Architectural proteins, transcription, and the three-dimensional organization of the genome

Abstract

Architectural proteins mediate interactions between distant sequences in the genome. Two well-characterized functions of architectural protein interactions include the tethering of enhancers to promoters and bringing together Polycomb-containing sites to facilitate silencing. The nature of which sequences interact genome-wide appears to be determined by the orientation of the architectural protein binding sites as well as the number and identity of architectural proteins present. Ultimately, long range chromatin interactions result in the formation of loops within the chromatin fiber. In this review, we discuss data suggesting that architectural proteins mediate long range chromatin interactions that both facilitate and hinder neighboring interactions, compartmentalizing the genome into regions of highly interacting chromatin domains.

Keywords: CCCTC-binding factor; Chromatin; Epigenetics; Insulator; Topologically associating domain.

FIGURE 1. The consequences of a single architectural protein interaction

Architectural proteins organize regulatory elements within the genome. The facilitating and inhibitory effects of a single architectural protein interaction between two genomic loci are shown. Regulatory elements are shown as gold boxes and architectural proteins are in blue. Facilitating interactions are depicted as green arrows, while insulating interactions are in red. (A) Architectural proteins bound to regulatory elements promote interactions between the regulatory sequences. In addition, polymer simulation studies have suggested that a single architectural protein interaction affects neighboring interactions as well (denoted by *). (B) Regulatory elements within chromatin loops formed by architectural protein interactions may interact more frequently. (C) By reducing the linear genomic distance between loci flanking a chromatin loop, architectural proteins may promote their interactions. (D) Regulatory elements within chromatin loops are insulated from interactions with elements outside the chromatin loops.

FIGURE 2. Multiple architectural protein-bound loci can interact in 3D space

Three distinct architectural-protein bound loci can form multiple different types of interactions and chromatin loops. The mechanisms regulating which architectural protein-bound loci interact are still poorly understood. Architectural proteins are shown in green. (APBS: Architectural protein binding site)

FIGURE 3. Architectural proteins mark TAD borders

Cartoon schematics depicting regions of highly associating chromatin called TADs, which are separated by TAD borders. Interaction frequency is shown as a continuum from white to dark red. (A) The strength of a TAD border, defined as the ratio between intra- and inter-TAD interactions around border sequences, depends on architectural protein occupancy (occupancy shown by peak size and a continuum from light to dark blue). A specific orientation of the CTCF motif is observed at TAD borders (purple arrows). (B) Individual TADs contain many different chromatin types depicted in green, blue, black and gold. Evidence suggests that TADs represent compartments for regulatory elements. Interacting regulatory elements in the two distinct TADs are shown in purple and cyan.

FIGURE 4. Architectural proteins regulate chromatin interactions within TADs

(A) Cartoon schematic depicting the regions of enriched chromatin interactions within TADs called subTADs. Intra-TAD interactions change during cellular differentiation and are strongly reduced after architectural protein depletion. Interaction frequency is shown as a continuum from white to dark red. (B) Cartoon schematic illustrating how architectural proteins bring distant enhancers and promoters together in 3D space.