Synergistic Enhancer Networks Revealed by Live-Cell 3D Chromatin Imaging and Perturbation

The 3D genome plays a critical role in regulating transcription, cellular functions, and diseases. We explore innovative technologies for perturbing the 3D genome organization and imaging interaction between regulatory elements in real-time. We systematically perturb enhancers and reveal a synergistic enhancer network that regulate oncogene expression. Genome profiling confirms that 3D genome structure is resistant to individual element perturbation but is significant altered when multiple elements are perturbed. To investigate real-time interaction between regulatory elements, we developed Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of dynamic chromatin interaction, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Combination of perturbation and live-cell imaging offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease.

Speaker: Stanley Qi, Stanford University