scNanoHi-C: a single-cell long-read concatemer sequencing method to reveal high-order chromatinstructures within individual cells

Abstract The high-order three-dimensional (3D) organization of regulatory genomic elements provides a topological basis for gene regulation, but it remains unclear how multiple regulatory elements across the mammalian genome interact within an individual cell. To address this, herein, we developed scNanoHi-C, which applies Nanopore sequencing to explore genome-wide proximal high-order chromatin contacts within individual cells. Evaluation of the method suggested that scNanoHi-C reliably and effectively profiled 3D chromatin structure and distinguished structure subtypes among single cells. This method could also be used to detect genomic variations,including CNVs and SVs, as well as to scaffold the de novo assembly of single-cell genomes. Importantly, our results suggested that extensive high-order chromatin structures exist in active chromatin regions across the genome, and multiway interactions between enhancers and their target promoters were identified within single cells. Altogether, scNanoHi-C offers new opportunities to investigate high-order 3D genome structures at the single-cell level.