Active promoters and insulators are marked by the centrosomal protein 190

Abstract

For the compact Drosophila genome, several factors mediating insulator function, such as su(Hw) and dCTCF, have been identified. Recent analyses showed that both these insulator-binding factors are functionally dependent on the same cofactor, CP190. Here we analysed genomewide binding of CP190 and dCTCF. CP190 binding was detected at CTCF, su(Hw) and GAF sites and unexpectedly at the transcriptional start sites of actively transcribed genes. Both insulator and transcription start site CP190-binding elements are strictly marked by a depletion of histone H3 and, therefore, a loss of nucleosome occupancy. In addition, CP190/dCTCF double occupancy was seen at the borders of many H3K27me3 'islands'. As before, these sites were also depleted of H3. Loss of either dCTCF or CP190 causes an increase of H3 and H3K27 trimethylation at these sites. Thus, for both types of cis-regulatory elements, domain borders and promoters, the chromatin structure is dependent on CP190.

The chromatin insulator CTCF and the emergence of metazoan diversity

“…To judge the specificity of the identified motifs, we repeated the analysis with four corrupted matrices (SI Appendix, Fig. S5) that differed from the original matrix by the reciprocal exchange of two highly conserved nucleotide positions (67).…”

“…To predict CTCF-binding motifs, we constructed position weight matrices (PWMs) on the basis of the CTCF-binding profiles determined by ChIP-seq from human HeLa cells and ChIP-chip data from D. melanogaster S2 cells (67). Fastq files corresponding to CTCF ChIP-seq experiments were downloaded from the Encode repository at the University of California, Santa Cruz (UCSC), genome portal (http://hgdownload.cse.…”

CTCF terminal segments are unstructured

“…[4][5][6] Furthermore, both context-dependent activity and ubiquitous global distribution are conserved throughout vertebrates and insects. [7][8][9][10][11][12][13] Recent studies of CTCF suggest that the mechanism of this multifunctional transcriptional regulation may involve higher order chromatin structure.…”

Insulators form gene loops by interacting with promoters in Drosophila

“…Certain types of insulators [the Su(Hw)-dependent 1A2, the Zw5-dependent scs, and Wari] can effectively interact with the yellow promoter, whereas others appear not to (the GAF-dependent Fab-7 and CTCF-dependent Mcp). GAF and CTCF are frequently found bound to promoter regions (Smith et al, 2009;Bartkuhn et al, 2009;Bushey et al, 2009;Nègre et al, 2010), which indicates that insulators that utilize these proteins are also involved in longdistance interactions with some promoters. For example, it is speculated that the Fab-7 insulator can interact with stalled promoters, such as the Abd-B promoter (Chopra et al, 2009;Core and Lis, 2009).…”

“…The stalled promoters of the bithorax complex display insulator activity in embryos (Chopra et al, 2009). Many insulator proteins, such as CTCF, CP190, Mod(mdg4)-67.2 [Mod(mdg4) -FlyBase] and BEAF (BEAF-32), are frequently found bound to the promoters (Smith et al, 2009;Bartkuhn et al, 2009;Jiang et al, 2009;Bushey et al, 2009;Nègre et al, 2010).…”