Forward Genetic Analysis of Human Nuclear Long Non-Coding RNAs

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PROJECT SUMMARY Certain human nuclear long non-coding RNAs (lncRNAs) represent well-established promising targets for the treatment of cancer, developmental and viral diseases; manipulating their levels is expected to provide therapeutic interventions for various human disorders. However, due to the lack of a reliable high-throughput screening technology to quantify nuclear lncRNA levels, human pathways of nuclear lncRNA biogenesis, regulation, and surveillance have been refractory to forward genetic identification. We developed an approach that enables the first successful forward genetic interrogation of the pathways of biogenesis and surveillance of the nuclear lncRNA MALAT1 in human cells. We identified human nuclear complexes required for MALAT1 3′ end surveillance and components required for MALAT1-associated small cytoplasmic RNA (mascRNA) maturation, as well as numerous candidate genes that require further investigation. We propose to expand this approach and perform comprehensive forward genetic identification of human nuclear pathways acting on the following lncRNAs: (i) cancer-associated lncRNA MALAT1, (ii) multiple endocrine neoplasia transcript 1 (MEN- β), which is up-regulated upon embryonic stem cell and neuronal differentiation, and (iii) polyadenylated nuclear lncRNA PAN, required for lytic production of new viral particles by the Kaposi’s sarcoma-associated herpesvirus (KSHV). This study is aimed to identify human pathways and regulatory networks acting on nuclear lncRNAs and uncover new targets for potential anti-cancer and anti-viral therapies.