Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.

ABSTRACT:

Background

DNase I is an enzyme which cuts duplex DNA at a rate that depends strongly upon its chromatin environment. In combination with high-throughput sequencing (HTS) technology, it can be used to infer genome-wide landscapes of open chromatin regions. Using this technology, systematic identification of hundreds of thousands of DNase I hypersensitive sites (DHS) per cell type has been possible, and this in turn has helped to precisely delineate genomic regulatory compartments. However, to date there has been relatively little investigation into possible biases affecting this data.

Results

We report a significant degree of sequence preference spanning sites cut by DNase I in a number of published data sets. The two major protocols in current use each show a different patt

SUBMITTER: Koohy H 

PROVIDER: S-EPMC3724795 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature