DIRECT: Digital Microfluidics for Isolation-Free Shared Library Construction of Single-Cell DNA Methylome and Transcriptome

Integrated single-cell transcriptome and DNA methylome profiling has provided insight into the complex regulatory networks of cells. Existing methods are based on picking a single-cell and performing library construction in a tube, which is costly and cumbersome. Here, we propose DIRECT, a digital microfluidics-based method for simultaneous analysis of the methylome and transcriptome in a single library construction. The accuracy of DIRECT is demonstrated in comparison with bulk and single-omics data, and the high CpG site coverage of DIRECT allows for precise analysis of copy number variation information, enabling expansion of single cell analysis from two- to three-omics. By applying DIRECT to monitor the dynamics of mouse embryonic stem cell differentiation, the relationship between DNA methylation and changes in gene expression during differentiation was revealed. DIRECT enables accurate, robust, and reproducible single-cell DNA methylation and gene expression co-analysis at a lower cost and with greater efficiency, broadening the application scenarios of single-cell multi-omics analysis and revealing a more comprehensive and fine-grained map of cellular regulatory landscapes. In total, 29 K562 cell line samples, 6 HL-60 cell line samples and 16 mESC samples were analyzed. We examined genome-wide DNA methylation and gene expression profiles of K562 and HL-60 cells, including 13 single-cell K562 and 6 single-cell HL-60 samples with DIRECT, three single-cell K562 samples in tube and two bulk K562 samples. We analyzed DNA methylome of 3 K562 cells. We detected transcriptome of 8 K562 cells with normal dNTP and cytosine-methylated dNTP, 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 for two passages. We collected mESCs at day 0 and differentiated cells at day 4.