Fig. 4: Mechanistic insights into transcriptional changes by catalytic histone acetylation.

Before analysis, THP-1 cells were treated with catalyst 1 (acetylated) or 2 (control) (10 µM) and acetyl donor 4 (1 mM) for 0–120 min in (a), or 45 min in (b–j). Red and blue dots or lines represent significantly upregulated (UP) and downregulated (DOWN) genes, respectively (P < 0.05 in Student’s two-sided t test, log₂FC > 1 or < 1). Gray dots or lines represent other genes (NS). a Immunoblot showing histone modification levels after catalytic histone acetylation (1 + 4) or SAHA (2 µM) treatment. b Scatter plot of the FPKM + 1 value of genes in RNA-seq analysis (n = 2). c, d Metagene profiles in ChIP-seq analyses of RNA polymerase II (Pol II) in (c), or H2BK120ac in (d). Gray lines represent other genes (NS). e Genome browser track example of the ChIP-seq data over the GADD45B and CITED2 loci visualized by the Integrated Genomics Viewer (IGV). f Top-5 enriched clusters of ENCODE TF ChIP-seq 2015 library from enrichment analysis of 124 upregulated genes (log₂FC > 1) The P-value was calculated by Fisher’s two-sided exact test. g Metagene profiles in ChIP-seq analyses of NELF. Venn diagram indicating overlapping upregulated (UP) genes and high NELFE genes, which had top-200 normalized tag count of NELFE ChIP-seq. The P-value was calculated by Fisher’s two-sided exact test. h Comparison of the change of normalized tag count of NELFE ChIP-seq after acetylation. Data are shown as mean ± SEM of the tag count for 13,710 genes. The P-value was calculated by the Student’s two-sided t test. i Immunoblot showing NELFE and H2BK120ac after catalytic histone acetylation. The loading amounts of proteins were visualized with Oriole staining. Representative blots in two independent experiments are shown. j Comparison of the fold change of mRNA levels after catalytic histone acetylation. Data are shown as mean ± SEM (n = 200 for high NELFE genes, 14,500 for low NELFE genes). The P-value was calculated by the Student’s two-sided t test. k A plausible mechanism of transcriptional activation of UP genes with high NELFE by the catalytic histone acetylation. See the Discussion section for details.