禽类转录因子与DNA互作的研究方法
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摘要
在禽类生长发育中,基因的适时适量表达起到至关重要的作用。研究转录因子与DNA的互作,对认识禽类生长发育过程具有重要意义。文章总结了禽类常用的转录因子与DNA互作研究方法,其中:生物信息学预测结合位点有助于针对性的开展后续研究;电泳迁移率变动分析(Electrophoretic mobility shift assay,EMSA)和染色质免疫共沉淀(Chromatin Immunoprecipitation,ChIP)能够分别从体外和体内验证转录因子与DNA结合;双荧光素酶报告基因可以鉴定对转录活性的影响。综合运用上述方法可有效开展转录因子-DNA互作研究,有助于揭示禽类生长发育调控机制。
Timely and proper gene expressions play a great part in poultry growth and development. Study the binding of transcription factors and DNA is contributed to recognize the poultry growth process. Our article summarized the current commonly methods of transcription factors and DNA interactions. Bioinformatics prediction of transcription factor binding sites help target to the follow-up experiments. Electrophoretic mobility shift assay(EMSA) and chromatin immunoprecipitation(ChIP) can respectively detect the binding of transcription factors and DNA in vitro and in vivo.Dual luciferase reporter gene assay could reveal the transcription activities of the binding sites. Together, combining the above methods could carry out the transcription factors and DNA interaction analysis effectively, and help to reveal the mechanism of poultry development and growth step by step.
Timely and proper gene expressions play a great part in poultry growth and development. Study the binding of transcription factors and DNA is contributed to recognize the poultry growth process. Our article summarized the current commonly methods of transcription factors and DNA interactions. Bioinformatics prediction of transcription factor binding sites help target to the follow-up experiments. Electrophoretic mobility shift assay(EMSA) and chromatin immunoprecipitation(ChIP) can respectively detect the binding of transcription factors and DNA in vitro and in vivo.Dual luciferase reporter gene assay could reveal the transcription activities of the binding sites. Together, combining the above methods could carry out the transcription factors and DNA interaction analysis effectively, and help to reveal the mechanism of poultry development and growth step by step.
引文
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[2]KIM T H,ABDULLAEV Z K,SMITH A D,et al.Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome[J].Cell,2007,128(6):1231-1245.
[3]BORNEMAN A R,GIANOULIS T A,ZHANG Z D,et al.Divergence of transcription factor binding sites across related yeast species[J].Science,2007,317(5839):815-819.
[4]ODOM D T,DOWELL R D,JACOBSEN E S,et al.Tissue-specific transcriptional regulation has diverged significantly between human and mouse[J].Nat Genet,2007,39(6):730-732.
[5]ZHANG Z W,CHEN Y C,PEI W Y,et al.Overexpression of Chicken Gata2 or Gata3 Suppressed the Transcription of PparγGene[J].Chinese Journal of Biochemistry and Molecular Biology,2012,28(9):835-842.
[6]ZHANG Z,WANG H,SUN Y,et al.Klf7 modulates the differentiation and proliferation of chicken preadipocyte[J].Acta Biochim Biophys Sin(Shanghai),2013,45(4):280-288
[7]DING N,GAO Y,WANG N,et al.Functional analysis of the chicken PPARgamma gene 5′-flanking region and C/EBPalpha-mediated gene regulation[J].Comp Biochem Physiol B Biochem Mol Biol,2011,158(4):297-303.
[8]KOTOVA E S,AKOPOV S B,DIDYCH D A,et al.Binding of Protein Factor CTCF within Chicken Genome Alpha-Globin Locus[J].Acta naturae,2016,8(1):90-97.
[9]ZHANG L,ZHU R,ZUO Q,et al.Activity analysis and preliminary inducer screening of the chicken DAZL gene promoter[J].Int J Mol Sci,2015,16(3):6595-6605.
[10]程敏,张文建,邢天宇,等.鸡mi R-17-92基因簇上游调控区功能分析[J].遗传,2016,8:724-735.
[11]DUAN K,SUN Y,ZHANG X,et al.Identification and characterization of transcript variants of chicken peroxisome proliferator-activated receptor gamma[J].Poult Sci,2015.
[12]陈鸿飞,王进科.转录因子相关数据库[J].遗传,2010,10:1009-1017.
[13]李婷婷,蒋博,汪小我,等.转录因子结合位点的计算分析方法[J].生物物理学报,2008,5:334-347.
[14]KOH K H,JEONG H.Electrophoretic Mobility Shift Assay(EMSA)and Supershift Assay of Cytochrome P4502B6 in Response to Estrogen[J].Methods Mol Biol,2016,1366:41-51.
[15]HELLMAN L M,FRIED M G.Electrophoretic mobility shift assay(EMSA)for detecting protein-nucleic acid interactions[J].Nat Protoc,2007,2(8):1849-1861.
[16]SMITH A J,HUMPHRIES S E.Characterization of DNAbinding proteins using multiplexed competitor EMSA[J].J Mol Biol,2009,385(3):714-717.
[17]PUGH B F,GILMOUR D S.Genome-wide analysis of protein-DNA interactions in living cells[J].Genome Biol,2001,2(4):REVIEWS1013.
[18]李敏俐,王薇,陆祖宏.Ch IP技术及其在基因组水平上分析DNA与蛋白质相互作用[J].遗传,2010,3:219-228.
[19]BAO Y,VINCIOTTI V,WIT E,et al.Accounting for immunoprecipitation efficiencies in the statistical analysis of Ch IP-seq data[J].BMC Bioinformatics,2013,14(11):169.
[20]GRENTZMANN G,INGRAM J A,KELLY P J,et al.A dual-luciferase reporter system for studying recoding signals[J].RNA,1998,4(4):479-486.
[21]WU C,SUZUKI-OGOH C,OHMIYA Y.Dual-reporter assay using two secreted luciferase genes[J].Biotechniques,2007,42(3):290,292.
[22]MULLER M,PERSSON A B,KRUEGER K,et al.The Wilms tumor protein WT1 stimulates transcription of the gene encoding insulin-like growth factor binding protein5(IGFBP5)[J].Gene,2017.
[23]PRADHAN S A,RATHER M I,TIWARI A,et al.Evidence that TSC2 acts as a transcription factor and binds to and represses the promoter of Epiregulin[J].Nucleic Acids Res,2014,42(10):6243-6255.
[24]ZHANG J J,ZHU Y,ZHANG X F,et al.Transcriptional regulation of human MUC4 gene:identification of a novel inhibitory element and its nuclear binding protein[J].Mol Biol Rep,2013,40(8):4913-4920.
[25]LIVYATAN I,AARONSON Y,GOKHMAN D,et al.BindDB:An Integrated Database and Webtool Platform for"Reverse-Ch IP"Epigenomic Analysis[J].Cell Stem Cell,2015,17(6):647-648.
[26]赵明明,齐锦生,栗彦宁.Reverse Ch IP:研究DNA-蛋白质相互作用的新方法[J].中国生物化学与分子生物学报,2010,5:407-410.