FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription

Abstract

Complex organisms require tissue-specific transcriptional programs, yet little is known about how these are established. The transcription factor FoxA1 is thought to contribute to gene regulation through its ability to act as a pioneer factor binding to nucleosomal DNA. Through genome-wide positional analyses, we demonstrate that FoxA1 cell type-specific functions rely primarily on differential recruitment to chromatin predominantly at distant enhancers rather than proximal promoters. This differential recruitment leads to cell type-specific changes in chromatin structure and functional collaboration with lineage-specific transcription factors. Despite the ability of FoxA1 to bind nucleosomes, its differential binding to chromatin sites is dependent on the distribution of histone H3 lysine 4 dimethylation. Together, our results suggest that methylation of histone H3 lysine 4 is part of the epigenetic signature that defines lineage-specific FoxA1 recruitment sites in chromatin. FoxA1 translates this epigenetic signature into changes in chromatin structure thereby establishing lineage-specific transcriptional enhancers and programs.

Figure 1. Genome-wide identification of FoxA1 binding sites reveals its global role in control of E2 signaling in breast cancer cells

A) Overlap analysis at FDR1% showing the number of binding sites specific to FoxA1 or ERα or shared between the two factors in MCF7 cells. B) Correlation between E2 up-regulated (left panel) or down-regulated (right panel) genes and binding of either ERα only (ERα unique), FoxA1 only (FoxA1 unique), both factors at different sites (ERα+FoxA1) or both factors at a shared site (ERα/FoxA1 overlapping sites) within 20 kb of the TSS of genes. Fold change is presented for instances where significant differences are observed between regulated (t-test p-value ≤ 10-3) versus non-regulated genes (t-test p-value ≥ 10-3). C) Correlation between ERα and FoxA1 binding sites and genes co-expressed with FoxA1 in primary breast tumors (Wang et al., 2005) were analyzed as in B. Fold change is presented for instances where significant differences are observed.

Figure 2. Cell type-specific recruitment of FoxA1 correlates with differential gene expression patterns

A) Cis-regulatory element annotation system (CEAS) (Ji et al., 2006) was used to determine the distribution of FoxA1 binding regions identified within chromosomes 8, 11 and 12 in MCF7 and LNCaP cells regarding known genes. B) Overlap analysis at FDR1% showing the number of FoxA1 binding sites specific to MCF7 or LNCaP or shared between the two cell-lines. C) Correlation between cell type-specific or shared FoxA1 binding sites and genes co-expressed with FoxA1 in primary breast (Wang et al., 2005) or prostate (Setlur, SR., Mertz, KD., Hoshida,Y., Demichelis, F., Lupien, M., Perner, S., Sboner, A., Pawitan, Y., Andren, O., Johnson, LA., et al. unpublished results) tumors. The occurrence of FoxA1 binding sites within 20 kb of the TSS of FoxA1 co-expressed genes was compared to that of non co-expressed genes. Fold change is presented for instances where significant differences are observed.

Figure 3. FoxA1 cell type-specific binding sites also recruit nuclear receptors ERα or AR and correlate with regulation of sex steroid signaling in breast and prostate cancer cells

A) Enrichment for the ERE, ERE half-site, FKHR, ARE and ARE half-site in the center of the binding sites specific to MCF7 cells (MCF7-only) or LNCaP cells (LNCaP-only) or shared between the two cell-lines (Both). The occurrence of the motifs (N motifs) was normalized to the number of sites in each subset (N binding sites). B) Venn diagrams depicting the overlap between FoxA1 (red) and ERα (blue) binding sites from MCF7 cells together with FoxA1 (green) and AR (orange) binding sites from LNCaP cells. C). Correlation between E2 or DHT regulated genes and binding sites for FoxA1 and ERα in MCF7 cells or for FoxA1 and AR in LNCaP cells. Analyses were performed as in Fig.1B using hormone regulated or non-regulated genes from chromosomes 8,11 and 12. Fold change is presented for instances where significant differences are observed between regulated versus non-regulated genes.

Figure 4. Methylation pattern of histone H3 lysine 4 correlates with cell type-specific FoxA1 recruitment

A) De novo determination of the sequence recognized by FoxA1 within its cell type-specific or shared binding sites. Logos show the consensus sequences of the enriched Forkhead motifs found by de novo analyses within the FoxA1 binding sites specific to MCF7 (MCF7-only) or LNCaP (LNCaP-only) cells or common to the two cell-lines (Both) in comparison to the Transfac FoxA1 matrix (http://www.gene-regulation.com/pub/databases.html#transfac). B-G) Levels of H3K9me2 (B-C) H3K4me1 (D-E) and H3K4me2 (F-G) on FoxA1 recruitment sites specific to MCF7 cells (MCF7-only) or LNCaP cells (LNCaP-only) or shared between the two cell-lines (Both) were determined by ChIP-qPCR. Box plots were generated from data obtained from three independent experiment testing 11 sites specific to MCF7 cells, 12 to LNCaP cells and 8 common to both cell-types. Statistical analyses of the difference between the non cell type-specific sites and the other sites are presented, *: p≤0.05 and **: p≤0.01. H) ChIP-chip analyses of H3K4me2 levels across chromosomes 8,11 and 12 in MCF7 cells. Two independent ChIP-chip experiments were combined and analyzed using the MAT algorithm. The signals given by the probes localized in the 200 bp central regions of the FoxA1 binding sites unique to MCF7 (MCF7-only) or LNCaP (LNCaP-only) or shared (Both) by the two cell-lines were compared (left graph). Similarly, H3K4me2 levels at 200bp regions containing the FoxA1 recognition motif bound by FoxA1 were compared to randomly selected FoxA1 unbound FoxA1 recognition motif containing regions (right graph). Means +/- S.E. of H3K4me2 levels given by MAT are shown as well as statistically significant differences with *** corresponding to p≤0.001.

Figure 5. FoxA1 silencing decreases chromatin accessibility of enhancers but not H3K4 methylation levels

A) Effect of ERα silencing on FoxA1 recruitment. Eight sites recruiting both ERα and FoxA1 in MCF7 cells were used to monitor the effect of ERα silencing on ERα and FoxA1 recruitment by ChIP-qPCR. Reduction in ERα protein levels by siERα was also demonstrated by western blot (Fig.S16A). B) DNaseI sensitivity assays were performed in both MCF7 and LNCaP cells and the percent change triggered by FoxA1 silencing from at least three independent experiments is reported. C) Effect of FoxA1 silencing on the levels of H3K4me1 and me2 at binding sites used in the DNaseI sensitivity assays in both MCF7 and LNCaP cells from three experiments is presented, * p≤0.05 and **: p≤0.01. D-E) Presence of H3K4me1/me2 at enhancer is not sufficient for transcriptional regulation of BIK and CCND1 in MCF7 cells. H3K4me1/2 levels at FoxA1 recruiting enhancers localized within or nearby FoxA1 target genes were determined by ChIP-qPCR in MCF7 cells transfected with siLuc or siFoxA1 (C). Even though FoxA1 silencing did not modulate the levels of H3K4 methylation, the expression of the target genes was significantly reduced (D).

Figure 6. Role of H3K4me2 in FoxA1 recruitment to the chomatin

A-C) Effect of KDM1 over-expression on H3K4 methylation (A), FoxA1 recruitment (B) and H3K9 methylation (C). H3K4me2 and H3K9me2 levels as well as FoxA1 recruitment were determined in control or KDM1 over-expressing cells by ChIP-qPCR. Box plots were generated from data obtained for 16 sites. Results from one representative experiment are presented with the statistical analyses of the difference between control and KDM1 over-expressing cells, **: p≤0.01. D) Western blots showing KDM1, FoxA1 and Calnexin (Control) levels in MCF7 cells transfected with an empty control plasmid or a plasmid coding for KDM1. E) Specific examples of genes regulated by E2, DHT or by both hormones. One gene specifically regulated by E2 in MCF7 cells (MCF7-only), by DHT in LNCaP cells (LNCaP only) and by both hormones in MCF7 and LNCaP cells respectively (both) are shown. E2 and DHT regulated genes were identified using expression array analyses performed in MCF7 and LNCaP cells, respectively. Significantly regulated genes were determined using a t-test and a p-value cut-off of 5×10^-3. ERα, AR and FoxA1 binding sites from ChIP-chip are indicated together with the occurrence of histone modifications derived from ChIP-qPCR at these sites. Enrichment for the various factors is presented by green and red blocks in LNCaP and MCF7 cells, respectively. White blocks indicate the absence of enrichment for the ChIPed factors or a decrease of more than two-fold for histone marks in MCF7 cells following KDM1 over-expression. A 4 kb wide view of the probe signals obtained by ChIP-chip for FoxA1, ERα and AR at the analyzed binding sites is also shown. Complete probe signal across the 3 genes selected is presented in Fig.S21.

Figure 7. Model of the cell type-specific interplay between the epigenetic signature and FoxA1 for the establishment of lineage specific transcriptional programs

Schematic representation of how FoxA1 recruitment occurs primarily on H3K9me2-poor but H3K4me1/me2-rich regions. H3K4me1/me2 could guide FoxA1 cell type-specific recruitment through direct physical interactions. FoxA1 regulation of differential transcriptional programs is subsequently achieved through transcriptional collaborations with cell type-specific (ERα and AR) as well as ubiquitously expressed (AP-1) transcription factors.