Long non-coding RNAs (lncRNAs) emerge to be critical regulators of cellular processes, but only a few out of thousands have been functionally characterized. We identified a novel heart-specific lncRNA, named cardiac hypertrophy associated epigenetics regulator (Chaer), which was both necessary and sufficient for hypertrophy of neonatal rat ventricular cardiomyocytes. RNA deep-sequencing revealed that Chaer contributed to the global transcriptome reprogramming during phenylephrine (50 μM)-induced hypertrophy, and regulated imprinted gene H19 expression independent of DNA methylation but dependent on histone tri-methylation at H3K27 (H3K27me3). RNA immunoprecipitation assay found that Chaer directly interacting with and negatively regulating PRC2 function on H3K27me3. Tagged RNA pull-dwon and RNA EMSA assays confirmed that Chaer directly bound to the catalytic subunit Ezh2 with a conserved 66-mer motif near its 5’ end in competition with and functionally interrupting other PRC2-binding lncRNAs. Interestingly, Chaer-PRC2 interaction was transiently enhanced at the onset of hypertrophy and responsible for hypertrophy fetal gene induction which was sensitive to Ezh2 inhibitor GSK126 (1 μM). Moreover, mTOR inhibitor rapamycin (20 nM) completely blocked the enhanced Chaer-PRC2 interaction, reversed the decrease of global H3K27me3, and abolished phenylephrine-induced expression of hypertrophy fetal genes. Finally, Chaer silence in vivo using chemically modified siRNA and nanoparticle transfection reagents significantly reversed the development of cardiac hypertrophy, pathological remodeling and H3K27m3-modification-mediated fetal gene induction under transaortic-constriction-induced pressure overload. The findings unveil Chaer as an epigenetic determinant of cardiac hypertrophy, and shed a light into the early molecular events under cardiac stress.
