Discovering chromatin motifs using FAIRE sequencing and the human diploid genome

Abstract

BackgroundSpecific 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.ResultsWe 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 reveal chromatin motifs that may directly modulate chromatin accessibility. In this study, we used DNA 6-10mer sequences to interrogate all DCSRs, and subsequently discovered conserved chromatin motifs with significant changes in the occurrence frequency. To investigate their likely roles in biology, we studied the annotated protein associated with each of the top ten chromatin motifs genome-wide, in the intergenic regions and in genes, respectively. As a result, we found that most of these annotated motifs are associated with chromatin remodeling, reflecting their significance in biology.ConclusionsOur method is the first one using fully phased diploid genome and FAIRE-seq to discover motifs associated with chromatin accessibility. Our results were collected to construct the first chromatin motif database (CMD), providing the potential DNA motifs recognized by chromatin-remodeling proteins and is freely available at http://syslab.nchu.edu.tw/chromatin.

Detect accessible chromatin using ATAC-sequencing, from principle to applications

“…The FAIRE-seq uses formaldehyde immobilization, phenol chloroform extraction and separation to obtain exposed DNA. However, its background is high, and sequencing signal-to-noise ratio is low [45–47].…”

Chromatin accessibility: a window into the genome

“…This assay has been instrumental for the identification of active regulatory elements in a number of human cell lines by ENCODE [ 26 ]. It has been used widely to detect open chromatin in normal and diseased cells [ 86 , 91 , 94 , 95 ], to associate specific chromatin states with known sequence variants of disease susceptibility [ 91 ] or allele-specific signatures [ 96 ], and to decipher the effects of TF binding to chromatin structure [ 97 , 98 ].…”

High-Resolution Breakpoint Analysis Provides Evidence for the Sequence-Directed Nature of Genome Rearrangements in Hereditary Disorders

“…Table S4), of which several are (to some extent) involved in chromatin state remodeling. Five shorter DREME motifs, GGAGTGCA, ATACAAA, CCACC, AGTAGC, and CTAAT have also been well tagged in the chromatin motif database [Yang et al., ], suggesting that sites of homologous recombination are not only determined by highly homologous sequences, but also by DNA motifs and proteins that bind to them thereby acting in the regulation of higher‐order states of genomic architecture.…”