A single-cell lncRNA atlas deciphers lncRNA-mediated gene regulatory network in the kidney and aging kidney (KAP230586)

Accumulated evidence demonstrates that long non-coding RNAs (lncRNAs) regulate cell differentiation and homeostasis, influencing kidney aging and disease. Despite their versatility, lncRNA functions are poorly understood because of several technical limitations. Accordingly, there have been only a few research studies conducted to identify lncRNAs in the aging kidney at the single-cell level. Here, we employed a method using targeted single-cell RNA-sequencing to increase the sensitivity of lncRNA detection. Using this method, we established an lncRNA atlas of various mouse tissues including the kidney at the single-cell level and generated a web interface (https://gist-fgl.github.io/sc-lncrna-atlas/). Our workflow enhanced the sensitivity of lncRNA detection in single cells, which enabled a comprehensive analysis of lncRNA, even in rare aging kidney cells. We identified unique and distinct lncRNA expression patterns across various cells and constructed gene regulatory networks (GRNs) in each cell type centered on interactions between lncRNA and transcription factors (TF), suggesting that lncRNAs have critical roles in maintaining transcriptional programs cooperatively with core TFs. Collectively, our data are a valuable resource for lncRNA studies and demonstrate how cell type-specific lncRNAs regulate various cell types, and provide a comprehensive understanding of their functions in the kidney and aging kidney.