Fig. 4.

Characterization of MBD9 chromatin binding. a Genomic distribution of MBD9-enriched peaks vs wild type (mac2 peak caller, q value <0.01). b Average distribution of DNA methylation levels in CG, CHG, and CHH contexts in wild type over MBD9-occupied peaks and MBD9 control peaks. c Heatmap of normalized MBD9 signal (log₂ RPKM) over wild-type control and normalized ATAC-seq signal (RPKM) from merged replicates in wild type and mbd9-3 mutant over MBD9-occupied peaks. d Upper: Distribution of normalized signal (RPKM) for MBD9-3xFlag ChIP-seq, wild-type Flag ChIP-seq control, H2A.Z, and H3 in wild type over protein-coding genes. Lower: Distribution of normalized signal (RPKM) for ATAC-seq in wild type over protein-coding genes. e Snapshot representing normalized read counts (RPKM) for MBD9-3xFlag ChIP-seq, wild-type Flag ChIP-seq control, ATAC-seq, H2A.Z, and H3. Signal for ATAC-seq, H2A.Z, and H3 is a merge of two biological replicates. f Distribution of normalized H2A.Z ChIP-seq signal (RPKM) from merged replicates in wild type, mbd9-3, arp6-1, and arp6-1 mbd9-3 over MBD9-occupied genes. g Heatmap ordered based on k-means clustering of H2A.Z ChIP-seq signal in wild type (cluster n = 5) at MBD9-occupied genes. Shown are corresponding H2A.Z ratio plots for wild type over mbd9-3, arp6-1, and arp6-1 mbd9-3 mutants and MBD9-3X Flag ChIP-seq over wild-type flag control in log₂ RPKM, ATAC-seq in wild type in RPKM, and H3K27me3 levels in wild type in RPKM. Source data are provided as Source Data file