Figure 5. Mbd3 and Mbd2 are required for each other’s binding in ES cells.

(A) Genome browser tracks of ChIP-seq experiments examining Mbd3 or Mbd2 occupancy in control (EGFP KD), Mbd2 KD, or Mbd3 KD ES cells over one example locus (Pitx1). (B) Aggregation plots of Mbd3 or Mbd2 ChIP-seq data showing occupancy over ICPs (top left panel), annotated TSSs (bottom left panel), LMR subset (top middle panel), gene-distal DHSs (bottom middle panel), Mbd2 peaks (top right panel), and Mbd3 peaks (bottom right panel) ± 2 kb in control (EGFP KD), Mbd3 KD, or Mbd2 KD ES cells. (C) Heatmaps of Mbd3 enrichment over Mbd3 binding sites ± 2 kb sorted by Mbd2 occupancy (top panel) and Mbd2 enrichment over Mbd2 binding sites ± 2 kb sorted by Mbd3 occupancy (bottom panel) in control (EGFP KD), Mbd2 KD, or Mbd3 KD ES cells. The profiles shown in the browser tracks, aggregation plots, and heatmaps represent the average of two biological replicates.

DOI: http://dx.doi.org/10.7554/eLife.21964.015

Figure 5—figure supplement 1. Interplay between Mbd3 and Mbd2.

(A–B) Genome browser tracks of replicate ChIP-seq experiments examining Mbd3 or Mbd2 occupancy in control (EGFP KD), Mbd2 KD, or Mbd3 KD ES cells over example loci (Hoxd cluster (A) and Tfap2a (B)) show reduced occupancy of Mbd3 in Mbd2 KD cells and of Mbd2 in Mbd3 KD cells over the promoter-proximal regions of Hoxd3, Hoxd11, and Tfap2a.

DOI: http://dx.doi.org/10.7554/eLife.21964.016

Figure 5—figure supplement 2. Mbd3 is required for Dnmt1 occupancy in ES cells.

(A) Western blot showing loss of Mbd3 expression in Mbd3 KO ES cell line. β-actin serves as a loading control. (B) Aggregation plots of Dnmt1 ChIP-seq over ICPs, annotated TSSs, gene-distal DHSs, the LMR subset, total LMRs, Mbd2 peaks, and Mbd3 peaks ± 2 kb in wild-type (WT), Dnmt1 KO, and Mbd3 KO ES cells.

DOI: http://dx.doi.org/10.7554/eLife.21964.017