Figure 8

Factors required for H2A.Z or H3.3 deposition are required for enhanced accessibility of regions normally bound by these histone variants. (A) Chromatin accessibility determined by RED-seq averaged over regions of the genome bound by H2A.Z, as in Figure 7. Shown are control (EGFP KD) and Ep400 KD ESCs. (B) Western blot of p400 in control (EGFP) or Ep400 KDs, indicating KD efficiency. Actin is shown as a loading control. (C) Average accessibilities over H2A.Z-marked nucleosomes were quantified for biological replicate experiments from –200 to +200 bp with respect to the H2A.Z peak. P-values indicating statistical significance of accessibility between EGFP and Ep400 KDs are indicated. (D) Chromatin accessibility determined by RED-seq averaged over regions of the genome bound by H3.3. Shown are control (EGFP KD) and Hira KD ESCs. (E) Western blot of Hira in control (EGFP) or Hira KDs, indicating KD efficiency. Actin is shown as a loading control. (F) Average accessibilities over H3.3-marked nucleosomes were quantified for biological replicate experiments from –200 to +200 bp with respect to the H3.3 peak. P-values indicating statistical significance of accessibility between EGFP and Hira KDs are indicated. (G) Effects of Ep400 or Hira KD on average nucleosome accessibility shown by plotting RED-seq data over the same 320,135 randomly selected nucleosomes as in Figure 7A. (H) Effects of Ep400 or Hira KD on chromatin accessibility over CTCF binding sites, as in Figure 3C. (I) Average accessibilities over CTCF-binding sites were quantified for biological replicate experiments from –200 to +200 bp with respect to the peak of CTCF-binding. P-values indicating statistical significance of accessibility between EGFP and Hira KDs are indicated.