In vivo functions of the long non-coding RNA (lncRNA) Fendrr in cardiac development during mouse embryogenesis

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The most abundant RNA transcripts in the vertebrate transcriptome are long noncoding RNAs (lncRNAs), transcripts that are longer than 200 nucleotides and do not encode proteins. LncRNAs have been associated with epigenetic changes, developmental defects and cancer, and knockouts are sometimes lethal. We showed previously that the lncRNA Fendrr is essential for mouse embryo development and mutant embryos die due to cardiac defects.We will further characterize the molecular roles of Fendrr in the development of the early cardiac cell lineage of the mouse embryo. This work will help us to understand how the loss of Fendrr leads to cardiac defects and how Fendrr, together with the polycomb repressive complex 2 (PRC2), regulates cardiac specific gene expression. Furthermore we will identify additional proteins and protein complexes that interact with Fendrr and will analyze their in vivo role in early cardiac development. In addition, certain elements of the Fendrr transcript can interact directly with the genome to regulate target gene expression and, eventually, aid in recruiting protein complexes to specific sites in the genome. We identified one such element in the Fendrr transcript. By CRISPR/Cas9 aided genome editing we removed this element in the genome from embryonic stem cells and embryos and mice derived from these ES cells exhibit a partial requirement of this element for Fendrr function. We will analyze additional potential elements in Fendrr in vivo. In addition, we will identify genome wide binding sites of Fendrr.The human orthologue of Fendrr is implicated to play a role in the human genetic disorder Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV). Patients with ACD/MPV exhibit numerous developmental defects such as cardiac defects, but ultimately die due to lung failure. We will use lung ex vivo culture of wild type and Fendrr mutant lungs to identify the developmental defects causing the lung failure of ACD/MPV patients and elucidate the molecular role of Fendrr in this process.The experiments proposed here aim to widen our understanding of the in vivo roles of the lncRNA Fendrr and uncover basic principles of genome regulation by lncRNAs in general.