Genomic SELEX for the genome-wide search of regulation targets by transcription factors: SELEX-clos and SELEX-chip procedures

T. Shimada, N. Fujita, Kaneyoshi Yamamoto, A. Ishihama
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引用次数: 1

Abstract

The pattern of genome transcription in prokaryotes is determined by selective distribution of RNA polymerase within the genome. The gene selectivity of RNA polymerase is modulated after interaction with DNA-binding transcription factors (TFs). Escherichia coli contains a total of about 300 TFs, but the regulatory function has not yet been identified for about one third. For quick and systematic search of the regulation target genes by TFs, we have developed a novel screening technology “Genomic SELEX”, in which the recognition DNA sequences by the test TF are isolated from a mixture of genome DNA fragments. The sequences were determined by either cloning-sequencing of SELX fragments (SELEX-clos) or high-density microarray (tilling array) analysis (SELEX-chip). Here we describe the application of these novel technologies for search of the whole set of regulation target genes on the E. coli genome by CRP (cAMP-binding protein).
基因组SELEX用于转录因子调控靶标的全基因组搜索:SELEX闭合和SELEX芯片程序
原核生物基因组转录的模式是由基因组内RNA聚合酶的选择性分布决定的。RNA聚合酶与dna结合转录因子(TFs)相互作用后,基因的选择性受到调控。大肠杆菌共含有约300个TFs,但其中约三分之一的调节功能尚未确定。为了快速系统地利用TF搜索调控靶基因,我们开发了一种新的筛选技术“Genomic SELEX”,该技术从混合基因组DNA片段中分离出被测试TF识别的DNA序列。通过SELX片段克隆测序(SELEX-clos)或高密度微阵列(tilling array)分析(SELEX-chip)确定序列。本文描述了这些新技术在利用CRP (camp结合蛋白)搜索大肠杆菌基因组上整套调控靶基因方面的应用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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