Developing in 3D: the role of CTCF in cell differentiation

Abstract

CTCF is a highly conserved zinc-finger DNA-binding protein that mediates interactions between distant sequences in the genome. As a consequence, CTCF regulates enhancer-promoter interactions and contributes to the three-dimensional organization of the genome. Recent studies indicate that CTCF is developmentally regulated, suggesting that it plays a role in cell type-specific genome organization. Here, we review these studies and discuss how CTCF functions during the development of various cell and tissue types, ranging from embryonic stem cells and gametes, to neural, muscle and cardiac cells. We propose that the lineage-specific control of CTCF levels, and its partnership with lineage-specific transcription factors, allows for the control of cell type-specific gene expression via chromatin looping.

Keywords: Cell differentiation; Development; Epigenetics; Genome organization; Transcription.

Fig. 1.

CTCF interacts with a variety of proteins. (A) Domain structure of CTCF, highlighting the three major domains: the N-terminal domain, the central zinc-finger domain (containing Zn-fingers 1-11) and the C-terminal domain. (B) A variety of CTCF-interacting proteins are known to bind to specific domains of CTCF. Multiple proteins interact with the zinc-finger domain, whereas only RNAPII, cohesin, RNA, Kaiso and TFII-I interact with the C-terminal domain. Likewise, only a handful of proteins interact with the N-terminal domain. A number of additional proteins have been shown to interact with CTCF, although their binding has not been mapped to specific domains.

Fig. 2.

The organization of the genome inside the nucleus. Eukaryotic chromosomes are organized within the three-dimensional space of the nucleus. They occupy positions in the nucleus termed chromosome territories, each of which can be further organized into two types of domains: compartmental domains, which reflect transcriptional and chromatin states; and loop domains, which depend on the occupancy of architectural proteins such as CTCF and cohesin. See also Box 2.

Fig. 3.

CTCF promotes the establishment of insulated neighborhoods to maintain proper gene expression in ESCs. (A) CTCF forms loop domains in ESCs to insulate pluripotency genes (such as those encoding Oct4, Sox2 and Nanog; OSN) from sequences located outside of the loops. An ESC super-enhancer and the miR-290-295 locus are located inside a chromatin loop anchored by CTCF. This topological structure restricts the stimulatory potential of the super-enhancer to the genes contained inside the loop. Removal (e.g. via CRISPR-Cas9-mediated approaches) of the CTCF-binding site at one of the loop anchors results in long-range interactions with a gene originally located outside the loop (Nlrp12) and a decrease in the transcription of the original target genes. (B) CTCF can also maintain the epigenetic silencing of Polycomb-repressed lineage-specifying genes through chromatin looping. For example, the disruption of looping (via the deletion of one of the CTCF sites) leads to ectopic expression of the Tcfap2e gene.

Fig. 4.

Modes of CTCF function during cell differentiation and development. (A-C) CTCF can promote the physical interaction between enhancers and promoters (A), insulate genes from neighboring regulatory signals by chromatin looping (B) or mediate transcriptional activation by binding at the promoter regions of certain genes (C). (D) During cell differentiation, CTCF can also promote the establishment of a basal, stable topology upon which regulatory transactions can take place. Some chromatin loops can be formed early in development and remain unchanged during differentiation, although genes inside could be subject to differential gene expression owing to the binding of specific transcription factors. (E,F) In addition, some chromatin loops can be lost (E) or formed de novo by recruitment of CTCF and perhaps cell type-specific transcription factors (F).