度(Ho)、杂合度(He)、有效等位基因数(Ne)及多态信息含量(PIC)分析表明:云南文山马的多态信息含量最高,并且处于高度多态(PIC>0.5),其它类型马(除设特兰马外)均为中度多态。
Referencing by the SHOX gene sequence in GenBank, Seven types of Xinan pony SHOX gene sequence containing partial CDS sequence were firstly cloned and sequenced using the PCR technique.The sequence of DB horse was submitted to GenBank.Its accession is EU556739.The compositions of nucleotide of SHOX gene was analysed.The polymorphisms of SHOX gene of different horse groups were analyzed by PCR-SSCP and directly sequencing of PCR products. The results were as follows:
1、The sequence of cloned pony SHOX gene was 520bp in length, included partial CDS sequence.
2、The homology analysis of this sequence by BLAST software in GenBank showed that this sequence has 95% identity with homo sapiens SHOX gene sequence, and analysis by the DNAman indicated that this region was mainly Exon2.
3、Submitted this sequence to the GenBank, and its accession number is EU556739.
4、The analysis of nucleotide composition showed that G/C content was abundant in horse SHOX gene,and in exon 2 of different species,the bases of biased were all G and C.
5、The analysis of PCR-SSCP showed that P2 site existed variations. The transversion of G→A in 268 and T→G in 431 led allelomorphic gene B→A. The dominant allele and genetype of WS were BB type and B, and the dominant allele and genetype of other horse types were AB. P2 site was in Hardy-Weinberg equilibrium in QB horse, WS horse ,JC horse and ST horse (P>0.05).
6、Analysis result of the genetic polymorphism parameters of different horse groups at P2 site showed: Polymorphism of WS was very abundant at this site.
1、克隆所得的序列长度为520bp,包含着CDS的部分序列。
2、通过GenBank中的Blast软件对此序列进行同源性比较以后发现,与人的矮小性状基因SHOX有95%的相似性。并通过DNAman等软件比较发现此片段主要是马矮小性状基因SHOX的第2外显子部分。
3、将序列提交到了GenBank,登陆号为EU556739。
4、西南马SHOX基因序列核苷酸组成富含GC,且马与其它物种的SHOX基因密码子在第2外显子上核苷酸均偏向使用G和C。
5、PCR-SSCP分析结果表明,在克隆所得序列上选择的两个位点中P2位点出现了多态性,经测序得知在第268处有一个G→A的突变,在431处有一个T→G的突变,由此导致等位基因B变为等位基因A。该位点除云南文山马的优势基因型和优势等位基因为BB型和B外,其余类群马均为AB型,且X2检验结果表明:云南丘北马、云南文山马、云南大理马、建昌马和设特兰马在P2位点上处于Hardy-Weinberg平衡状态。
6、不同类型马SHOX基因P2位点的纯合度(Ho)、杂合度(He)、有效等位基因数(Ne)及多态信息含量(PIC)分析表明:云南文山马的多态信息含量最高,并且处于高度多态(PIC>0.5),其它类型马(除设特兰马外)均为中度多态。
Referencing by the SHOX gene sequence in GenBank, Seven types of Xinan pony SHOX gene sequence containing partial CDS sequence were firstly cloned and sequenced using the PCR technique.The sequence of DB horse was submitted to GenBank.Its accession is EU556739.The compositions of nucleotide of SHOX gene was analysed.The polymorphisms of SHOX gene of different horse groups were analyzed by PCR-SSCP and directly sequencing of PCR products. The results were as follows:
1、The sequence of cloned pony SHOX gene was 520bp in length, included partial CDS sequence.
2、The homology analysis of this sequence by BLAST software in GenBank showed that this sequence has 95% identity with homo sapiens SHOX gene sequence, and analysis by the DNAman indicated that this region was mainly Exon2.
3、Submitted this sequence to the GenBank, and its accession number is EU556739.
4、The analysis of nucleotide composition showed that G/C content was abundant in horse SHOX gene,and in exon 2 of different species,the bases of biased were all G and C.
5、The analysis of PCR-SSCP showed that P2 site existed variations. The transversion of G→A in 268 and T→G in 431 led allelomorphic gene B→A. The dominant allele and genetype of WS were BB type and B, and the dominant allele and genetype of other horse types were AB. P2 site was in Hardy-Weinberg equilibrium in QB horse, WS horse ,JC horse and ST horse (P>0.05).
6、Analysis result of the genetic polymorphism parameters of different horse groups at P2 site showed: Polymorphism of WS was very abundant at this site.
引文
1 刘建文,动物生长轴的激素调控,畜牧兽医学报,2006,2:12-13;
2 刘德武,猪神经内分泌生长轴各因子及相关基因的研究进展,农业生物技术学报 2004 01 期;
3 Attie KM, julius JR , stoppani C , et al . National cooperative growth study substudy V: the clinic utility of growth - hormone- binding protein , insulin - like growth factor I , and insulin -like growth factor - binding protein 3measurements [J ] . Journal of pediatrics ,1997 ,131(1) - part 2 :s56 - s601
4 Binder G, Schwarze CP ,Ranke MB Identification of short stature caused by SHOX defects and threapeutic effect of recombinant human growth hormone[J ] . The Journal of Clinical Endocrinology Metabolism ,2001
5 Rao E , Weiss B , Fukami M, et al . Pseudoautosomal deletions encompassing a novel homeobox gene cause growth failure in idiopathic short stature and Turner syndrome [ J ] . Nat Genet ,1997 ,16 :54 – 631
6 Ogata T1SHOX: Pseudoautosomal homeobox containing gene for short stature and dyschondrosteosis [J ] . Growth Horm IGF Res1999 , 9(Suppl B) :53 – 571
7 孙逊,朱尚权. 生长激素的结构与功能.国外医学,生理、病理科学与临床分册,1999,19(1):
8 贺淹才. 生长激素和生长激素受体的分子生物学.生命的化学,2002,22(1):29-32;
9 王星, 吴红专, 贺东生, 等. 鸡生长激素研究进展[J]. 中国家禽, 1998, 20(10): 25-26.
10 曾礼华, 周安国, 杨凤. 动物生长激素与肉畜生产[J]. 动物营养学报, 1999, 11(4): 1-8.
11 Attie KM. Genetic studies in idiopathic short stature [J ] . Current Opinion In Pediatrics ,2000 ,12 :400 - 4041
12 生长激素受体基因单核苷酸多态性与特发性矮小的相关性,医学综述,2007,13(11),833～834;
13 Chan J M, Stampfer M J, Giovanucci E, et al. Plasma insulin-like growth factor-I and prostate cancer risk: a prospective study[J]. Science, 1998, 279: 563-566.
14 Clement-JonesM,Schiller S,Rao E,et al.The short stature homeobox gene SHOX is involved in skeletal abnormalities in Turner syndrome[J].HumMol Genet,2000,9(5):695-702.
15 Deng HW,Xu FH,Liu YZ,et a1.A whole-genome linkage scan suggests several genomic regions potentially containing QTIs underlying the variation of stature[J].Am J Med Genet,2002,113(1):29-39.
16 Hirschhorn JN,Lindgren CM,DaIy MJ,et al.Genomewide linkage analysis of stature in multiple populations reveals several regions with evidence of linkageto adult height[J].Am J Hum Genet,2001,69(1):106-116.
17 陈晓丽 特发性矮小的相关基因研究进展,国外医学妇幼保健,2002 年第 13 卷第 5 期
18 Zuffardi, O.; Maraschio, P.; Lo Curto, F.; Muller, U.; Giarola, A.; Perotti, L. :The role of Yp in sex determination: new evidence from X/Y translocations. Am. J. Med. Genet. 12: 175-184, 1982.
19 Ogata, T.; Goodfellow, P.; Petit, C.; Aya, M.; Matsuo, N. : Short stature in a girl with a terminal Xp deletion distal to DXYS15: localisation of a growth gene(s) in the pseudoautosomal region. J. Med. Genet. 29: 455-459, 1992.
20 Ogata, T.; Petit, C.; Rappold, G.; Matsuo, N.; Matsumoto, T.; Goodfellow, P. : Chromosomal localisation of a pseudoautosomal growth gene(s). J. Med. Genet. 29: 624-628, 1992.
21 Ellison, J. W.; Wardak, Z.; Webster, M.; Chiong, W. : PHOG, a candidate gene for involvement in the short stature of Turner syndrome. (Abstract) Am. J. Hum. Genet. 59 (suppl.): A32, 1996.
22 Rao, E.; Weiss, B.; Fukami, M.; Mertz, A.; Meder, J.; Ogata, T.; Heinrich, U.; Garcia-Heras, J.; Schiebel, K.; Rappold,A. :FISH-deletion mapping defines a 270-kb short stature critical interval in the pseudoautosomal region PAR1 on human sex chromosomes. Hum. Genet. 100: 236-239, 1997.
23 Kawai M,Momoi T,Yorifuji T,et a1,Unfavorable effects of growth hormone treatment on final height of boys with short sture not caused by growth hormone deficiency[J].J Pediatrics,1997,130:205.
24 Blaschke 1tJ, Monaghan AP, Schiller S .SHOT, a SHOX-related homeobox gene, is implicated in craniofacial, brain, heart, and limb development .Genetics, 1998, 95 :240f}2411.
25 Clement-JonesM,Schiller S,Rao E,et al.The short stature homeobox gene SHOX is involved in skeletal abnormalities in Turner syndrome[J].HumMol Genet,2000,9(5):695-702.
26 Rao, E.; Blaschke, R. J.; Marchini, A.; Niesler, B.; Burnett, M.; Rappold, G. A. : The Leri-Weill and Turner syndrome homeobox gene SHOX encodes a cell-type specific transcriptional activator. Hum. Molec. Genet. 10: 3083-3091, 2001.
27 Wilson D.Sheng ,G.,(1993); Cooperative dimerization of paired class homeodomain dimmer on DNA.Genes Dev,.7,2120-2134 .
28 Blaschke RJ,Topfer C,Marchini A,et a1.Transcriptional and translational regulation of the Leri-Weill and Turner syndrome homeobox gene SHOX[J].J Biol Chem,2003,278(48):47820-47826.
29 Munns CJ, Haase HR, Crowther LM, et al. Expression of SHOX in human fetal and childhood growth plate.J Clin Endocrinol Metab,2004,89(8):4130-5.
30 Marchini A, Marttila T, Winter A, et al.The short stature homeodomain protein SHOX induces cellular growth arrest and apoptosis and is expressed in human growth plate chondrocytes.J Biol Chem,2004,279(35):37103-14.
31 Rao E,Blaschke RJ,Marchini A,et a1.TheLeri-Weill and Turner syndrome homeobox gene SHOX encodes a cell-type specific transcriptional activator [J].Hum Mol Genet,2001,10(26):3083-3091.
32 Sabherwal N, Schneider KU, Blaschke RJ, et al. Impairment of SHOX nuclear localization as a cause for Leri-Weill syndrome.J Cell Sci, 2004,117(14):3041-8.
33 Niesler B,Fischer C,Rappold, human SHOX mutation database[J].Hum Mutat ,2002,20(5):338-341.
34 Sabherwal N, Blaschke RJ, Marchini A, et a1.A novel point mutation A170P in the SHOX gene defines impaired nuclear translocation as a molecular cause for Lzri-Weill dyschondrosteosis and Langer dysplasia.J Med Genet,2004,41(6):e83.
35 Kanaka-Gantenbein C, Kitsiou S, Mavrou A, et a1.Ta11 stature, insulin resistance, and disturbed behavior in a girl with the triple X syndrome harboring three SHOX genes: offspring of a father with mosaic Klinefelter syndrome but with two maternal X chromosomes.Horm Res,2004,61(5):205-10.
36 林剑军,109 例身材矮小儿童骨龄分析,广西医科大学学报 ,2006 年 01 期
37 Ogata T, Matsuo N, Fukushima Y, et al. FISH analysis for apparently simple terminal deletions of the X chromosome: identification of hidden structural abnormalities.Am J Med Genet,2001,104(4):307-311.
38 Morizio E, Stuppia L, Gatta V, et al. Deletion of the SHOX gene in patients with short stature of unknown cause.Am J Med Genet,2003,119A(3):293-296.
39 Rappold GA, Fukami M, Niesler B,et al. Deletions of the homeobox gene SHOX (short stature homeobox) are an important cause of growth failure in children with short stature.J Clin Endocrinol Metab,2002,87(3):1402-1406.
40 Ezquieta B, Cueva E, Oliver A, et al. SHOX haploinsufficiency SHOX intragenic microsatellite analysis in patients with short stature.J Pediatr Endocrinol Metab,2002,15(2):139-48.
41 Ogata T. SHOX haploinsufficiency and its modifying factors.J Pediatr Endocrinol Metab,2002 Dec;15 Suppl 5:1289-94. Review.
42 Munns CF, Glass IA, Flanagan S, et al. Familial growth and skeletal features associated with SHOX haploinsufficiency. J Pediatr Endocrinol Metab, 2003,16(7):987-96.
43 Fukami M, Nishi Y, Hasegawa Y, et al. 5tatural growth in 31 Japanese patients with SHOX haploinsufficiency: support for a disadvantageous effect of gonadal estrogens.Endocr J,2004,51(2):197-200.
44 Ogata T, Kosho T, Wakui K, et al. Short Stature Homeobox-Containing Gene Duplication on the der(X) Chromosome in a Female with 45,X/46,X,der(X), Gonadal Dysgenesis, and Tall Stature J Clin Endocrinol Metab, 2000, 85:2927-2930.
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2 刘德武,猪神经内分泌生长轴各因子及相关基因的研究进展,农业生物技术学报 2004 01 期;
3 Attie KM, julius JR , stoppani C , et al . National cooperative growth study substudy V: the clinic utility of growth - hormone- binding protein , insulin - like growth factor I , and insulin -like growth factor - binding protein 3measurements [J ] . Journal of pediatrics ,1997 ,131(1) - part 2 :s56 - s601
4 Binder G, Schwarze CP ,Ranke MB Identification of short stature caused by SHOX defects and threapeutic effect of recombinant human growth hormone[J ] . The Journal of Clinical Endocrinology Metabolism ,2001
5 Rao E , Weiss B , Fukami M, et al . Pseudoautosomal deletions encompassing a novel homeobox gene cause growth failure in idiopathic short stature and Turner syndrome [ J ] . Nat Genet ,1997 ,16 :54 – 631
6 Ogata T1SHOX: Pseudoautosomal homeobox containing gene for short stature and dyschondrosteosis [J ] . Growth Horm IGF Res1999 , 9(Suppl B) :53 – 571
7 孙逊,朱尚权. 生长激素的结构与功能.国外医学,生理、病理科学与临床分册,1999,19(1):
8 贺淹才. 生长激素和生长激素受体的分子生物学.生命的化学,2002,22(1):29-32;
9 王星, 吴红专, 贺东生, 等. 鸡生长激素研究进展[J]. 中国家禽, 1998, 20(10): 25-26.
10 曾礼华, 周安国, 杨凤. 动物生长激素与肉畜生产[J]. 动物营养学报, 1999, 11(4): 1-8.
11 Attie KM. Genetic studies in idiopathic short stature [J ] . Current Opinion In Pediatrics ,2000 ,12 :400 - 4041
12 生长激素受体基因单核苷酸多态性与特发性矮小的相关性,医学综述,2007,13(11),833～834;
13 Chan J M, Stampfer M J, Giovanucci E, et al. Plasma insulin-like growth factor-I and prostate cancer risk: a prospective study[J]. Science, 1998, 279: 563-566.
14 Clement-JonesM,Schiller S,Rao E,et al.The short stature homeobox gene SHOX is involved in skeletal abnormalities in Turner syndrome[J].HumMol Genet,2000,9(5):695-702.
15 Deng HW,Xu FH,Liu YZ,et a1.A whole-genome linkage scan suggests several genomic regions potentially containing QTIs underlying the variation of stature[J].Am J Med Genet,2002,113(1):29-39.
16 Hirschhorn JN,Lindgren CM,DaIy MJ,et al.Genomewide linkage analysis of stature in multiple populations reveals several regions with evidence of linkageto adult height[J].Am J Hum Genet,2001,69(1):106-116.
17 陈晓丽 特发性矮小的相关基因研究进展,国外医学妇幼保健,2002 年第 13 卷第 5 期
18 Zuffardi, O.; Maraschio, P.; Lo Curto, F.; Muller, U.; Giarola, A.; Perotti, L. :The role of Yp in sex determination: new evidence from X/Y translocations. Am. J. Med. Genet. 12: 175-184, 1982.
19 Ogata, T.; Goodfellow, P.; Petit, C.; Aya, M.; Matsuo, N. : Short stature in a girl with a terminal Xp deletion distal to DXYS15: localisation of a growth gene(s) in the pseudoautosomal region. J. Med. Genet. 29: 455-459, 1992.
20 Ogata, T.; Petit, C.; Rappold, G.; Matsuo, N.; Matsumoto, T.; Goodfellow, P. : Chromosomal localisation of a pseudoautosomal growth gene(s). J. Med. Genet. 29: 624-628, 1992.
21 Ellison, J. W.; Wardak, Z.; Webster, M.; Chiong, W. : PHOG, a candidate gene for involvement in the short stature of Turner syndrome. (Abstract) Am. J. Hum. Genet. 59 (suppl.): A32, 1996.
22 Rao, E.; Weiss, B.; Fukami, M.; Mertz, A.; Meder, J.; Ogata, T.; Heinrich, U.; Garcia-Heras, J.; Schiebel, K.; Rappold,A. :FISH-deletion mapping defines a 270-kb short stature critical interval in the pseudoautosomal region PAR1 on human sex chromosomes. Hum. Genet. 100: 236-239, 1997.
23 Kawai M,Momoi T,Yorifuji T,et a1,Unfavorable effects of growth hormone treatment on final height of boys with short sture not caused by growth hormone deficiency[J].J Pediatrics,1997,130:205.
24 Blaschke 1tJ, Monaghan AP, Schiller S .SHOT, a SHOX-related homeobox gene, is implicated in craniofacial, brain, heart, and limb development .Genetics, 1998, 95 :240f}2411.
25 Clement-JonesM,Schiller S,Rao E,et al.The short stature homeobox gene SHOX is involved in skeletal abnormalities in Turner syndrome[J].HumMol Genet,2000,9(5):695-702.
26 Rao, E.; Blaschke, R. J.; Marchini, A.; Niesler, B.; Burnett, M.; Rappold, G. A. : The Leri-Weill and Turner syndrome homeobox gene SHOX encodes a cell-type specific transcriptional activator. Hum. Molec. Genet. 10: 3083-3091, 2001.
27 Wilson D.Sheng ,G.,(1993); Cooperative dimerization of paired class homeodomain dimmer on DNA.Genes Dev,.7,2120-2134 .
28 Blaschke RJ,Topfer C,Marchini A,et a1.Transcriptional and translational regulation of the Leri-Weill and Turner syndrome homeobox gene SHOX[J].J Biol Chem,2003,278(48):47820-47826.
29 Munns CJ, Haase HR, Crowther LM, et al. Expression of SHOX in human fetal and childhood growth plate.J Clin Endocrinol Metab,2004,89(8):4130-5.
30 Marchini A, Marttila T, Winter A, et al.The short stature homeodomain protein SHOX induces cellular growth arrest and apoptosis and is expressed in human growth plate chondrocytes.J Biol Chem,2004,279(35):37103-14.
31 Rao E,Blaschke RJ,Marchini A,et a1.TheLeri-Weill and Turner syndrome homeobox gene SHOX encodes a cell-type specific transcriptional activator [J].Hum Mol Genet,2001,10(26):3083-3091.
32 Sabherwal N, Schneider KU, Blaschke RJ, et al. Impairment of SHOX nuclear localization as a cause for Leri-Weill syndrome.J Cell Sci, 2004,117(14):3041-8.
33 Niesler B,Fischer C,Rappold, human SHOX mutation database[J].Hum Mutat ,2002,20(5):338-341.
34 Sabherwal N, Blaschke RJ, Marchini A, et a1.A novel point mutation A170P in the SHOX gene defines impaired nuclear translocation as a molecular cause for Lzri-Weill dyschondrosteosis and Langer dysplasia.J Med Genet,2004,41(6):e83.
35 Kanaka-Gantenbein C, Kitsiou S, Mavrou A, et a1.Ta11 stature, insulin resistance, and disturbed behavior in a girl with the triple X syndrome harboring three SHOX genes: offspring of a father with mosaic Klinefelter syndrome but with two maternal X chromosomes.Horm Res,2004,61(5):205-10.
36 林剑军,109 例身材矮小儿童骨龄分析,广西医科大学学报 ,2006 年 01 期
37 Ogata T, Matsuo N, Fukushima Y, et al. FISH analysis for apparently simple terminal deletions of the X chromosome: identification of hidden structural abnormalities.Am J Med Genet,2001,104(4):307-311.
38 Morizio E, Stuppia L, Gatta V, et al. Deletion of the SHOX gene in patients with short stature of unknown cause.Am J Med Genet,2003,119A(3):293-296.
39 Rappold GA, Fukami M, Niesler B,et al. Deletions of the homeobox gene SHOX (short stature homeobox) are an important cause of growth failure in children with short stature.J Clin Endocrinol Metab,2002,87(3):1402-1406.
40 Ezquieta B, Cueva E, Oliver A, et al. SHOX haploinsufficiency SHOX intragenic microsatellite analysis in patients with short stature.J Pediatr Endocrinol Metab,2002,15(2):139-48.
41 Ogata T. SHOX haploinsufficiency and its modifying factors.J Pediatr Endocrinol Metab,2002 Dec;15 Suppl 5:1289-94. Review.
42 Munns CF, Glass IA, Flanagan S, et al. Familial growth and skeletal features associated with SHOX haploinsufficiency. J Pediatr Endocrinol Metab, 2003,16(7):987-96.
43 Fukami M, Nishi Y, Hasegawa Y, et al. 5tatural growth in 31 Japanese patients with SHOX haploinsufficiency: support for a disadvantageous effect of gonadal estrogens.Endocr J,2004,51(2):197-200.
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