等位基因特异性表达形成机制及其应用的研究进展
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摘要
基因作为遗传信息的介质,决定了生物的性状表现。基因序列变异的发生是生物体适应环境变化的必然趋势。在二倍体生物中等位基因是一对控制着相对性状的基因,因此,等位基因特异性表达效应根据细胞类型和发育阶段的不同而变化,表现出不同个体之间的差异。等位基因差异表达对基因的表达起到重要的调控作用,并最终可能与生物的表型多态性联系起来。等位基因特异性表达分析已经在动物研究中得到广泛应用,有助于提高鉴定调控遗传变异的能力。对等位基因特异性表达的形成机制及其应用研究进展进行了综述,以期为进一步揭示等位基因特异性表达的遗传学机制,以及加快其在动物生产中的应用提供理论依据。
Genes, as mediators of genetic information, determine the performance of the creature′ s traits. The occurrence of genetic sequence variation is an inevitable trend of organisms to adapt to the environmental changes. The allele in the diploid organism is a pair of genes that controls relative traits. Therefore, the effect of allele specific expression varies depending on the cell type and its developmental stage, showing differences between different individuals. Differential expression of alleles plays an important role in the regulation of gene expression and may ultimately be linked to phenotypic polymorphisms in organisms.Allele specific expression analysis has been widely used in animal studies to help improve the ability to identify and regulate genetic variation. The research progress on the formation mechanism of allele specific expression and its application is reviewed,in hoping to provide a theoretical basis for further revealing the genetic mechanism of allele specific expression and accelerating its application in animal production.
Genes, as mediators of genetic information, determine the performance of the creature′ s traits. The occurrence of genetic sequence variation is an inevitable trend of organisms to adapt to the environmental changes. The allele in the diploid organism is a pair of genes that controls relative traits. Therefore, the effect of allele specific expression varies depending on the cell type and its developmental stage, showing differences between different individuals. Differential expression of alleles plays an important role in the regulation of gene expression and may ultimately be linked to phenotypic polymorphisms in organisms.Allele specific expression analysis has been widely used in animal studies to help improve the ability to identify and regulate genetic variation. The research progress on the formation mechanism of allele specific expression and its application is reviewed,in hoping to provide a theoretical basis for further revealing the genetic mechanism of allele specific expression and accelerating its application in animal production.
引文
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[2]CHESS A,SIMON I,CEDAR H,et al.Allelic inactivation regulates olfactory receptor gene expression[J].Cell,1994,78(5):823-834.
[3]PAI A A,PRITCHARD J K,GILAD Y,et al.The genetic and mechanistic basis for variation in gene regulation[J].PLoS Genetics,2015,11(1):e1004857.
[4]GARTLER,STAN LEY M,GOLD MAN,et al.Biology of the X chromosome[J].Current Opinion in Pediatrics,2001,13(4):340-345.
[5]GREGG C.Known unknowns for allele-specific expression and genomic imprinting effects[J].F1000Prime Reports,2014,6:75.
[6]WANG X,CLARK A G.Using next-generation RNA sequencing to identify imprinted genes[J].Heredity,2014,113(2):156-166.
[7]HAI Y,WEISHI Y,VELCULESCU V E,et al.Allelic variation in human gene expression[J].Science,2002,297(5584):1143.
[8]OSHLACK A,ROBINSON M D,YOUNG M D.From RNA-seq reads to differential expression results[J].Genome Biology,2010,11(12):220.
[9]WOOD D L A,HONES K,STEPTOE A,et al.Recommendations for accurate resolution of gene and isoform allele-specific expression in RNA-seq data[J].PLoS One,2015,10(5):e0126911.
[10]王志敏,王大志,施锦秀,等.等位基因不平衡表达的检测及应用[J].中华预防医学杂志,2011,45(1):9-11.
[11]KUKURBA K R,ZHANG R,LI X,et al. Allelic expression of deleterious protein-coding variants across human tissues[J].PLoS Genetics,2014,10(5):e 1004304.
[12]BJORNSSON H T,ALBERT T J,LADD-ACOSTA CM,et al.SNP-specific array-based allele-specific expression analysis[J].Genome Research,2008,18(5):771-779.
[13]DAELEMANS C,RITCHIE M E,SMITS G,et al.Highthroughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta[J].BMC Genetics,2010(11):25.
[14]SERRE D,GURD S,GE B,et al.Differential allelic expression in the human genome:a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression[J].PLoS Genetics,2008,4(2):e1000006.
[15]VIJAYA S R,ZAVALJEVSKI N,REIFMAN J.A new strategy to reduce allelic bias in RNA-seq readmapping[J].Nucleic Acids Research,2012,40(16):e127.
[16]ROZOWSKY J,ABYZOV A,WANG J,et al.AlleleSeq:analysis of allele-specific expression and binding in a network framework[J].Molecular Systems Biology,2014(7):522.
[17]SKELLY D A,JOHANSSON M,MADEOY J,et al.A powerful and flexible statistical framework for testing:hypotheses of allele-specific gene expression from RNA-seq data[J].Genome Research,2011,21(10):1728-1737.
[18]DEGNER J F,MARIONI J C,PAI A A,et al.Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data[J].Bioinformatics,2009,25(24):3207-3212.
[19]MCGRATH J,SOLTER D.Completion of mouse embryogenesis requires both the maternal and paternal genomes[J].Cell,1984,37(1):179-183.
[20]SIGURDSSON M I,SADDIC L,HEYDARPOUR M,et al.Allele-specific expression in the human heart and its application to postoperative atrial fibrillation and myocardial ischemia[J].Genome Medicine,2016,8(1):127.
[21]SEAN M E,MUIR W M,CROSBY S D,et al.Genomewide identification and quantification of cis-and transregulated genes responding to Marek's disease virus infection via analysis of allele-specific expression[J].Frontiers in Genetics,2012(2):113.