Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.

ABSTRACT: The expression of eukaryotic genes is regulated by cis-regulatory elements such as promoters and enhancers, which bind sequence-specific DNA-binding proteins. One of the great challenges in the gene regulation field is to characterise these elements. This involves the identification of transcription factor (TF) binding sites within regulatory elements that are occupied in a defined regulatory context. Digestion with DNase and the subsequent analysis of regions protected from cleavage (DNase footprinting) has for many years been used to identify specific binding sites occupied by TFs at individual cis-elements with high resolution. This methodology has recently been adapted for high-throughput sequencing (DNase-seq). In this study, we describe an imbalance in the DNA strand-specific alignme

SUBMITTER: Piper J 

PROVIDER: S-EPMC3834841 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature