H3.3 is enriched at transcribed genes and has a strong 3′ bias. (A) Genes with at least one H3.3 nucleosome (right) have higher transcript abundance than genes without H3.3 (left). Horizontal bars indicate median values. Expression data are from  and in logarithmic scale. (B,C) H3.3 nucleosome (B) and total nucleosome (C) occupancy were measured as H3.3-YFP-ChIP and histone-ChIP signals, respectively. Metagene plots across gene bodies (blue bar) were constructed between -3 kb and +3 kb. Genes were grouped according to transcript abundance from low (red) to high (violet). (D) Validation of H3.3 at promoters by ChIP-qPCR. 5′ Upstream regions of 10 genes that had H3.3-enrichment at promoters in the ChIP-chip experiment were tested. ACTIN7 and a CINFUL-like locus served as controls. Error bars represent standard error of mean, n = 3. GFP, green fluorescent protein.