(158x) Simultaneous Quantification of Protein-DNA Contacts and Transcriptomes in Single Cells

The epigenome plays a critical role in regulating gene expression in mammalian cells. On the transcriptional level, packaging of DNA into chromatin can control access of transcriptional regulators to functional DNA elements such as enhancers and promoters. Higher levels of organization that contribute to the regulation of gene expression involve the spatial segmentation of the genome into compartments with transcriptionally permissive or repressive gene regulatory activities. Failure to integrate and coordinate the multi-layered regulatory control of gene expression can result in developmental defects and diseases. However, understanding how cell-to-cell heterogeneity in these epigenetic features influences gene expression variability and cellular phenotypes remains a major challenge. Therefore, to directly link heterogeneity in upstream elements such as 3D genome organization, DNA accessibility or transcriptional factor/chromatin modifying factor binding to transcriptional output, we developed a new technology to simultaneously quantify protein-DNA interactions and mRNA from the same cell (scDam&T-seq)^1,2. scDam&T-seq enables us to directly correlate protein-DNA contacts to a particular gene expression program in a cell. By profiling lamina-associated domains (LADs) in human KBM7 cells, we reveal different dependencies between genome-nuclear lamina (NL) association and gene expression in single cells. Specifically, we find that gene expression heterogeneity is dependent on NL positioning for genomic regions that infrequently contact the lamina. Surprisingly though, for genomic regions that frequently contact the NL, we find that gene expression is not sensitive to NL positioning. In addition, we use the E. coli methyltransferase, Dam, as an in vivo marker of DNA accessibility in single cells and show that scDam&T-seq can be used to simultaneously map DNA accessibility and the transcriptome in single cells. Further, we show that scDam&T-seq can be used to map the genome-wide binding patterns of chromatin modifying factors by quantifying the genome binding landscape of a polycomb-group protein, RING1B, and the associated transcriptome. Finally, using mouse embryonic stem cells, we show that this approach can be used as a general technology to identify cell types in silico using the transcriptome of single cells and simultaneously determine the underlying chromatin landscape of each cell type using the corresponding protein-DNA interaction maps. Thus, scDam&T-seq is a multiomics single-cell method that enables systematic investigation of gene regulatory mechanisms on the acquisition of cell type specific transcriptional programs in heterogeneous tissues.

References:

1. Rooijers, K, [...] Dey, S.S.*, Kind, J.* et al. Nature Biotechnology (2019).

2. Markodimitraki, C.M., [...] Dey, S.S.*, Kind, J.* et al. Nature Protocols (2020).