Genome-wide binding profiles of Drosophila melanogaster insulator proteins in Kc and Mbn2 cells

ChIP-chip experiments with NimbleGen whole-genome tiling arrays to compare Su(Hw), dCTCF, BEAF, and CP190 localization on DNA in Kc and Mbn2 cells revealed that BEAF is a third subclass of CP190-containing insulators. The DNA binding proteins, Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line specific localization sites for all three DNA binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression. Three replicates of Su(Hw), dCTCF, and CP190 ChIP-chip experiments in both Kc and Mbn2 cells as well as two replicates of BEAF ChIP-chip experiments in both Kc and Mbn2 cells were compared.