Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.

ABSTRACT: DNaseI footprinting is an established assay for identifying transcription factor (TF)-DNA interactions with single base pair resolution. High-throughput DNase-seq assays have recently been used to detect in vivo DNase footprints across the genome. Multiple computational approaches have been developed to identify DNase-seq footprints as predictors of TF binding. However, recent studies have pointed to a substantial cleavage bias of DNase and its negative impact on predictive performance of footprinting. To assess the potential for using DNase-seq to identify individual binding sites, we performed DNase-seq on deproteinized genomic DNA and determined sequence cleavage bias. This allowed us to build bias corrected and TF-specific footprint models. The predictive performance of these models de

SUBMITTER: Yardımcı GG 

PROVIDER: S-EPMC4231734 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature