XL-DNase-seq: improved footprinting of dynamic transcription factors.

ABSTRACT:

Background

As the cost of high-throughput sequencing technologies decreases, genome-wide chromatin accessibility profiling methods such as the assay of transposase-accessible chromatin using sequencing (ATAC-seq) are employed widely, with data accumulating at an unprecedented rate. However, accurate inference of protein occupancy requires higher-resolution footprinting analysis where major hurdles exist, including the sequence bias of nucleases and the short-lived chromatin binding of many transcription factors (TFs) with consequent lack of footprints.

Results

Here we introduce an assay termed cross-link (XL)-DNase-seq, designed to capture chromatin interactions of dynamic TFs. Mild cross-linking improved the detection of DNase-based footprints of dynamic TFs but interfered

SUBMITTER: Oh KS 

PROVIDER: S-EPMC6547507 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature