CTCF: an architectural protein bridging genome topology and function - PubMed (original) (raw)

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CTCF: an architectural protein bridging genome topology and function

Chin-Tong Ong et al. Nat Rev Genet. 2014 Apr.

Abstract

The eukaryotic genome is organized in the three-dimensional nuclear space in a specific manner that is both a cause and a consequence of its function. This organization is partly established by a special class of architectural proteins, of which CCCTC-binding factor (CTCF) is the best characterized. Although CTCF has been assigned various roles that are often contradictory, new results now help to draw a unifying model to explain the many functions of this protein. CTCF creates boundaries between topologically associating domains in chromosomes and, within these domains, facilitates interactions between transcription regulatory sequences. Thus, CTCF links the architecture of the genome to its function.

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Figures

Figure 1

Figure 1. Features of CTCF binding sites in the genome

CTCF binding sites are associated with different genetic elements. The majority of sites are intergenic and co-localize with cohesin. In addition, a fraction of CTCF binding sites are located near RNA polymerase III (RNAPIII) type II genes (e.g. tRNA and SINE elements) and ETC loci, suggesting that TFIIIC and CTCF may cooperate in some aspects of the function of this protein. The 12 bp consensus sequence of CTCF sites is embedded within binding modules 2 and 3 as determined by the ChIP-exo technique. DNA methylation (filled red ball) of cytosine residues occurs at positions 2 and 12 of the consensus sequence in a subset of CTCF sites.

Figure 2

Figure 2. Regulation of CTCF binding to DNA

Constitutive CTCF sites present in cells from different tissues are present in non-methylated and nucleosome-free regions. Cell-type specific CTCF binding is partly regulated by differential DNA methylation and nucleosome occupancy across different cell-types. This suggests that cells may use ATP-dependent chromatin remodeling complexes to regulate nucleosome occupancy at specific CTCF sites and control the interaction of this protein with DNA. In addition, the methylation status of cell-type-specific CTCF binding sites may be determined by a combination of activities of de novo methyltransferases and TET enzymes that regulate the presence and levels of 5mC at specific sites. Immortalized cancer cell lines contain high levels of 5mC at CTCF sites, which correlates with the low CTCF occupancy in these cells (Filled red circle: methylated DNA; open circle: unmethylated DNA).

Figure 3

Figure 3. CTCF regulates enhancer-promoter interactions in a multi-gene cluster

The human _Pcdh_α gene cluster contains 13 similar, tandemly arranged, variable first exons (1 to 13, shown in blue if they are transcribed or in white if they are not) and two related c-type ubiquitous first exons (c1 and c2, shown in yellow). Each of these 15 variable first exons is adjacent to its own promoter and is spliced to three downstream constant exons (1 to 3, shown in black). _Pcdh_α alternate isoforms are expressed stochastically, whereas all the c-type isoforms are expressed ubiquitously in all cells. The SK-N-SH cells depicted here express isoforms 4, 8 and 12. Promoter choice and the formation of an active chromatin hub is mediated by CTCF-cohesin DNA looping between the distal HS5-1 enhancer and distinct promoters at the _Pcdh_α gene cluster. Individual variable exons (blue and white rectangles) or ubiquitous exons (yellow rectangles) may be expressed and joined to the three exons from the constant region (black rectangles) by pre-mRNA splicing. Binding of CTCF to the promoter preceding individual exons is correlated with the level of gene activity. The active promoters are distinguished from the inactive promoters by an enrichment for H3K4me3 and a depletion of DNA methylation, which leads to expression of the downstream genes (blue rectangles).

Figure 4

Figure 4. CTCF facilitates endodermal enhancer-promoter interactions in ESCs

Recruitment of TAF3 at endodermal enhancers by CTCF and chromatin looping activates Mapk3 in ESCs. Apart from being a component of TFIID at core promoters, TAF3 may also associate with other transcription factors across the genome in ESCs. For instance, TAF3 represses the activity of pluripotency-associated transcription factors (OCT4, SOX2 and NANOG).

Figure 5

Figure 5. CTCF regulates V(D)J recombination

V(D)J recombination at antigen receptor loci is regulated by chromatin accessibility, which correlates with active histone modifications and transcription. CTCF may influence the outcome of V(D)J recombination by regulating enhancer-promoter interactions and locus compaction. At the IgH locus, CTCF-mediated looping of DH-JH-CH segments imposes ordered recombination (DH-to-JH) by controlling the communication of enhancers (Eμ and 3'RR) with distinct gene segments. Binding of CTCF at IGCR1 blocks the influence of the Eμ enhancer on proximal VH segments and prevents the spread of active histone modification from DH into the proximal VH region. In addition, it inhibits the level of antisense transcription within the DH region and modulates locus compaction in collaboration with other factors (e.g. YY1, Ikaros, Pax5, E2A). As a consequence, CTCF within IGCR1 may bias the rearrangement of distal (over proximal) VH segments with DJH joins.

Figure 6

Figure 6. CTCF promotes alternative mRNA splicing

Mutually exclusive DNA methylation and CTCF binding may regulate alternative splicing. At the CD45 gene, DNA methylation at exon 5 inhibits CTCF binding, which leads to fairly unimpeded transcriptional elongation by RNA polymerase II (RNAPII) and subsequent exclusion of exon 5 during splicing of the resultant mRNA (upper panel). By contrast, hypomethylation of exon 5 leads to CTCF binding and RNAPII stalling, which promotes the inclusion of exon 5 (lower panel).

Figure 7

Figure 7. CTCF regulates three-dimensional genome architecture

A) Cartoon of an interaction heat map of a chromosome segment around 2.5 Mb in length depicting data generated by Hi-C in mammalian cells. The TADs and their borders are indicated. B) The presence of multiple CTCF and TFIIIC binding sites at TAD borders may contribute to the establishment of the border. This arrangement may explain the observed function of CTCF as an enhancer blocker. On the other hand, CTCF binding sites within TADs may facilitate enhancer-promoter looping through the recruitment of cohesin. The blue box denotes the promoter of the gene. C) Chromatin features of TAD borders in mammals and Drosophila melanogaster. The TAD borders in mammals are enriched for housekeeping and tRNA genes, SINE elements and CTCF binding sites. In D. melanogaster, they are enriched for highly transcribed genes and clusters of binding sites for various architectural proteins. The role of TFIIIC, cohesin and condensin proteins in mediating TAD border formation remains to be determined.

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