A05: LncRNAs controlling chromatin remodeller complexes in the cardiovascular system

Little is known about the function of long non-coding RNAs in mitochondria of cells in the cardiovascular system. In the previous funding period, we determined the role of a nuclear encoded ncRNA – mito-lnc – that is imported into mitochondria of cardiomyocytes to interact and control activity of the branched-chain alpha-ketoacid dehydrogenase (BCKDH) complex, which is essential for branched chain amino acid (BCAA) catabolism. Absence of mito-lnc in cardiomyocytes reduces BCKDH activity, resulting in accumulation of BCAAs, which activates mTOR and leads to cardiac hypertrophy. We now focus on two novel nuclear encoded lncRNA mito-lnc-c6 and mito-lnc-c11 that are imported into mitochondria of cardiomyocytes and a nuclear encoded lncRNA mito-lnc-sm that translocates into mitochondria of vascular smooth muscle cells. We will identify interaction partners of mito-lnc-c6, mito-lnc-C11 and mito-lnc-sm by RNA-protein pull-down and RNA in-situ hybridisation proximity ligation experiments. RNA-seq of newly generated mouse mutants for mitolnc-c6 and mito-lnc-c11 indicates major changes in G2/M cell cycle control, mTOR signalling and expression of genes relevant for cardiac metabolism. We will explore the molecular mechanism causing metabolic changes in lncRNA-mutant cardiomyocytes and investigate whether mito-lnc-c6 and mito-lnc-c11 have a direct role for the regulation of cell cycle specific genes or whether alterations in cell cycle control are induced by lncRNAdependent regulation of cardiomyocyte metabolism. Additional mouse models will be generated for mitolnc-sm localized in mitochondria of smooth muscle cells. We will investigate the metabolic changes caused by inactivation of mito-lnc-c6 and mito-lnc-c11 and identify the pathways potentially regulated by mito-lnc-c6 and mito-lnc-c11, using a combination of RNA-seq, proteome and metabolome analysis. Manipulation of the newly discovered mitochondrial lncRNAs may provide novel opportunities to adjust deranged metabolic processes in diseased hearts or to stimulate cardiomyocyte proliferation and heart regeneration. We will also take advantage of the Cryo-EM expertise within the consortium to gain a better understanding of conformational changes in protein complexes induced by lncRNAs. In vivo HyperTRIBE approaches in the mouse, pursued during the last funding period, identified lncRNAs including Airn that interact with the chromatin remodeling complex INO80. We will investigate the functional relevance of the Airn-INO80 interactions in smooth muscle cells, focusing on the imprinted IFG2R/Slc22A2/A3 locus, which is involved in the transport of phosphorylated lysosomal enzymes and metformin responses amongst other processes. Similar studies will be conducted in cardiomyocytes to unravel cell-type specific functions of the interactions between lncRNAs and INO80.