Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 May 8:14:310.
doi: 10.1186/1471-2164-14-310.

Discovering chromatin motifs using FAIRE sequencing and the human diploid genome

Chia-Chun Yang  1 , Michael J Buck, Min-Hsuan Chen, Yun-Fan Chen, Hsin-Chi Lan, Jeremy J W Chen, Chao Cheng, Chun-Chi Liu
Affiliations

Discovering chromatin motifs using FAIRE sequencing and the human diploid genome

Chia-Chun Yang et al. BMC Genomics. .

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 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.

Conclusions: Our 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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Overview of the algorithm. (A) To identify accessible and inaccessible chromatin regions, we mapped FAIRE-seq reads to a diploid genome (GM12878) using Bowtie without any mismatch. (B) We identified differential chromatin-state regions (DCSRs) and then separated DCSRs into accessible and inaccessible chromatin groups. (C) To discover chromatin motifs, we used all combinations of DNA sequences from 6mer to 10mer (motif candidates) to scan all of the DCSRs, each of which has 41 bases in total. For each motif candidate, we calculated occurrence frequency, and then performed paired t-tests between frequency vectors of the inaccessible chromatin group and accessible chromatin group. We selected chromatin motifs with P values < 0.01 by the paired t-tests. (D) To annotate the motifs, we used the motif sequences and then performed BLAST alignment against the entire transcription factor binding site sequences in both the TFe and hPDI databases. For each motif, we annotated the motif using the best E-value of alignment and homology > 0.8. (E) To provide more accurate annotation, we filtered out the transcript factors that are not expressed (FPKM < 1) by the RNA-seq data (SRP007417).
Figure 2
Figure 2
The hypothesis of chromatin motifs. (A) A chromatin motif in the inaccessible state. The TF may bind to the motif with co-activators and then make the chromatin accessible. (B) A chromatin motif in the accessible state. The TF may bind to the motif with co-repressors and then make the chromatin inaccessible.
Figure 3
Figure 3
An example motif CTC. Assume that a motif candidate is the sequence CTC. We calculated the number of hits (frequency of sequences) among all sliding windows for each DCSR. The frequency vectors of the inaccessible and accessible chromatin groups are [2, 2, 0] and [1, 0, 0], respectively. Next, we performed a paired t-test between these two frequency vectors to determine the significance of this motif in terms of differential chromatin states.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Grewal SI, Jia S. Heterochromatin revisited. Nat Rev Genet. 2007;8(1):35–46. doi: 10.1038/nrg2008. - DOI - PubMed
    1. Taberlay PC, Kelly TK, Liu CC, You JS, De Carvalho DD, Miranda TB, Zhou XJ, Liang G, Jones PA. Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell. 2011;147(6):1283–1294. doi: 10.1016/j.cell.2011.10.040. - DOI - PMC - PubMed
    1. Han H, Cortez CC, Yang X, Nichols PW, Jones PA, Liang G. DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Hum Mol Genet. 2011;20(22):4299–4310. doi: 10.1093/hmg/ddr356. - DOI - PMC - PubMed
    1. Henikoff S. Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet. 2008;9(1):15–26. - PubMed
    1. Wallrath LL, Lu Q, Granok H, Elgin SC. Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. Bioessays. 1994;16(3):165–170. doi: 10.1002/bies.950160306. - DOI - PubMed

Publication types

LinkOut - more resources