启动子结构、功能预测和验证方法的研究进展  

Research Advances in Prediction and Validation Methods for Structures and Functions of Promoters

作　　者：曾晓玲 赵昶灵[1] 文国松[1] 丁灿[2] 张洪玲 徐率 古朝山 Zeng Xiaoling;Zhao Changling;Wen Guosong;Ding Can;Zhang Hongling;Xu Shuai;Gu Chaoshan(College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201;College of Tobacco Sciences, Yunnan Agricultural University, Kunming, 650201)

机构地区：[1]云南农业大学生物与技术学院,昆明650201 [2]云南农业大学烟草学院,昆明650201

出　　处：《分子植物育种》2018年第12期3915-3925,共11页Molecular Plant Breeding

基　　金：国家自然科学基金(31460065);云南省科技厅2016-2017年度"三区"人才支持计划(A3008427-87)共同资助

摘　　要：本综述总结了启动子结构、功能预测和验证的主要方法及其选用的研究进展。已知或克隆到靶基因的5'端上游序列后,应首先用生物信息学方法预测序列中的启动子,分析、预测其结构元件及其功能,再用实验方法验证元件的功能。生物信息学分析、预测是指单独或结合选用若干软件以及真核生物启动子、植物DNA顺式作用调控元件、植物顺式作用调控元件、Plant Prom、转录因子和转录调控区数据库;实验方法验证是指在综合考虑特定方法的原理、目标内涵和操作流程等多方面优劣势的基础上合理选用表达分析、染色质免疫共沉淀法、DNaseⅠ足迹法、电泳迁移率变动分析法和酵母单杂交法,但是,各方法均在运用中被不断改进,且目前使用最广泛的是表达分析法。启动子结构、功能预测和验证常选用两个或两个以上软件、数据库和方法,但可能会涉及到对不同数据库和方法产生的不一致或矛盾结果的甄别,将来应研发新的、更有效的研究DNA-蛋白互作的技术,与上述经典实验方法结合、用于启动子的功能研究。本综述可为启动子结构和功能的研究提供方法学参考。This review summarized the main methods and research advances in the prediction and validation methods for the structures and functions of promoters. After the upstream sequence of the 5＇-terminal of the target gene was known or cloned, bioinformatics methods should be first employed to predict the promoter in the sequence, further analyze and predict the structural elements and their functions of the promoter, and experimental methods were utilized to validate the functions of the elements. The analysis and prediction based on bioinformatics referred to individually or integratively select and applicate several softwares and eukaryotic promoter, plant cis-acting regulatory DNA elements（PLACE）, plant cis-acting regulatory element（Plant CARE）, Plant Prom, transcription factor（TRANSFAC） and transcription regulatory region database（TRRD）. The experimental method verification referred to reasonably select the expression analysis, chromatin immuno-precipitation（ChIP）, DNase Ⅰfootprinting, electrophoretic mobility shift assay（EMSA） and yeast one-hybrid（Y1H） on the basis of comprehensive consideration on the superior and inferior positions with respect to the principles, objective connotations, and operation procedures of the specific methods. However, all experimental methods were ceaselessly improved in applications and at present the expression analysis was applied most extensively. Two or more than two softwares,databases and methods were usually employed in the prediction and validation of the structures and functions, but it was possible to involve the discrimination in the inconsistent or contradictory results deriving from different databases and methods. In the future, new and more effective technologies studying DNA-protein interactions should be researched and developed to be applied in the study on promoter functions combined with above-mentioned classical experimental methods. This research could provide a methodological reference for the study of the structures and functions

关 键 词：启动子 结构 功能 预测和验证方法 研究进展 

分 类 号：Q75[生物学—分子生物学]