AMAR-seq: automated multimodal sequencing of DNA methylation, chromatin accessibility, and RNA expression with single-cell resolution

Parallel single-cell multimodal sequencing is the most intuitive and precise tool for cellular status research. In this study, we propose AMAR-seq to automate methylation, chromatin accessibility and RNA sequencing on a chip with single-cell precision. We validated the accuracy and robustness of AMAR-seq in comparison with standard single-omics methods. The high gene detection rate and genome coverage of AMAR-seq enabled us to establish a genome-wide gene expression regulatory atlas, implement single-cell copy number variation analysis, and construct a single-gene, single-base resolution gene expression, DNA methylation, and chromatin accessibility landscape. Applying AMAR-seq to investigate the process of mouse embryonic stem cell differentiation, we revealed the dynamic coupling of the epigenome and transcriptome which may contribute to the unravelling of the molecular mechanisms of early embryonic development. Collectively, these results illustrate that the employment of AMAR-seq can deeply and accurately establish single-cell multi-omics regulatory networks in a single-cell context in a cost-efficient and automated manner, which paves the way for incisive dissection of complex life procedures. In total, 19 K562 cell line samples and 24 mESC samples were analyzed. We examined genome-wide DNA methylation, gene expression and chromatin accessibility profiles of 12 K562 single cells, two bulk K562 samples and 24 mESC single cells. We analysed DNA methylome of 3 K562 single cells by scBS-seq and transcriptome of 4 K562 single cells with smart-seq2 workflow, respectively. Mouse embryonic stem cells were grown on 6-cm culture dishes with MEF feeder cells and cultured in a complete medium supplemented with leukemia inhibitory factor (LIF) to prevent differentiation. To induce undirectional differentiation, mESCs were dissociated and replated onto 0.1% gelatin-coated dishes, and cultured without LIF in a feeder-free manner. We collected mESCs at day 0 and differentiated cells at day 3, day 6 day 9. For library construction methods: NOMe-seq (http://www.genome.org/cgi/doi/10.1101/gr.143008.112) scNOMe-seq (https://elifesciences.org/articles/23203)