Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice [olfactory, single-cell RNA & Hi-C]

The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding our genome's structure–function relation, yet is extremely challenging for existing methods. Here we present Linking mRNA to Chromatin Architecture (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 profiled the developing mouse olfactory epithelium and reported the first chromatin accessibility profiles and the first paired 3D genome structures and gene expression information of single neurons. We greatly 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. Overall design: simultaneous 3D genome and gene expression within the same single cell by LiMCA Each cell was named according to the developmental stage/age and mouse strain information. For example, "p007" indicates that the developmental stage/age of the mouse from which this neuron was derived is postnatal day 7. "bc" and "bdf1" indicate the mouse strain. We labeled F1 hybrids of C57BL/6J (female) and DBA/2J (male) as bdf1 and F1 hybrids of C57BL/6J (female) and CAST/EiJ (male) as bc.