TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.

ABSTRACT: Transcription is tightly regulated by cis-regulatory DNA elements where transcription factors (TFs) can bind. Thus, identification of TF binding sites (TFBSs) is key to understanding gene expression and whole regulatory networks within a cell. The standard approaches used for TFBS prediction, such as position weight matrices (PWMs) and chromatin immunoprecipitation followed by sequencing (ChIP-seq), are widely used but have their drawbacks, including high false-positive rates and limited antibody availability, respectively. Several computational footprinting algorithms have been developed to detect TFBSs by investigating chromatin accessibility patterns; however, these also have limitations. We have developed a footprinting method to predict TF footprints in active chromatin element

SUBMITTER: Ouyang N 

PROVIDER: S-EPMC7397869 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature