Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice

Abstract The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding genome’s structure–function relation, yet is extremely challenging for existing methods. Here we present L inking m RNA to C hromatin A rchitecture (LiMCA), which jointly profiles 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we were able to profile the chromatin accessibility and the paired 3D genome structures and gene expression information of single neurons within the developing mouse olfactory epithelium. We expanded the repertoire of known OR enhancers, and discovered unexpected rules of their dynamics: ORs and their enhancers are most accessible during early differentiation, and the active OR typically does not associate with the largest enhancer hub. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the “one neuron–one receptor” selection process.