Comprehensive Mapping of Transcriptionally-active Enhancers During Murine Cardiogenesis at Single Cell Resolution

An in-depth understanding of the complex mechanisms that orchestrate normal embryonic heart development is required to disambiguate the origin of congenital heart disease. However, the epigenetic landscapes governing cell type-specific gene expression patterns during heart development at single cell resolution has yet to be revealed. Here we use simultaneous single cell RNA and assay for transposase accessible chromatin sequencing to construct a comprehensive multimodal map of embryonic murine heart development, profiling cell type- and timepoint-specific epigenetic regulatory elements as well as their gene targets. Furthermore, we compare these regulatory elements with published GWAS hits to map variants implicated in key developmental processes and clinical phenotypes to enhancers for genes that are actively transcribed during cardiac development. Taken together, our work provides a rich resource for the broader scientific community that empowers future studies in heart development and disease and offers a simple computational framework for integrating and profiling multiomic data in single cells. Overall design: Mouse embryonic hearts were harvested at embryonic days 8.5, 10.5, and 16.5 and dissociated into single cells. Nuclei were extracted from cell suspensions and underwent ATAC transposition followed by single nuclei capture using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CG000338 Rev F) protocol. ScRNA and scATAC libraries were generated using the 10X Genomics protocol. Subsequent sequencing was conducted using an Illumina NOvaSeq 6000 at 20,000 read pars per nuclei for the gene expression library and 25,000 read pairs per nuclei for the ATAC library.