Extensive HoxA spatial chromatin remodeling during cellular differentiation involves the transcriptionally regulated 5' end region. (a) 5C chromatin interaction profiles with the greatest differences between undifferentiated and differentiated states were extracted from 5C datasets. The normalized interaction frequency is plotted logarithmically on the y-axis to emphasize differences between cellular states. The x-axis shows genomic position relative to the start of the domain analyzed. The linear HoxA cluster diagram and predicted BglII restriction pattern are shown to scale above the graphs, and are as described in Figures 2b, 5 & 6. Solid orange vertical lines identify the position of 'fixed' 5C interaction profiles presented in each graph. Shaded green vertical lines highlight position of putative 3'-5' looping regions. Each data point is the average of at least three array interaction frequencies. Error bars represent the standard error of the mean. (b) 5C chromatin compaction of a gene desert control region does not change during differentiation. The y-axis indicates interaction frequency and the x-axis shows genomic distance between interacting fragments. The average log ratio of corresponding contacts in undifferentiated and differentiated cells from this dataset was used to normalize HoxA 5C datasets shown in Figures 5 & 6 and in (a). Interaction frequencies represent the average of at least three array interaction frequencies and error bars represent the standard error of the mean.
Fraser et al. Genome Biology 2009 10:R37 doi:10.1186/gb-2009-10-4-r37