Figure 4.

Hox gene clusters are mis-regulated in Dnmt1^-/- mouse embryonic fibroblasts. Browser shots from the UCSC genome browser showing H3K27me3 (red) and H3K4me3 (green) ChIP-seq data, and strand-specific mRNA-seq data for the (A) Actb, (B) HoxC, (C) HoxA and (D) HoxD loci in Dnmt1^+/+ and Dnmt1^-/- MEFs. The position of RefSeq genes (blue) is shown along with the direction of sense transcription for the Hox genes (black arrow). The position of UCSC CpG islands (green) is shown. ChIP-seq data is represented as the number of reads that overlap genomic windows. Note the different scales used for H3K4me3 data. mRNA-seq data is represented as the number of reads that overlap genomic windows (log2) on each strand (above and below the dashed line).