{"title":"染色质中的动态增强子功能。","authors":"Ido Goldstein, Gordon L Hager","doi":"10.1002/wsbm.1390","DOIUrl":null,"url":null,"abstract":"<p><p>Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding. More recently, fluorescent microscopy techniques, including fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, and single molecule tracking (SMT), reveal a highly dynamic binding behavior for these factors in live cells. Furthermore, a refined analysis of genomic footprinting suggests that many transcription factors leave minimal or no footprints in chromatin, even when present and active in a given cell type. In this study, we review the implications of these new approaches for an accurate understanding of enhancer function in real time. In vivo SMT, in particular, has recently evolved as a promising methodology to probe enhancer function in live cells. Integration of findings from the many approaches now employed in the study of enhancer function suggest a highly dynamic view for the action of enhancer activating factors, viewed on a time scale of milliseconds to seconds, rather than minutes to hours. WIREs Syst Biol Med 2018, 10:e1390. doi: 10.1002/wsbm.1390 This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > Imaging.</p>","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":null,"pages":null},"PeriodicalIF":7.9000,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1390","citationCount":"20","resultStr":"{\"title\":\"Dynamic enhancer function in the chromatin context.\",\"authors\":\"Ido Goldstein, Gordon L Hager\",\"doi\":\"10.1002/wsbm.1390\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Enhancers serve as critical regulatory elements in higher eukaryotic cells. 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引用次数: 20
摘要
增强子在高等真核细胞中起着关键的调节元件的作用。增强子功能的表征主要来自全基因组方法,包括染色质免疫沉淀(ChIP-seq)、DNA酶-I超敏反应(DNA酶-seq)、数字基因组足迹(DGF)和染色体构象捕获技术(3C、4C和Hi-C)。这些基于群体的测定平均了数百万细胞的信号,并产生了以静态和顺序结合为特征的增强子模型。最近,荧光显微镜技术,包括光漂白后的荧光回收、荧光相关光谱和单分子跟踪(SMT),揭示了这些因子在活细胞中的高度动态结合行为。此外,对基因组足迹的精细分析表明,即使在给定的细胞类型中存在并具有活性,许多转录因子也会在染色质中留下最小或没有足迹。在这项研究中,我们回顾了这些新方法对实时准确理解增强子功能的影响。特别是体内SMT,最近已经发展成为一种很有前途的方法来探测活细胞中的增强子功能。整合目前用于研究增强子功能的许多方法的发现,表明增强子激活因子的作用具有高度动态性,从毫秒到秒的时间尺度来看,而不是从分钟到小时。WIREs Syst Biol Med 2018,10:e1390。doi:10.1002/wsbm.1390本文分类在:分析和计算方法>计算方法实验室方法和技术>遗传/基因组方法实验室方法与技术>成像。
Dynamic enhancer function in the chromatin context.
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding. More recently, fluorescent microscopy techniques, including fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, and single molecule tracking (SMT), reveal a highly dynamic binding behavior for these factors in live cells. Furthermore, a refined analysis of genomic footprinting suggests that many transcription factors leave minimal or no footprints in chromatin, even when present and active in a given cell type. In this study, we review the implications of these new approaches for an accurate understanding of enhancer function in real time. In vivo SMT, in particular, has recently evolved as a promising methodology to probe enhancer function in live cells. Integration of findings from the many approaches now employed in the study of enhancer function suggest a highly dynamic view for the action of enhancer activating factors, viewed on a time scale of milliseconds to seconds, rather than minutes to hours. WIREs Syst Biol Med 2018, 10:e1390. doi: 10.1002/wsbm.1390 This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > Imaging.
期刊介绍:
Journal Name:Wiley Interdisciplinary Reviews-Systems Biology and Medicine
Focus:
Strong interdisciplinary focus
Serves as an encyclopedic reference for systems biology research
Conceptual Framework:
Systems biology asserts the study of organisms as hierarchical systems or networks
Individual biological components interact in complex ways within these systems
Article Coverage:
Discusses biology, methods, and models
Spans systems from a few molecules to whole species
Topical Coverage:
Developmental Biology
Physiology
Biological Mechanisms
Models of Systems, Properties, and Processes
Laboratory Methods and Technologies
Translational, Genomic, and Systems Medicine