Single-nucleus multiomic mapping of mA methylomes and transcriptomes in native populations of cells with sn-m6A-CT.

N-methyladenosine (mA) RNA modification plays important roles in the governance of gene expression and is temporally regulated in different cell states. In contrast to global mA profiling in bulk sequencing, single-cell technologies for analyzing mA heterogeneity are not extensively established. Here, we developed single-nucleus m6A-CUT&Tag (sn-m6A-CT) for simultaneous profiling of mA methylomes and transcriptomes within a single nucleus using mouse embryonic stem cells (mESCs). m6A-CT is capable of enriching mA-marked RNA molecules in situ, without isolating RNAs from cells. 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 mA methylome landscapes from heterogeneous populations. These indicate that sn-m6A-CT provides additional dimensions to multimodal datasets and insights into epitranscriptomic landscape in defining cell fate identity and states.