Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

Abstract

We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different transcription factors: STAT1 in the immortalized HeLa S3 cell line, with and without interferon-gamma (IFNG) stimulation; and FOXA2 in mouse adult liver tissue. In unstimulated and stimulated HeLa cells, respectively, we determined approximately 270,000 and approximately 301,000 H3K4me1-enriched regions, and approximately 54,500 and approximately 76,100 H3K4me3-enriched regions. In mouse adult liver, we determined approximately 227,000 and approximately 34,800 H3K4me1 and H3K4me3 regions. Seventy-five percent of the approximately 70,300 STAT1 binding sites in stimulated HeLa cells and 87% of the approximately 11,000 FOXA2 sites in mouse liver were distal to known gene TSS; in both cell types, approximately 83% of these distal sites were associated with at least one of the two histone modifications, and H3K4me1 was associated with over 96% of marked distal sites. After filtering against predicted transcription start sites, 50% of approximately 26,800 marked distal IFNG-stimulated STAT1 binding sites, but 95% of approximately 5800 marked distal FOXA2 sites, were associated with H3K4me1 only. Results for HeLa cells generated additional insights into transcriptional regulation involving STAT1. STAT1 binding was associated with 25% of all H3K4me1 regions in stimulated HeLa cells, suggesting that a single transcription factor can interact with an unexpectedly large fraction of regulatory regions. Strikingly, for a large majority of the locations of stimulated STAT1 binding, the dominant H3K4me1/me3 combinations were established before activation, suggesting mechanisms independent of IFNG stimulation and high-affinity STAT1 binding.

Figure 1.

Association and concordance rates. Concordance rates between unstimulated and IFNG-stimulated HeLa cells for H3K4me1 (A), H3K4me3 (B), and STAT1 (C), using FDR ∼0.01 profiles, with random expectations in parentheses. Association rates between STAT1 and H3K4me1/me3 in unstimulated (D) and stimulated (E) HeLa cells. (F) Association rates between STAT1 in IFNG-stimulated cells and H3K4me1/H3K4me3 in unstimulated cells. (G) Association rates between FOXA2, H3K4me1, and H3K4me3 in adult mouse liver. (A–C) Concordance rates relative to numbers of both unstimulated and stimulated regions (e.g., for H3K4me1, 72.0% and 67.4%). (D–G) Percentages in red are relative to the TF (e.g., in E, 32.7% of IFNG-stimulated STAT1 binding sites are associated with H3K4me1 and not H3K4me3), while those in blue and green are relative to H3K4me1 and H3K4me3, respectively, and refer to modified regions that are not associated with the TF (e.g., in E, 7.1% of the H3K4me1 regions that are not associated with STAT1 are associated with H3K4me3).

Figure 2.

Relationships between regions enriched in STAT1 or FOXA2 and in H3K4me1 and H3K4me3. (A,C) Number and fraction of all, proximal, and distal STAT1 binding sites, and distal binding sites filtered by predicted TSS (DEE) in IFNG-stimulated HeLa cells. (B,D) As for STAT1, but for distal FOXA2 binding sites in mouse adult liver. A binding site was distal if the location of its maximum coverage was farther than ±2.5 kb from a transcriptional start site of UCSC known gene.

Figure 3.

Spatial relationships for TF-associated H3K4me1 and H3Kme3. Coverage profiles associated with STAT1 in IFNG-stimulated HeLa cells (A) and FOXA2 in mouse adult liver (B). Density distributions for distances between the location of maximal coverage for a region enriched in STAT1 (C) or FOXA2 (D) and the closest H3K4me1- or H3K4me3-enriched region. (Blue lines) H3K4me1; (green lines) H3K4me3; (solid lines) profiles for distal TF regions; (dashed lines) profiles for proximal TF regions. We distinguished these groups using a ±2.5-kb threshold distance from UCSC hg18 or mm8 known gene TSS. The area under each curve was normalized to 1.0.

Figure 4.

Examples of TF, histone modification, and read mappability profiles. (A) A 15-kb UCSC hg18 genome browser view around the 5′-end of the STAT1 gene (chr2:191,581,501–191,596,500). The gene is transcribed from right to left. Custom tracks are XSET coverage profiles for (from the top) STAT1, H3K4me1, and H3K4me3. Pairs of profiles show IFNG-stimulated cells above and unstimulated cells below. (B,C) Overall 25-kb (chr5:91,517,001–91,542,000) and detailed 8-kb (chr5:91,519,901–91,527,900) UCSC mm8 genome browser views that include a known and a novel enhancer for the albumin (Alb1) gene (Wederell et al. 2008). The gene is transcribed from left to right. ChIP-seq coverage profiles are (from the top) FOXA2, H3K4me1, and H3K4me3 in mouse adult liver. (A–C) The final custom track is a profile for (gray) 27-mer exact match mappability; (black horizontal lines) coverages (heights) that correspond to profile-specific FDR thresholds of ∼0.01 (Table 1).