Differences of DNA methylation and chromatin accessibility during human skin Treg differentiation
BEUMER N. 1,2,3,4,5,7, DELACHER M. 6, IMBUSCH C. 7, WEICHENHAN D. 8, BÄHR M. 8, PLASS C. 8, BRORS B. 7,10,11, FEUERER M.
1 Division of Personalized Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; 2 Faculty of Biosciences (Heidelberg University), Heidelberg, Germany; 3 DKFZ-Hector Cancer Institute at the University Medical Center Mannheim, Mannheim, Germany; 4 German Center for Lung Research (DZL), Heidelberg, Germany; 5 University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; 6 University Medical Center Mainz, Mainz, Germany; 7 Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; 8 Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany; 9 National Center for Tumor Diseases (NCT), Heidelberg, Germany; 10 German Cancer Consortium (DKTK), Heidelberg, Germany; 11 Leibniz Institute for Immunotherapy, Regensburg, Germany
Tissue-resident regulatory T cells (Tregs) can participate in tissue homeostasis and repair. Previous research has highlighted several epigenetic traits that underlie tissue-residency and associated functions. However, the corresponding DNA methylation landscape has not been characterized in humans and its relationship with chromatin accessibility is so far unclear. To shed light on methylation changes during human tissue-Treg development, we profiled DNA methylation in blood naïve Tregs and skin Tregs using whole-genome bisulfite sequencing. We then identified genomic regions displaying differential methylation between the two cell types and investigated enrichment of transcription factor binding motifs in such regions. Genomic regions that lose methylation during skin Treg differentiation are enriched for motifs associated with a group of basic helix-loop-helix (bHLH) transcription factors that includes c-Myc and USF1. This suggests a demethylation program that specifically targets binding sites of these transcription factors. In order to align this finding with the chromatin accessibility level, we utilized single-cell ATAC-seq data for the same cell types. Remarkably, motifs associated with the aforementioned transcription factors display an accessibility signal in both cell types and do not exhibit notable changes during skin Treg differentiation. Together, our results indicate that binding sites for specific bHLH transcription factors are primarily affected by methylation changes during skin Treg differentiation. This suggests different roles of methylation and chromatin accessibility during this process. Further investigations may identify other discrepancies between the two epigenetic levels and thus lead to an in-depth understanding of the different epigenetic mechanisms that guide the development of tissue-resident Tregs.