Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription

Abstract

DNA sequence variation has been associated with quantitative changes in molecular phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. To understand the interplay between chromatin and genetic control of gene regulation, we quantified allelic variability in transcription factor binding, histone modifications, and gene expression within humans. We found abundant allelic specificity in chromatin and extensive local, short-range, and long-range allelic coordination among the studied molecular phenotypes. We observed genetic influence on most of these phenotypes, with histone modifications exhibiting strong context-dependent behavior. Our results implicate transcription factors as primary mediators of sequence-specific regulation of gene expression programs, with histone modifications frequently reflecting the primary regulatory event.

Figure 1. Allele-specific (AS) activity within transcriptional and chromatin layers

(A) Proportion of accessible heterozygous SNP sites showing significant AS activity (median across all individuals, n=3–14). (B) Consistency of allelic effects within genomic regions of TF binding and histone modification. Bars represent the proportion of peaks with a consistent allelic direction at two or more SNP sites.

Figure 2. DNA sequence properties at allele-specific (AS) PU.1 binding sites

(A) SNPs in PU.1- and cooperative TF motifs are predictive of AS PU.1 binding (5% FDR) (5). (B) PU.1-bound regions (peaks) with homotypic PU.1 motifs show a weak response towards motif-disrupting SNPs. Motif-disrupting SNPs were split into two classes (one or two PU.1 motifs per peak) and grouped based on their motif impact (1, lowest; 10 highest).

Figure 3. Genetic component of allele-specific (AS) transcriptional and chromatin activity

(A) Distribution of pairwise correlation coefficients of significant AS sites between all unrelated CEU individuals (n=10) for each molecular phenotype. Correlation of the reference allele ratio is calculated at shared significant AS SNP sites using Spearman rank correlation. (B–D) Correlation of the paternal allele ratio of the child and that inferred from the parents at SNP sites where parents are opposite homozygotes and the child has a significant allelic effect. (B) Examples of transmitted PU.1 and H3K27ac SNP sites. (C) Genome-wide transmission results. GRO-seq signal was analyzed separately for each strand (filled and empty points, forward and reverse strand, respectively; P-value represents combined data). (D) Transmission results of H3K4me1 and H3K27ac near DNase I sensitivity QTLs (+/− 1 kb window around the dsQTL).

Figure 4. Local, short- and long-range coordination between transcriptional and chromatin layers

Results of allelic coordination (A) and haplotypic coordination (B) analysis at gene regions (genes +/− 50 kb) (5). Coordination of the allelic effect was considered between all pairs of assays. SNP sites within genomic regions were required to show a significant AS effect in both assays. Only assay pairs with >=20 SNPs were considered for the analysis. Significant Spearman rank correlation coefficients (P < 0.05) between the paternal allele ratios of the SNP pairs are indicated with colored lines ranging in intensity from ρ = −1.0 (blue) to ρ = 1.0 (red). Non-significant correlations are indicated with grey lines and missing lines indicate lack of sufficient data points for analysis.