SU(HW) Fine-Tunes Nuclear Lamina Interactions Figure 2. SU(HW) sites are enriched at LAD borders and within LADs. (A) Binding maps of insulator proteins along a 1 Mb region on chromosome 2L. Y-axes depict the Dam-insulator over Dam-only methylation ratio (high values are truncated at 10). Grey rectangles represent LADs. (B) Theoretical profiles of features that are respectively enriched at LAD borders, enriched inside LADs or depleted from LADs (upper panels). Profiles of insulator and EcR binding peaks across aligned LAD borders. 824 borders, left and mirrored right borders combined (lower panels). The region around each border from which data was taken ranges from the center of the inter-LAD region to the center of the LAD; this ensures that each data point is used only once. X-axis depicts the position relative to the nearest LAD border; positive coordinates inside LADs and negative coordinates outside LADs. Y-axes depict the median number of binding peaks within a running window of 10 kb. Y-axes are scaled to frequencies within the plotted window, depending on the genome-wide frequency of the feature. (C) Percentage of insulator binding peaks within LADs (top) and percentage of inter-LAD peaks within a 10 kb region just outside LADs (bottom). Black horizontal lines represent the percentage expected by chance. **significantly enriched or *depleted compared to random permutation simulations; p,1023. (D) Model of the chromatin organization in LADs, with SU(HW) binding mainly at LAD borders and inside LADs; and DWG, BEAF-32, GAF and CTCF preferentially located in inter-LAD regions. doi:10.1371/journal.pone.0015013.g002 This revealed that the distributions of these three insulator proteins and their cognate motifs are highly similar when aligned to LADs and LAD borders. The motifs of CTCF and GAF are depleted in LADs and not specifically enriched in border regions. In contrast, the motif of SU(HW) is enriched within LADs as well as in border regions. Importantly, the SU(HW) motif shows the same prominent enrichment inside LADs at ,40 kb from LAD borders as was observed for SU(HW) binding. Thus, the enrichments of SU(HW) at LAD borders and at the +40 kb position are to a large extent ‘‘hard-coded’’ in the sequence of the Drosophila genome. PLoS ONE | www.plosone.org 5 November 2010 | Volume 5 | Issue 11 | e15013