A highly sensitive in vivo footprinting technique for condition-dependent identification of cis elements.

ABSTRACT: Knowing which regions of a gene are targeted by transcription factors during induction or repression is essential for understanding the mechanisms responsible for regulation. Therefore, we re-designed the traditional in vivo footprinting method to obtain a highly sensitive technique, which allows identification of the cis elements involved in condition-dependent gene regulation. Data obtained through DMS methylation, HCl DNA cleavage and optimized ligation-mediated PCR using fluorescent labelling followed by capillary gel electrophoresis are analysed by ivFAST. In this work we have developed this command line-based program, which is designed to ensure automated and fast data processing and visualization. The new method facilitates a quantitative, high-throughput approach because it enables

SUBMITTER: Gorsche R 

PROVIDER: S-EPMC3874196 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature