Figure 6

Finding potential cis-regulatory elements. (A) Heat maps of H3K4me1 and H3K27ac marks in regions located within 50 kb of the 5^′ end of genes with significant changes in expression in the course of 7 days of chondrogenic differentiation in donors 2–4. Data for donor 1 are not available due to a failed experiment. Definition of rows, sorting of rows and clustering of columns as described in the Legend to Figure 2B. Each column has 262 533 rows. (B) Profiles of the regulatory histone modification marks for selected chondrogenic and mesenchymal signature genes. Shown is the 500 bp bin with the highest histone enrichment ratio for the indicated genes in a 50 kb area as mean value of three donors. Error bars are SD. (C) ChIP-seq signal tracks for H3K4me1 and H3K27ac in a 50 kb area on either side of the TSS of the COL2A1 gene. Validated (green) and potential new [29] regulatory areas are highlighted. (D) Left side: Motif scanning for transcription factor binding sites in regions enriched for H3K27ac in differentiated cells. Example motif shown from Jaspar database. The members of the TF families are TFs known to be involved in chondrogenesis which share similar binding motifs. Right side: Motif hits in regulatory areas around the COL2A1 gene