Figure 2. KDM4A preserves maternal epigenome integrity and prevents against widespread co-occurrence of H3K4me3-H3K9me3 in oocytes.

(a) Immunofluorescence imaging of H3K9me3 in maternal pronuclei of Kdm4a^+/- and Kdm4a^-/-(MZ) zygotes where DNA is counterstained using DAPI. Representative images of a mid-section zygote are shown with both parental pronuclei (left panel). Maternal pronuclei H3K9me3 intensity levels and volume are compared for significance using a two-tailed unpaired t-test with Welch correction (right panel). Violin plots show data distribution with median and quartiles for 12 zygotes assessed for each genotype. (Scale bar: 10μm).

(b) Heat maps (left) and line graphs (right) of averaged H3K9me3 ChIP-Seq signal in Kdm4a^+/+ (blue) and Kdm4a^-/- (red) MII oocytes at previously defined bdH3K4me3 (>= 20kb size) and surrounding loci, all adjusted to fit the same visual space. The bdH3K4me3 set of regions is ordered according to H3K9me3 levels in a wild-type replicate with signal enrichment shown in FPKM.

(c) Heat maps (left panel) and line graphs (right panel) of averaged (bottom) H3K9me3 ChIP-seq signal in Kdm4a^+/+ (blue) and Kdm4a^-/- (red) MII oocytes at genes including transcription start-sites (TSS), entire gene bodies and surrounding loci. All non-redundant genes annotated in UCSC database were adjusted to fit the same visual space. The genes are ordered according to H3K9me3 levels in a wild-type replicate with signal enrichment shown in FPKM.

(d) Heat maps (left panel) and line graphs (right panel) of averaged H3K4me3 ChIP-Seq signal in Kdm4a^-/- (red) and Kdm4a^+/+ (blue) MII oocytes at bdH3K4me3 and surrounding loci as defined in panel (b).

(e) Heat maps (left panel) and line graphs (right panel) of averaged H3K4me3 ChIP-seq signal in Kdm4a^-/- (red) and Kdm4a^+/+ (blue) MII oocytes at non-redundant UCSC genes ordered as in panel (c). The ChIP-seq assays in b-e were performed on two independent pools of oocytes. Statistical source data are provided in source data fig. 2.