Abstract
Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. We induce endothelial cell (EC) dysfunction with high glucose and TNFα (H + T), that mimic the common stress in diabetes mellitus. We characterize the H + T-induced changes in gene expression by single cell (sc)RNA-seq, DNA interactions by Hi-C, and RNA-chromatin interactions by iMARGI. H + T induce inter-chromosomal RNA-chromatin interactions, particularly among the super enhancers. To test the causal relationship between H + T-induced RNA-chromatin interactions and the expression of EC dysfunction-related genes, we suppress the LINC00607 RNA. This suppression attenuates the expression of SERPINE1, a critical pro-inflammatory and pro-fibrotic gene. Furthermore, the changes of the co-expression gene network between diabetic and healthy donor-derived ECs corroborate the H + T-induced RNA-chromatin interactions. Taken together, caRNA-mediated dysregulation of gene expression modulates EC dysfunction, a crucial mechanism underlying numerous diseases.
Highlights
Chromatin-associated RNA has been proposed as a type of epigenomic modifier
Given that many enhancers are actively transcribed into RNAs that remain bound to chromatins[15], it is curious what regulatory role these enhancer/super enhancers (SEs)-embedded Chromatin-associated RNA (caRNA) play in transcriptional regulation of endothelial cell (EC) dysfunction
This design is based on three premises: (1) hyperglycemia and chronic inflammation are two key culprits in diabetes to cause EC dysfunction[17,18]; (2) the prolonged and combined treatment would induce robust EC changes, encompassing endothelial nitric oxide synthase (eNOS) suppression, pro-inflammatory activation, extracellular matrix (ECM) remodeling, and endothelial–mesenchymal transition (EndoMT), in which ECs manifest a phenotypic transition into mesenchymal-like cells[19,20]; and (3) the time course will allow temporal mapping of EC changes in transcriptome, genomic interactions, and RNA–genome interactions
Summary
Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. This feature helped to reveal a large number of caRNAs, including those attached to other chromosomes[7,12] It is unknown whether these RNA–chromatin contacts are altered in a dynamic cellular process, and how these interactions impact transcriptional output and functional outcome in the context of health and disease remains unclear. Correlational analysis performed with scRNA-seq data from H + T-treated ECs and diabetic donor-derived ECs reveal that LINC00607 and SERPINE1 are coexpressed in the same single cells more often in the dysfunctional ECs than in healthy control ECs. Collectively, our data suggest that RNA–chromatin interactions contribute to transcriptional regulation during endothelial dysfunction, a biological process closely implicated in various diseases
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