Viral expression of HOX-TFs in chicken micromass culture (chMM) modifies chondrogenic cell differentiation.

<p>(A) Individual HOX-TF expressing chMM cultures stained with Alcian blue (top) and Eosin (bottom). Alcian Blue staining of four biological replicates was quantified and compared to mock-infected chMM. Error bars indicate standard deviation from four replicates. (B) Hierarchical clustering of differentially regulated genes in the nine HOX-TF expressing cultures (all RNA-seq shown in replicates). The top 50 differentially regulated genes from each sample were selected (Criteria: p-Val ≤10e-5, base mean≥30, fold change≥2) and for each replicate, the log2-transformed fold changes relative to mock-infected cultures of these 205 genes were subjected to hierarchical clustering.</p

AP1 and CTCF binding sites are overrepresented in Group 1 HOX-TF binding sites.

<p>(A) <i>De novo</i> motif analysis of all Group 1 HOX-TF peaks (here, HOXA10 results) identifies overrepresented binding sites. A comparison of these motifs to known AP1 and CTCF motifs is shown below. (B) Centrimo analysis identifies the position of best binding site matches in all peak sequences. Blue and black lines indicate enrichment of the given HOXA10 or HOXD13 motif shown below, respectively. Yellow lines indicate enrichment for CTCF motif shown below. (C) The overlap of peaks containing a HOX (Group 1- blue, Group 2- black) or a CTCF (yellow) binding site. The red overlap indicates peaks containing a HOX and a CTCF binding site.</p