Parallel profiling of genome mutations and multiple chromatin modalities in single cells by scNanoCT&ATAC-seq

Profiling multiple histone modifications alongside chromatin accessibility at single-cell resolution has been enabled by technologies such as multi-CUT&Tag, scGET-seq, and nano-CUT&Tag. Here, we developed Nanopore sequencing based single-cell CUT&Tag and ATAC co-profiling (scNanoCT&ATAC-seq), which allows for the simultaneous mapping of genome mutations, histone modifications and chromatin accessibility within the same individual cells. scNanoCT&ATAC-seq achieves comparable sensitivity and fragment yield per cell as previous single-modal methods. Anchoring by the ATAC module, a comprehensive epimap that includes multiple histone marks is characterized, generating a cell type specific annotation of chromatin status for genomic regulatory elements, which specified different H3K9me3 modes and identified enhancer-promoter interactions at single-molecular level, specifying genomic structure variations lead to novel regulatory elements in cancer cells. Applying to lung adenocarcinoma, scNanoCT&ATAC-seq clearly captured the tumor subclones and revealed the coordination of genomic and epigenetic regulations. Together, scNanoCT&ATAC-seq reveals the interplay between genomic and multiple epigenetic modalities underlying any cellular processes.