Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions

Abstract

Insulators are protein-bound DNA elements that are thought to play a role in chromatin organization and the regulation of gene expression by mediating intra-and interchromosomal interactions. Suppressor of Hair-wing [Su(Hw)] and Drosophila CTCF (dCTCF) insulators are found at distinct loci throughout the Drosophila melanogaster genome and function by recruiting an additional protein, Centrosomal Protein 190 (CP190). We performed chromatin immunoprecipitation (ChIP) and microarray analysis (ChIP-chip) experiments with wholegenome tiling arrays to compare Su(Hw), dCTCF, boundary element-associated factor (BEAF), and CP190 localization on DNA in two different cell lines and found evidence 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. These findings suggest a model in which insulator subclasses may have distinct functions that together organize the genome in a cell type-specific manner, resulting in differential regulation of gene expression.[Keywords: Insulators; chromatin organization; BEAF; CTCF; gypsy] Supplemental material is available at http://www.genesdev.org.

Opening Pathways for Underrepresented High School Students to Biomedical Research Careers: The Emory University RISE Program

“…Previous studies have shown that Drosophila insulator proteins are present at hundreds of sites throughout the genome that colocalize to distinct foci predominantly around the nuclear periphery in diploid cells (Ramos et al 2006;Gerasimova et al 2007). A number of proteins have been identified that interact with insulator DNA but additional components may be required to explain all the properties of these sequences (Pai et al 2004;Capelson and Corces 2005;Lei and Corces 2006;Bushey et al 2009). The research project carried out by students in the RISE program seeks to find novel protein components of insulator complexes as well as other proteins that may have unique roles in nuclear organization.…”

Drosophila BTB/POZ Domains of “ttk Group” Can Form Multimers and Selectively Interact with Each Other

“…28 This protein is essential for enhancer blocking of the Su (Hw) insulator and also interacts with other Drosophila insulator proteins, dCTCF 29,30 and BEAF. 31 Although the BTB domain of CP190 does not belong to the ttk group, it is suggested to play a significant role in supporting long-distance interactions between insulators.…”

Cell type specificity of chromatin organization mediated by CTCF and cohesin

“…Although insulators would be expected to reside primarily in intergenic regions where they could provide boundary or enhancer blocking activity, genome scans of CTCF enrichment show that CTCF sites are overrepresented in genes and promoter regions, with only 41-56% at intergenic locations (5). In Drosophila, between about 49% and 64% of insulator sites are located in intergenic regions (4). Thus, although CTCF sites are proposed to be insulators, their in vivo functions may not be limited to insulation.…”

“…Evidence also suggests that insulators are involved in higher-order chromatin organization by clustering together with other insulators. Such "insulator bodies" can be visualized at the nuclear periphery of certain cells in Drosophila and are thought to coalesce through the interaction of proteins such as Su(Hw) and Drosophila CTCF (3,4).…”