利用基因芯片技术筛选秦川牛公牛与阉牛肌肉组织差异表达基因

doi:10.3724/SP.J.1005.2010.01166

遗传 ›› 2010, Vol. 32 ›› Issue (11): 1166-1174.doi: 10.3724/SP.J.1005.2010.01166

利用基因芯片技术筛选秦川牛公牛与阉牛肌肉组织差异表达基因

张莺莺¹, 昝林森^1,2, 王洪宝^1,2

1. 西北农林科技大学动物科技学院, 杨凌 712100; 2. 国家肉牛改良中心, 杨凌 712100

收稿日期:2010-01-12 修回日期:2010-09-30 出版日期:2010-11-20 发布日期:2010-11-25
通讯作者: 昝林森 E-mail:zanls@yahoo.com.cn
基金资助:
国家高技术研究发展计划项目(863计划)(编号：2006AA10Z1A1, 2008AA101010, 2010AA10Z101)和国家转基因生物新品种培育重大专项(编号：2008ZX08007-02)资助

Genome array on differentially expressed genes of muscle tissue in intact male and castrated Qinchuan cattle

ZHANG Ying-Ying¹, ZAN Lin-Sen^1,2, WANG Hong-Bao^1,2

1. College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; 2. National Beef Cattle Improvement Center in China, Yangling 712100, China

Received:2010-01-12 Revised:2010-09-30 Online:2010-11-20 Published:2010-11-25
Contact: ZAN Lin-Sen E-mail:zanls@yahoo.com.cn

摘要/Abstract

摘要： 为了筛选秦川牛公牛和阉牛肌肉组织差异表达的基因, 探讨二者肉质差异的分子生物学机理, 文章利用Affymetrix公司生产的牛基因组芯片技术, 分别检测了3头36月龄秦川牛公牛与阉牛背最长肌肌肉组织的mRNA 表达水平变化; 运用Significance Analysis of Microarrays (SAM) 法对秦川牛公牛和阉牛基因表达谱进行了差异分析; 并通过分子注释系统平台(MAS 2.0)对差异表达基因进行了功能富集类分析和调控通路分析; 最后应用实时定量PCR 技术对部分差异表达基因进行了验证。基因表达谱分析结果显示, 在36月龄秦川牛的肌肉组织中, 共检测到约11 000个探针, 代表大约10 000个基因。共筛选出差异表达基因143条, 主要涉及胶原纤维的组织和合成、细胞粘附、细胞生长调控、泛素介导的蛋白分解代谢和横纹肌收缩等生物学过程; 在分子注释系统数据库中注释到的显著调控通路为细胞外基质受体反应、细胞通讯、焦点粘连和紧密连接等; 所验证的差异表达基因的荧光定量 PCR结果与芯片结果基本一致。结合已有的文献报道, 文章初步认为ECM受体反应、细胞通讯、焦点粘连、紧密接头等调控通路及COL3A1、COL1A1、COL1A2、SPP1、FBN1、MMP2、ECM1、MYH3、MYH8、S100A4、ASPN、CFD等基因可能是参与调控秦川牛阉割前后肉质性状差异的重要调控通路和基因。此外, 还筛选出一些尚未在GenBank上登陆的序列, 推测可能是未知的新基因, 它们在牛肉质代谢过程中的作用还需进一步的研究证明。

关键词: 秦川牛, 基因芯片, 肌肉, 基因表达谱

Abstract: Bovine Genome Array was used to construct gene expression profile to screen differentially expressed genes of the Longuissimus dorsi muscle (LDM) tissue between intact male and castrated Qinchuan cattle and investigate the molecular mechanism related to meat quality differences between the two groups. Significance Analysis of Microarray (SAM) methods was used to identify the differentially expressed genes. Go (Gene Ontology) and the pathway analyses were con-ducted on differentially expressed genes using a free web-based Molecular Annotation System 2.0 (MAS 2.0). About 11 000 probe sets represented about 10 000 genes were detected in LDM of 36 months old Qinchuan cattle. A total of 143 genes were identified to be differentially expressed genes. They were mainly involved in collagen fibril organization and synthesis, regulation of cell growth and development, ubiquitin-dependent protein catabolism, and striated muscle contrac-tion etc. The enriched pathways mainly included ECM-receptor interaction, cell communication, and focal adhesion etc. Subsequently, real-time PCR was performed to validate eight differentially expressed genes screened out by the microarray approach and sufficient consistency was observed between the two methods. According to our study and published papers, the regulated pathways including ECM-receptor interaction, cell communication, focal adhesion, tight junction and genes including COL3A1, COL1A1, COL1A2, SPP1, FBN1, MMP2, ECM1, MYH3, MYH8, S100A4, ASPN, CFD etc were con-sidered as the most important parthways and genes involved in meat quality differences between males and castrated Qin-chuan cattle. Moreover, some genes had no annotation in GenBank were screened out, which were presumed to be unknown new genes. The roles that they may play in muscle metabolism need to be clarified in future.

Key words: gene expression profile, muscular tissues, microarray, Qinchuan cattle

张莺莺，昝林森，王洪宝. 利用基因芯片技术筛选秦川牛公牛与阉牛肌肉组织差异表达基因[J]. 遗传, 2010, 32(11): 1166-1174.

ZHANG Ying-Ying, ZAN Lin-Sen, WANG Hong-Bao. Genome array on differentially expressed genes of muscle tissue in intact male and castrated Qinchuan cattle[J]. HEREDITAS, 2010, 32(11): 1166-1174.

参考文献

[1] 符金录, 刘汉卿. 秦川牛肉用性能开发前景及对策. 黄牛杂志, 2005, 31(5): 39-41. [2] GB 5797-2003, 秦川牛. 北京: 中国标准出版社, 2003. [3] Li C, Wong WH. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detec-tion. Proc Natl Acad Sci USA, 2001, 98(1): 31-36. [4] Li C, Wong WH. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error ap-plication. Genome Biol, 2001, 2(8): research0032.1-0032.11. [5] Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA, 2001, 98(9): 5116-5121. [6] Qin LX, Beyer RP, Hudson FN, Linford NJ, Morris DE, Kerr KF. Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. BMC Bioinformatics, 2006, 7: 23-34. [7] Field, RA. Effect of castration on meat quality and quan-tity. J Anim Sci, 1971, 32(5): 849-858. [8] Ende C, Gebhardt R. Inhibition of matrix metallopro-teinase-2 and -9 activities by selected flavonoids. Planta Med, 2004, 70(10): 1006-1008. [9] Dietz HC, Pyeritz RE. Mutations in the human gene for fi-brillin-1 (FBN1) in the Marfan syndrome and related disorders. Hum Mol Genet, 1995, 4(Review 1): 1799-1809. [10] Okamoto O, Suzuki Y, Kimura, S, Shinkai H. Extracellular matrix 22-kDa protein interacts with decorin core protein and is expressed in cutaneous fibrosis. J Biochem (Tokyo), 1996, 119(1): 106-114. [11] Forbes EG, Cronshaw AD, MacBeath JRE, Hulmes DJS. Tyrosine-rich acidic matrix protein (TRAMP) is a tyro-sine-sulphated and widely distributed protein of the extracel-lular matrix. FEBS Lett, 1994, 351(3): 433-436. [12] MacBeath JR, Shackleton DR, Hulmes DJ. Tyrosine-rich acidic matrix protein (TRAMP) accelerates collagen fibril formation in vitro. J Biol Chem, 1993, 268(26): 19826-19832. [13] Oberhauser AF, Marszalek PE, Erickson HP, Fernandez JM. The molecular elasticity of the extracellular matrix protein tenascin. Nature, 1998, 393(6681): 181-185. [14] Riley RR, Savell JW, Murphey CE, Smith GC, Stiffler DM, Cross HR. Palatability of beef from steer and young bull car-casses as influenced by electrical stimulation, subcutaneous fat thickness and marbling. J Anim Sci, 1983, 56(3): 592-597. [15] Vanderwert W, McKeith FK, Bechtel PJ, Berger LL. Influ-ence of zeranol implants and electrical stimulation on the pal-atability traits of five muscles in Angus and Limousin bulls and steers. J Anim Sci, 1986, 63(1): 114-120. [16] Lepetit J. Collagen contribution to meat toughness: Theo-retical aspects. Meat Sci, 2008, 80(4): 960-967. [17] Lepetit J. A theoretical approach of the relationships be-tween collagen content, collagen cross-links and meat tenderness. Meat Sci, 2007, 76(1): 147-159. [18] Cross HR, Schanbacher BD Crouse JD. Sex, age and breed related changes in bovine testosterone and intramuscular collagen. Meat Sci, 1984, 10(3): 187-195. [19] McCormick RJ. The flexibility of the collagen compart-ment of muscle. Meat Sci, 1994, 36(1-2): 79-91. [20] Crouse JD, Cross HR, Seideman SC. Effects of sex condi-tion, genotype, diet and carcass electrical stimulation on the collagen content and palatability of two bovine mus-cles. J Anim Sci, 1985, 60(5): 1228?1234. [21] Gerrard DE, Jones SJ, Aberle ED, Lemenager RP, Diekman MA, Judge MD. Collagen stability, testosterone secretion and meat tenderness in growing bulls and steers. J Anim Sci, 1987, 65(5): 1236–1242. [22] Fritsche S, Steinhart H. Differences in natural steroid hormone patterns of beef from bulls and steers. J Anim Sci, 1998, 76 (6): 1621-1625. [23] Boccard RL, Naudé RT, Cronje DE, Smit MC, Venter HJ, Rossouw EJ. The influence of age, sex and breed of cattle on their muscle characteristics. Meat Sci, 1979, 3(4): 261-280. [24] Warrick HM, Spudich JA. Myosin structure and function in cell motility. Cell Biol, 1987, 3: 379–421. [25] Schiaffino S, Reggani C．Myosin isoforms in mammalian skeletal muscle. J Appl phys, 1994, 77(2): 493–501. [26] Tidyman W E, Moore L A, Bandman E．Expression of fast myosin heavy chain transcripts in developing and dystrophic chicken skeletal muscle. Dev Dynam, 1997, 208(4): 491–504. [27] Xiong YL. Myofibrillar protein from different muscle fi-ber types: implications of biochemical and functional properties in meat processing. Crit Rev Food Sci Nutr, 1994, 34(3): 293–320. [28] 朱砺, 李学伟, 李芳琼, 张克英, 陈代文, 胡祖禹. 肌纤维生长发育规律的研究. 四川农业大学学报, 2002, 20(1): 47-48. [29] 王天辉, 刘洪涛. 钙结合蛋白 S100A4 与分子靶标相互作用. 中国公共卫生, 2009, 25(11): 1330-1332. [30] Henry SP, Takanosu M, Boyd TC, Mayne PM, Eber-spaecher H, Zhou W, de Crombrugghe BD, Höök M, Mayne R. Expression pattern and gene characterization of asporin. a newly discovered member of leucine-rich repeat protein family. J Biol Chem, 2001, 276(15): 12212-12221. [31] Lorenzo P, Aspberg A, Önnerfjord P, Bayliss MT, Neame PJ, Heinegärd D. Identification and characterization of asporin. A novel member of the leucine-rich repeat protein family closely related to decorin and biglycan. J Biol Chem, 2001, 276(15): 12201-12211. [32] Kou I, Nakajima M, Ikegawa S. Expression and regulation of osteoarthritis-associated protein asporin. J Biol Chem, 2007, 282(44): 32193-32199. [33] Lazzaroni C, Biagini D. Effect of pre- and post-pubertal castration on Piemontese male cattle. II: Carcass measures and meat yield. Meat Sci, 2008 80(2): 422-448. [34] Zembayashi M, Nishimura K, Lunt DK, Smith SB. Effect of breed type and sex on the fatty acid composition of sub-cutaneous and intramuscular lipids of finishing steers and heifers. J Anim Sci, 1995, 73(11): 3325-3332. [35] Rosen, SD. Lymphocyte homing: progress and prospects. Curt Opin Cell Biol, 1989, 1(5): 913-919. [36] Choy LN, Rosen BS, Spiegelman BM. Adipsin and an endogenous pathway of complement from adipose cells. J Biol Chem, 1992, 267(18): 12736-12741. [37] 邱怀, 王科. 秦川牛选育、保种、改良及开发利用工作总结. 黄牛杂志, 1995, 76: 17-22. [38] Ilian MA, Morton JD, Kent MP, Le Couteur CE, Hickford J, Cowley R, Bickerstaffe R. Intermuscular variation in tender-ness: Association with the ubiquitous and muscle-specific calpains. J Anim Sci, 2001, 79(1): 122-132. [39] Hopkins DL, Thompson JM. Inhibition of protease activity. Part 1. The effect on tenderness and indicators of proteolysis in ovine muscle. Meat Sci, 2001, 59(2): 175-185. [40] Morgan JB, Wheeler TL, Koohmaraie M, Crouse DJ, Savell JW. Effect of castration on myofibrillar protein turnover, en-dogenous proteinase activities, and muscle growth in bovine skeletal muscle. J Anim Sci, 1993, 71(2): 408-414. [41] Sha G., Wu D, Zhang L, Chen X, Lei M, Sun H, Lin S, Lang J. Differentially expressed genes in human endo-metrial endothelial cells derived from eutopic endo-metrium of patients with endometriosis compared with those from patients without endometriosis. Hum Reprod, 2007, 22(12): 3159−3169. [42] Romer LH, Birukov KG, Garcia JGN. Focal adhesions: para-digm for a signaling nexus. Circ Res, 2006, 98(5): 606-616. [43] Dallas PB, Gottardo NG, Firth MJ, Beesley AH, Hoffmann K, Terry PA, Freitas JR, Boag JM, Cummings AJ, Kees UR. Gene expression levels assessed by oligonucleotide microar-ray analysis and quantitative real-time RT-PCR- how well do they correlate? BMC Genomics, 2005, 6(1): 59. [44] Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC. Accuracy and calibration of commercial oligonucleo-tide and custom cDNA microarrays. Nucl Acids Res, 2002, 30(10): e48.

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

利用基因芯片技术筛选秦川牛公牛与阉牛肌肉组织差异表达基因

Genome array on differentially expressed genes of muscle tissue in intact male and castrated Qinchuan cattle

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	禹奇超,宋彬,邹轩轩,王岭,刘德权,李波,马昆. 乳腺癌癌旁组织特异性表达基因分析[J]. 遗传, 2019, 41(7): 625-633.
[2]	陈应坚,廖苑君,林帆,孙胜南,赵小蕾,覃继恒,饶绍奇. 基于转录组数据的网络分析挖掘鼻咽癌与口腔鳞癌的共享功能模块[J]. 遗传, 2019, 41(2): 146-157.
[3]	秦辰雨, 蔡禾, 卿涵睿, 李利, 张红平. 长链非编码RNA H19对哺乳动物肌肉生长发育的调控[J]. 遗传, 2017, 39(12): 1150-1157.
[4]	储黄伟, 牛付安, 程灿, 周继华, 王新其, 罗小金, 袁勤, 曹黎明. 杂交粳稻花优14及其亲本孕穗期剑叶的基因表达谱芯片分析[J]. 遗传, 2015, 37(9): 932-938.
[5]	蒲强,罗嘉,沈林園,李学伟,张顺华,朱砺. 蛋白质修饰组学在肉品质研究中的应用[J]. 遗传, 2015, 37(4): 327-335.
[6]	刘欣, 张洁, 赵春晖, 李铁松, 王继红, 李庆伟. 日本七鳃鳗物种特异性microRNAs及其前体识别与验证[J]. 遗传, 2015, 37(3): 283-291.
[7]	宋晓燕, 张德祥, 张文武, 季从亮, 张细权, 罗庆斌. 鸡3种组织中热应激相关基因的表达谱芯片分析[J]. 遗传, 2014, 36(8): 800-808.
[8]	周文婷. 运动能力的遗传学研究进展[J]. 遗传, 2014, 36(4): 301-308.
[9]	冉茂良,陈斌,尹杰,杨岸奇,李智,蒋明. 猪microRNA组学研究进展[J]. 遗传, 2014, 36(10): 974-984.
[10]	曹随忠岳成鹤李西睿冯冲龙川潘登科. 锌指核酸酶技术制备肌肉生长抑制素基因敲除的五指山小型猪成纤维细胞[J]. 遗传, 2013, 35(6): 778-785.
[11]	解敏敏，龚达平，李凤霞，刘贯山，孙玉合. 烟草细胞色素P450的基因组学分析[J]. 遗传, 2013, 35(3): 379-387.
[12]	郭新军. 人类（Homo sapiens）肌肉增强因子2（MEF2）生物信息学特性比较及其进化分析[J]. 遗传, 2011, 33(9): 975-981.
[13]	郭昊，朱云平，李栋，贺福初. 肿瘤相关生物学通路的发现和建模[J]. 遗传, 2011, 33(8): 809-819.
[14]	刘阳，吴望军，左波，任竹青，熊远著. 猪PRDX6基因编码区的多态性及遗传效应分析[J]. 遗传, 2011, 33(7): 743-748.
[15]	包文斌，叶兰，潘章源，朱璟，杜子栋，蔡家嘉，黄小国，朱国强，吴圣龙. 大肠杆菌F18菌株敏感和抵抗基因型仔猪十二指肠基因表达谱差异分析[J]. 遗传, 2011, 33(1): 60-66.