The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart

Abstract

Long noncoding RNAs (lncRNAs) are emerging as critical regulators of heart physiology and disease, although the studies unveiling their modes-of-action are still limited to few examples. We recently identified pCharme, a chromatin-associated lncRNA whose functional knockout in mice results in defective myogenesis and morphological remodelling of the cardiac muscle. Here, we combined Cap-Analysis of Gene Expression (CAGE), single-cell (sc)RNA sequencing and whole-mount in situ hybridization analyses to study pCharme cardiac expression. Since the early steps of cardiomyogenesis, we found the lncRNA being specifically restricted to cardiomyocytes, where it assists the formation of specific nuclear condensates containing MATR3, as well as important RNAs for cardiac development. In line with the functional significance of these activities, pCharme ablation in mice results in a delayed maturation of cardiomyocytes, which ultimately leads to morphological alterations of the ventricular myocardium. Since congenital anomalies in myocardium are clinically relevant in humans and predispose patients to major complications, the identification of novel genes controlling cardiac morphology becomes crucial. Our study offers unique insights into a novel lncRNA-mediated regulatory mechanism promoting cardiomyocyte maturation and bears relevance to Charme locus for future theranostic applications.

Exploring the landscape of tools and resources for the analysis of long non-coding RNAs

“…In line with this, the output may serve as a starting point for conducting further experimental validations, such as performing cross-linking immunoprecipitation (CLIP) or reciprocal RNA pull-down approaches [94] , [95] .…”

Epigenetic Regulation of Mammalian Cardiomyocyte Development

“…Several other lncRNAs, such as CARMA and Platr4, also regulate cardiomyocyte differentiation by modulating the Notch and Hippo signaling pathways, respectively [ 184 , 185 ]. More recently, another lncRNA, Charme, emerged as significant for cardiomyocyte proliferation, via the formation of active nuclear condensates containing RNAs critical for cardiomyocyte development [ 186 ].…”