Many facades of CTCF unified by its coding for three-dimensional genome architecture

CCCTC-binding factor(CTCF)is a multifunctional zinc finger protein that is conserved in metazoan species.CTCF is consistently found to play an important role in many diverse biological processes.CTCF/cohesin-mediated active chromatin‘loop extrusion’architects three-dimensional(3D)genome folding.The 3D architectural role of CTCF underlies its multifarious functions,including developmental regulation of gene expression,protocadherin(Pcdh)promoter choice in the nervous system,immunoglobulin(Ig)and T-cell receptor(Tcr)V(D)J recombination in the immune system,homeobox(Hox)gene control during limb development,as well as many other aspects of biology.Here,we review the pleiotropic functions of CTCF from the perspective of its essential role in 3D genome architecture and topological promoter/enhancer selection.We envision the 3D genome as an enormous complex architecture,with tens of thousands of CTCF sites as connecting nodes and CTCF proteins as mysterious bonds that glue together genomic building parts with distinct articulation joints.In particular,we focus on the internal mechanisms by which CTCF controls higher order chromatin structures that manifest its many fa?ades of physiological and pathological functions.We also discuss the dichotomic role of CTCF sites as intriguing3D genome nodes for seemingly contradictory‘looping bridges’and‘topological insulators’to frame a beautiful magnificent house for a cell’s nuclear home.

Genetic evidence for asymmetric blocking of higher-order chromatin structure by CTCF/cohesin

Dear Editor,Similar to higher-order folding of polypeptide chains into functional proteins,linear DNA molecules are spatially folded in a hierarchical and dynamic manner into three-dimensional(3D)functional chromatin structures in eukaryotic nuclei(Huang and Wu,2016;Rowley and Corces,2018).This dynamic folding is closely related to many nuclear processes such as DNA replication and repair,chromosomal translo­cation,recombination,and segregation,as well as RNA transcription,splicing,and transport.In particular,dynamic long-distance chromatin looping interactions,which result in close spatial contacts between distal enhancers and target promoters,are thought to play a role in controlling precise spatiotemporal as well as cell-type specific gene expression during animal development(Rowley and Corces,2018).Mammalian genomes contain numerous noncoding regula­tory elements that regulate these dynamic long-distance chromatin looping interactions.

Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus

During development, gene expression is spatiotemporally regulated by long-distance chromatin interactions between distal enhancers and target promoters. However, how specificity of the interactions between enhancers and promoters is achieved remains largely unknown. As there are far more enhancers than promoters in mammalian genomes, the complexities of enhancer choice during gene regulation remain obscure. CTCF, the CCCTC-binding factor that directionally binds to a vast range of genomic sites known as CBSs(CTCF-binding sites), mediates oriented chromatin looping between a substantial set of distal enhancers and target promoters. To investigate mechanisms by which CTCF engages in enhancer choice, we used CRISPR/Cas9-based DNA-fragment editing to duplicate CBS-containing enhancers and promoters in the native genomic locus of the clustered Pcdhα genes. We found that the promoter is regulated by the proximal one among duplicated enhancers and that this choice is dependent on CTCF-mediated directional enhancer-promoter looping. In addition, gene expression is unaltered upon the switch of enhancers. Moreover, after promoter duplication, only the proximal promoter is chosen by CTCF-mediated directional chromatin looping to contact with the distal enhancer. Finally, we demonstrated that both enhancer activation and chromatin looping with the promoter are essential for gene expression. These findings have important implications regarding the role of CTCF in specific interactions between enhancers and promoters as well as developmental regulation of gene expression by enhancer switching.

Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering

Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s,the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development.In particular,the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes.CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries.Recent studies revealed,however,that the CRISPR genomeediting system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA.Here,we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes.Specifically,we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering.We then summarize different types of chromosomal rearrangements by DNA fragment editing.Finally,we review significant progress from precise ID gene editing toward predictable 3D genome engineering and synthetic biology.The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.