To investigate the causal relationships between chromosome conformation and genome functions, we developed a method in budding yeast, Chemically Induced Chromosomal Interaction (CICI), to engineer long-distance chromosomal interactions selectively and dynamically. CICI consists of a chemically induced dimerization (CID) system, the fluorescence repressor operator system (FROS), and LacO and TetO arrays. The CID system establishes interactions between LacO and TetO arrays by rapamycin mediated dimerization between FKBP12 and FRB. The FROS system uses fluorescence and repressor fusion proteins to visualize the arrays. Essentially we added velcro straps to pairs of loci in the genome, and when they stick with each other, it perturbs the 3D genome conformation. We have implemented CICI at multiple intra- and inter-chromosomal loci pairs and found that CICI can form even between loci with very low Hi-C contact frequencies. When we studied the functional consequences of CICI formation, we concluded that chromosome conformation plays an important role in donor selection during DNA repair, but has little effect on the timing of replication origins. Overall, our results demonstrate that CICI is a powerful tool to study chromosome dynamics and the 3D genome function.

Related papers:

  • Chemically Induced Chromosomal Interaction (CICI): A New Tool to Study Chromosome Dynamics and Its Biological Roles
    Du MY*, Zou F*, Yan YJ, & Bai L (2022) 
    Nat Commun, 13: 757.
  • Enhancement of LacI Binding in vivo
    Du MY, Kodner S, & Bai L (2019)
    Nucleic Acid Research, 47:9609-18