Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data.

ABSTRACT: Transcription factors (TFs) are crucial epigenetic regulators, which enable cells to dynamically adjust gene expression in response to environmental signals. Computational procedures like digital genomic footprinting on chromatin accessibility assays such as ATACseq can be used to identify bound TFs in a genome-wide scale. This method utilizes short regions of low accessibility signals due to steric hindrance of DNA bound proteins, called footprints (FPs), which are combined with motif databases for TF identification. However, while over 1600 TFs have been described in the human genome, only ~ 700 of these have a known binding motif. Thus, a substantial number of FPs without overlap to a known DNA motif are normally discarded from FP analysis. In addition, the FP method is restricted to or

SUBMITTER: Schultheis H 

PROVIDER: S-EPMC11039736 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature