Discovering chromatin motifs using FAIRE sequencing and the human diploid genome.

ABSTRACT:

Background

Specific chromatin structures are associated with active or inactive gene transcription. The gene regulatory elements are intrinsically dynamic and alternate between inactive and active states through the recruitment of DNA binding proteins, such as chromatin-remodeling proteins.

Results

We developed a unique genome-wide method to discover DNA motifs associated with chromatin accessibility using formaldehyde-assisted isolation of regulatory elements with high-throughput sequencing (FAIRE-seq). We aligned the FAIRE-seq reads to the GM12878 diploid genome and subsequently identified differential chromatin-state regions (DCSRs) using heterozygous SNPs. The DCSR pairs represent the locations of imbalances of chromatin accessibility between alleles and are ideal to rev

SUBMITTER: Yang CC 

PROVIDER: S-EPMC3655836 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature