Cell type specificity of chromatin organization mediated by CTCF and cohesin

Abstract

CTCF sites are abundant in the genomes of diverse species but their function is enigmatic. We used chromosome conformation capture to determine long-range interactions among CTCF/cohesin sites over 2 Mb on human chromosome 11 encompassing the β-globin locus and flanking olfactory receptor genes. Although CTCF occupies these sites in both erythroid K562 cells and fibroblast 293T cells, the long-range interaction frequencies among the sites are highly cell type specific, revealing a more densely clustered organization in the absence of globin gene activity. Both CTCF and cohesins are required for the cell-type-specific chromatin conformation. Furthermore, loss of the organizational loops in K562 cells through reduction of CTCF with shRNA results in acquisition of repressive histone marks in the globin locus and reduces globin gene expression whereas silent flanking olfactory receptor genes are unaffected. These results support a genome-wide role for CTCF/cohesin sites through loop formation that both influences transcription and contributes to cell-type-specific chromatin organization and function.chromatin loops | insulator | CTCF | globin | transcription E ukaryotic chromatin is dynamically organized to form distinct transcriptionally active or silent domains (1). Chromatin insulators are proposed to play a role in the establishment of such domains within which proper enhancer-gene interactions occur and improper ones are excluded (2). Insulators can function as boundary elements between active and silent chromatin domains and can also interfere with enhancer-gene interaction when placed between them. 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).In mammalian cells, insulators are bound by CTCF, a protein with 11 zinc fingers through which it can bind to a range of DNA sequences, to itself, and to nuclear structural proteins such as nucleophosmin and matrix attachment regions (MARs) (2). 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. Recently, cohesin has been reported to colocalize at most sites of CTCF enrichment and to play a role in transcriptional insulation, but the significance of this joint occupancy to higher-order chromatin structures is unknown (6).In the Igf2/H19 locus, CTCF binding to the imprinting control region on the maternal allele is required to loop ...

Chromatin Loop Formation in the β-Globin Locus and Its Role in Globin Gene Transcription

“…A similar effect was observed in the mouse β-globin locus when CTCF binding sequences at 3′HS1 were mutated. Reduction of CTCF by shRNA or siRNA in K562 cells decreased the interaction frequency between HS5 and 3′HS1 of the human β-globin locus (Chien et al, 2011;Hou et al, 2010).…”

“…Recent data indicate that the cohesion complex interacts with CTCF and co-occupies CTCF sites in chromatin including at the β-globin locus (Hou et al, 2010;Wendt and Peters, 2009). This complex participates in chromatin loop formation in the β-globin locus.…”

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

“…First, CTCF and the cohesin complex, consisting of the core subunits SMC3, SMC1, RAD21, and STAG1/SA1 or STAG2/SA2, were found to colocalize extensively throughout mammalian genomes (3)(4)(5). Second, both factors are involved in mediating long-range interactions (6)(7)(8)(9)(10)(11). Finally, cohesin was shown to be important for CTCF's chromatin insulation function (3)(4)(5), whereas CTCF is necessary to recruit cohesin to the shared binding sites but not to chromatin (3).…”

Cohesin and chromatin organisation

“…High-resolution chromatin conformation studies have revealed that cohesin forms long-range interactions between its binding sites (Figure 2) [13-18, [67][68][69][70]. Current models support the idea 6 that cohesin controls gene expression by contributing to the organisation of higher-order chromatin structure.…”

“…Current models support the idea 6 that cohesin controls gene expression by contributing to the organisation of higher-order chromatin structure. Communication between gene regulatory elements is believed to be a major mechanism for transcriptional control [71] and it is conceivable that interactions between cohesin binding sites that involve gene regulatory elements such as enhancers, promoters or insulators, would favour or inhibit gene expression [12][13][14][15][16][17][18][67][68][69]. These studies only survey a tiny proportion of the genome (Figure 2), and attempts to visualise cohesin effects on global chromatin organisation have to date been at low resolution.…”