Stress-induced RNA–chromatin interactions promote endothelial dysfunction

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.

Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells

“…caRNA can regulate gene transcription 8–17 and post-transcriptional RNA processing and localization 18,19 . These regulatory roles often depend on caRNA’s nuclear localization 7,13,20–22 . However, the spatial organization of caRNAs has not been systematically characterized.…”

Emerging Role of Long Non-Coding RNAs in Diabetic Vascular Complications

“…lncRNA-CCL2 and LINC00607 are involved in regulating inflammation in human umbilical vein ECs (HUVECs) ( 55 , 56 ). LncRNA-CCL2 , a divergent transcript expressed adjacent to CCL2 , was induced by the pro-inflammatory cytokine IL-1β in primary ECs, immortalized HUVECs and dermal microvascular ECs.…”

“…An integrative Omics study characterized HG plus TNF-α induced changes in ECs using a combination of single-cell RNA-seq, Hi-C (to identify DNA-DNA interactions), and in situ mapping of RNA–genome interactome (iMARGI) (to identify RNA-chromatin interactions genome-wide). HG + TNF-α treatment induced inter-chromosomal RNA-chromatin interactions that were particularly clustered around super enhancers from many chromosomes ( 56 ). One of the key chromatin-associated lncRNAs induced by HG and TNF-α, LINC00607 , regulated SERPINE1 , a known pro-inflammatory and pro-fibrotic gene.…”

Stress as a Chromatin Landscape Architect

“…The endothelial cells line the blood vessels and are one of the first to be exposed to stress. A recent study looked at the 3D chromatin alterations in the endothelial cells in the presence of a combination of components that mimic inflammatory response causing endothelial dysfunction during diabetes mellitus, namely, high glucose and pro-inflammatory cytokine tumor necrosis factor alpha (TNF-alpha) ( Calandrelli et al, 2020 ). The induced endothelial dysfunction was assessed by single-cell RNA-sequencing and further analyzed by the Hi-C method for DNA–DNA interactions, while RNA–DNA interactions were evaluated by the iMARGI method ( Calandrelli et al, 2020 ).…”