Mitochondrial RNA‐Chromatin Interactome Regulates Endothelial‐Mesenchymal Transition

Endothelial cells (ECs) play a central role in vascular function and diabetes‐induced endothelial dysfunction leads to the development of cardiovascular diseases. In response to hyperglycemic and inflammatory (high‐glucose + TNFα; HT) stimuli, we found that ECs undergo dysfunction and endothelial‐mesenchymal transition (EndoMT) characterized by upregulation of inflammatory, fibrotic, and mesenchymal genes. To determine whether interaction between regulatory RNAs and chromatin contributes to the induction of EndoMT, we profiled the global changes in RNA‐chromatin interactome in HT‐treated ECs using iMARGI (in‐situ Mapping of RNA‐Genome Interactions). iMARGI revealed extensive chromatin binding of RNAs, particularly at genomic regions containing super enhancers (SEs). SE overlapping SMAD3 (a known regulator of EndoMT) becomes an active SE‐hub, while SMAD3 expression is significantly induced at the single‐cell level with HT treatment. In parallel, iMARGI revealed significant chromatin binding of mitochondrial RNAs with the degree of MT‐RNR2‐binding increasing in a time‐dependent manner with HT treatment. The most enriched SE region for MT‐RNR2‐binding also overlaps with SMAD3. Further preliminary experiments by cell fractionation verified the chromatin‐localized MT‐RNR2‐derived transcripts and their increase in response to HT treatment. Perturbation of mitochondrial function or genetic ablation of mitochondrial transcripts suggests a role for mitochondrial RNAs in regulating EC function and HT‐induced EndoMT. Collectively, our study provides novel insights into the potential involvement of mitochondrial RNAs in retrograde signaling and linking mitochondria to functional genomics important for endothelial regulation and vascular disease. Support or Funding Information Ella Fitzgerald Foundation, NIH grants R00HL122368, R01HL108735, R01HL145170, and NIH 4D Nucleome U01CA200147