哺乳动物转录因子DNA结合谱

doi:10.3724/SP.J.1005.2012.00950

遗传 ›› 2012, Vol. 34 ›› Issue (8): 950-968.doi: 10.3724/SP.J.1005.2012.00950

哺乳动物转录因子DNA结合谱

谷光明, 王进科

东南大学生物电子学国家重点实验室, 南京210096

收稿日期:2011-12-20 修回日期:2012-05-06 出版日期:2012-08-20 发布日期:2012-08-25
通讯作者: 王进科 E-mail:wangjinke@seu.edu.cn
基金资助:
国家自然科学基金项目(编号：60871014, 61171030)资助

DNA-binding profiles of mammalian transcription factors

GU Guang-Ming, WANG Jin-Ke

The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China

Received:2011-12-20 Revised:2012-05-06 Online:2012-08-20 Published:2012-08-25

摘要/Abstract

摘要： 基因差异表达是生物发育和对刺激作出应答的分子基础, 转录因子在这种基因差异表达中发挥着重要的调控作用。因此, 要弄清楚转录因子调控基因差异表达的机理, 就必须鉴定出它们全部的靶基因并构建其操纵的转录调控网络。对基因组DNA的序列特异性结合是转录因子调控基因转录的关键环节, 因此, 要鉴定转录因子的靶基因, 就必须从它们与DNA相互作用的分子水平, 鉴定它们能够识别并结合的全部DNA序列, 即转录因子DNA结合谱。近年来随着DNA微阵列芯片和高通量DNA测序技术的产生和快速发展, 出现了建立转录因子体内及体外DNA结合谱的一系列革命性的新技术, 对该领域的研究带来重大影响。这些新技术主要包括建立转录因子体内DNA结合谱的染色质免疫沉淀-芯片技术(ChIP-chip)和染色质免疫沉淀-测序技术(ChIP-Seq), 以及建立转录因子体外DNA结合谱的双链DNA微阵列芯片技术(dsDNA microarray)、指数富集配体系统进化-系列分析基因表达技术(SELEX-SAGE)、结合-n-测序技术(Bind-n-Seq)、多重大规模并行SELEX技术(MMP-SELEX)、凝胶迁移实验-测序技术(EMSA-Seq)和高通量测序-荧光配体互作图谱分析技术(HiTS-FLIP)。文章将对这些新技术做一综述。

关键词: 哺乳动物转录因子, DNA结合谱, DNA微阵列芯片, 高通量DNA测序

Abstract: The differential gene expression is the molecular base of development and responses to stimuli of organisms. Transcription factors (TFs) play important regulatory roles in this kind of differential gene expression. Therefore, to elucidate how these TFs regulate the complex differential gene expression, it is necessary to identify all target genes of them and construct the gene transcription regulatory network controlled by them. DNA binding is a key step for TFs regulating gene transcription. Therefore, in order to identify their target genes, it is indispensable to identify all possible DNA sequences that can be recognized and bound by TFs at the molecular level of their interactions with DNA, i.e., construction of the DNA-binding profiles of TFs. In recent years, along with the development of DNA microarray and high-throughput DNA sequencing techniques, there appeared some revolutionary new techniques for constructing DNA-binding profiles of TFs, which greatly promotes studies in this field. These techniques include ChIP-chip and ChIP-Seq for constructing in vivo DNA-binding profiles of TFs, dsDNA microarray, SELEX-SAGE, Bind-n-Seq, MMP-SELEX, EMSA-Seq, and HiTS-FLIP for constructing in vitro DNA-binding profiles of TFs. This paper reviewed these techniques.

Key words: mammalian transcription factor, DNA-binding profile, DNA microarray, high-throughput DNA se-quencing

谷光明，王进科. 哺乳动物转录因子DNA结合谱[J]. 遗传, 2012, 34(8): 950-968.

GU Guang-Ming, WANG Jin-Ke. DNA-binding profiles of mammalian transcription factors[J]. HEREDITAS, 2012, 34(8): 950-968.

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哺乳动物转录因子DNA结合谱

DNA-binding profiles of mammalian transcription factors

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