增强子预测及靶向测序技术研究进展

Research Progress on Enhancer Forecast and Targeted Sequencing Technology

增强子在传统上被定义为不依赖转录方向及与目标启动子的相对位置来调控一个或多个基因转录的基因组顺式调控序列,其活性对生长发育、基因表达多样性、进化及人类疾病发生起到关键的调控作用,因此,了解增强子的功能特性不仅有利于理解基因表达的时空特异性,也有助于最终揭示细胞分化、物种进化及非编码区域变异导致疾病等关键的生物学问题。随着高通量测序技术的快速发展,增强子的预测鉴定、识别及功能注释的方法和工具也呈现出多样性,包括序列基序分析、转录因子和辅因子的体内结合位点、特征染色质和组蛋白修饰、大规模并行增强子分析,以及CRISPR(clustered regularly interspaced short palindromic repeats)相关技术。文章就高通量测序技术在全基因组水平上利用调节因子结合位点、染色质可接近性、组蛋白修饰、增强子与启动子的相互作用、增强子RNAs(eRNAs)和体外荧光素酶等技术对增强子鉴定、识别、预测的6种方法进行了综述,并就如何利用基因编辑技术靶向研究增强子进行了详细阐述,最后展望了全基因组水平上的增强子研究和个体研究增强子的作用,并详细描述了靶向预测增强子的方法,比较了每种方法的优势和局限性,为深入开展该领域的研究工作提供参考。

Enhancers have traditionally been defined as genomic cis-regulatory sequences that regulate the transcription of one or more genes independently of the transcription direction and relative position to the target promoter.The activity of enhancers plays a key regulatory role in growth and development,gene expression diversity,evolution and human disease occurrence.Therefore,understanding the functional characteristics of enhancers will not only help us understand the space-time specificity of gene expression,but also help us finally reveal the key biological issues such as cells differentiate,species evolve,and non-coding region variation leads to disease.With the rapid development of high-throughput sequencing technology,the methods and tools for the prediction,identification and functional annotation of enhancers also show diversity,including sequence motif analysis,in vivo binding sites of transcription factors and cofactors,feature chromatin and histone modification,large-scale parallel enhancer analysis,and CRSPR related technologies.This article reviews six methods of enhancer identification,recognition and prediction based on high-throughput sequencing technology at the whole genome level using regulatory factor binding sites,chromatin accessibility,histone modification,enhancer-promoter interaction,eRNAs and in vitro luciferase,and expounds in detail how to target enhancer research using gene editing technology.Finally,the role of enhancer research and individual research enhancer at the whole genome level is prospected,and the methods of targeted prediction of enhancer are described in detail,and the advantages and limitations of each method are compared,providing a reference for further research in this field.