Figure 3.

Extensive spatial chromatin remodeling accompanies 5' HoxA gene repression during cellular differentiation. (a) Conventional 3C analysis of transcriptionally regulated HoxA genes. Chromatin contacts between the HoxA9, A10, A11, or A13 genes and surrounding genomic domain were measured in undifferentiated and differentiated cells. The y-axis indicates normalized interaction frequency; the x-axis shows genomic position relative to start of domain characterized. The genomic domain is shown to scale above the graphs, and is as described in Figure 2b. Solid orange vertical lines identify the position of the 'fixed' 3C region analyzed in each graph. Shaded green vertical lines highlight the position of putative DNA looping contacts. Each data point is the average of at least three PCRs. Error bars represent the standard error of the mean. (b) Chromatin contact changes during cellular differentiation. 3C interactions between the HoxA9, A10, A11, or A13 genes and surrounding genomic domain presented in (a) were compared in both cellular states by calculating fold differences (log ratio differentiated/undifferentiated). Areas above and below horizontal dashed lines represent increased and reduced interactions in differentiated cells, respectively (black and white vertical arrows). The genomic domain is shown to scale above the graphs as in (a). Interaction frequencies represent the average of at least three PCRs and error bars represent the standard error of the mean.