Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human Regulatory T cells

The epigenome and transcriptome constitute a critical element of a tightly regulated, cell-type specific gene expression program, and subtle perturbations in the regulation of this program can result in pathology. Epigenetic features such as DNA accessibility dictate transcriptional regulation in a cell type- and cell state- specific manner, and mapping this in health vs. disease in clinically relevant material is opening the door to new mechanistic insights and new targets for therapy. Here we demonstrate the robustness and reproducibility of an ATAC-seq protocol comparing fresh or cryopreserved primary Treg cells, and comparing their profile in the steady state and in response to stimulation. We extend this method to explore the feasibility of conducting simultaneous quantitation of chromatin accessibility and transcriptome from a single aliquot of 50,000 Treg cells from cryopreserved PBMCs. Our study profiled chromatin accessibility of Treg cells recovered from fresh and frozen PBMC samples from healthy adult donors using ATAC-seq, as well as gene expression changes between RNA recovered from whole cells and ATAC supernatant fractions.