Extended Data Fig. 1: Characterization and validation of H3.3 ULI-NChIP-seq data.
From: Reprogramming of the histone H3.3 landscape in the early mouse embryo
a, Western blotting showing the specificity of antibodies. Anti-H3.1/H3.2, anti-H3.3 and anti-pan-H3 antibodies were used to label recombinant H3.1 or H3.3. Results from two biological replicates are shown. Uncropped blot images are shown in the Source Data. b, Genome browser snapshots of the H3.3 ULI-NChIP-seq data. The H3.3 UNI-NChIP-seq data generated from 300 mESCs (this study) with prior H3.3 ChIP-seq data (GSE59189)4 shown for comparison. Enrichment is shown by log2 ratios between H3.3 ULI-NChIP and input. The midline corresponds to log2 ratio = 0. Higher and lower enrichment over input is indicated in magenta and blue, respectively. c, Hierarchical clustering and correlation analysis of H3.3 ULI-NChIP-seq data. Correlation between the data was analyzed by considering H3.3 enrichment in genome-wide 10-kb bins. Heatmaps show Spearman’s correlation coefficients between the samples. d, Plots showing average H3.3 enrichment at genic regions of the indicated samples. e, Plots showing CpG methylation level around genic regions. Genes were categorized by indicated CpG density at promoters as well as their expression levels. DNA methylation data was obtained from GSE63417 (zygote) and GSE56697 (2-cell and 4-cell). f, Plots showing average H3.3 enrichment at distal DNase I-hypersensitive sites. DNase I-hypersensitive sites distal to genic regions (top) were identified using previously published data (GSE76642)23. Bottom, H3.3 enrichment at the distal DNase I-hypersensitive sites. g, Genome browser snapshots of the H3.3 ULI-NChIP-seq data. Arrows indicate the positions of indicated repetitive elements.
