Comparative evaluation of DNase-seq footprint identification strategies.

ABSTRACT: DNase I is an enzyme preferentially cleaving DNA in highly accessible regions. Recently, Next-Generation Sequencing has been applied to DNase I assays (DNase-seq) to obtain genome-wide maps of these accessible chromatin regions. With high-depth sequencing, DNase I cleavage sites can be identified with base-pair resolution, revealing the presence of protected regions ("footprints"), corresponding to bound molecules on the DNA. Integrating footprint positions close to transcription start sites with motif analysis can reveal the presence of regulatory interactions between specific transcription factors (TFs) and genes. However, this inference heavily relies on the accuracy of the footprint call and on the sequencing depth of the DNase-seq experiment. Using ENCODE data, we comprehensively eval

SUBMITTER: Barozzi I 

PROVIDER: S-EPMC4133688 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature