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. Author manuscript; available in PMC: 2008 Apr 20.
Published in final edited form as: Cell. 2008 Mar 21;132(6):958–970. doi: 10.1016/j.cell.2008.01.018

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

Figure 4

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.