PMC

(A) Histograms showing that the distributions of peaks for all four ChIP-seq experiments are centered on transcription start sites; the X-axis represents distance from transcription start sites and the Y-axis represents frequency. H3K56ac is H3K56 acetylation (B) Sequence motifs associated with the enriched regions in each ChIP-seq experiment. Only the highest ranked motif is shown. Cross-validation errors (“CV error”) and p-values were calculated as described in Methods.

(A) H3K56 acetylation modifications were found on the promoters and gene body of C/EBPα, C/EBPβ and C/EBPδ. Background represents the mock IgG experiment reads. Rectangular boxes below the H3K56 acetylation peaks represent the enriched regions. The Y-axis represents the number of reads per million sequenced, note that each ChIP experiment was plotted on a different scale on the Y-axis. Arrows indicate the direction of transcription. (B) Profiles from gene set enrichment analysis. Left: HSA4920 Adipocytokine signaling pathway. Right: HSA04930 Type II Diabetes Mellitus. Genes were ranked based on the number of acetylated sites per gene. Black lines represent genes with the specified annotation. The Y-axis represents the enrichment score (see ).

(A) DUSP1 is bound by multiple transcription factors and also has multiple H3K56 acetylation enrichment regions. The rectangular boxes below the peaks represent the enriched regions. (B) Histogram showing the correlation coefficients representing similarity between the relative locations of C/EBPα and E2F4 enrichment signal (left) and E2F4 and H3K56 acetylation enrichment signal (right). (C) Heatmaps showing the intensity of bound regions centered on E2F4 peaks, indicated by an asterisk. Each row in the heatmap represents each binding region, which has been divided into fifteen bins of one hundred base pairs. The color scale indicates the Z score of the number of reads in each bin. The immunoprecipitated proteins are E2F4 (left), C/EBPα (middle) and H3K56 acetylation (right).

(A) The left panel shows 4x phase contrast microscope images of undifferentiated human bone marrow mesenchymal stem cells and the right panel shows the differentiated adipocytes at day 19. (B) Cellomics image analysis of the human bone marrow mesenchymal stem cells-derived adipocytes after 19 days of differentiation, fixed and stained with DAPI (nuclei-blue), Nile red (a selective fluorescent stain for intracellular lipid droplets-yellow), and specific antibodies for PPARγ (Alexa 647-magenta). The left panel shows the lipid and nuclei staining and the right panel has additional PPARγ staining, three of which are indicated with red arrows.

(A) Comparison of the expression level of all genes (left panel) to genes that have (red) or do not have (blue) H3K56 acetylation or transcription factor binding sites. The dark band in the middle of the each box represents the median expression value of all gene that have/do not have an H3K56 acetylation or transcription factor binding sites. Asterisks represent statistical significance with p-values<1e-16. (B) The top panel shows the distribution of expression values for genes that have been categorized based on the distance from their transcription start sites to the nearest H3K56 acetylation peak. The number within each box represents the number of genes in each category. The bottom panel is similar to the top one, zooming in around -1000 to +1000 base pair window.