Single-nucleus multiomic mapping of m6A methylome and transcriptome in native populations of cells with sn-m6A-CT [Bulk CUT&Tag]

N6-methyladenosine (m6A) RNA modification plays important roles in the governance of gene expression and is temporally regulated in different cell states. In contrast to global m6A profiling in bulk sequencing, technologies for analyzing m6A heterogeneity across single-cells are not extensively established. Here, we report single-nucleus m6A CUT-Tag (sn-m6A-CT) for simultaneous profiling of m6A methylome and transcriptome within a single nucleus. m6A-CT is capable of enriching m6A-marked RNA molecules in situ, without isolating RNAs from cells, in a highly efficient manner. We adapted m6A-CT to the droplet-based single-cell omics platform and demonstrated high throughput performance in analyzing nuclei isolated from thousands of cells from various cell types. We show that sn-m6A-CT profiling is sufficient to determine cell identity and allows the generation of cell-type-specific m6A methylome landscapes from heterogeneous populations. Further, we exemplified the robust deconvolution capabilities in m6A heterogeneities with stem cells in multiple distinct pluripotency states. These indicate that sn-m6A-CT provides additional dimensions to multimodal datasets and new insights into epitranscriptomic landscape in defining cell fate identity and states. Bulk CUT&Tag or single-nucleus CUT&Tag followed by Illumina sequencing