Biology and dysregulation of IncRNAs in disease
Long non-coding RNAs (lncRNAs) are emerging as important regulators of tissue physiology and disease processes, especially cancers. Although dysregulated lncRNA expression has been associated with cancer progression, the contribution of lncRNAs to oncogenesis is poorly understood because their molecular and biological functions are obscure. We recently identified a novel lncRNA and its interacting proteins important for melanoma invasion. Projects are available to understand how this lncRNA functions at the molecular level, which may be important for determining why more males than females die from melanomas.
More broadly, the Novina lab is attempting to understand lncRNA biology and its roles in oncogenesis by systematically identifying lncRNA-associated proteins. It is virtually impossible to bioinformatically predict lncRNA function (or interacting proteins) by sequence analysis because (1) lncRNAs are poorly conserved and (2) proteins bind to RNAs by a poorly understood combination of RNA sequence and secondary structure. Traditional methods to define lncRNA-protein interactions focus on immunoprecipitating one candidate RNA with an RNA tag or antisense DNA oligos, or incubating cell lysates with biotinylated in vitro transcribed RNAs followed by mass spectrometry or western blotting. Not only are these methods low throughput, but the protein identification step is extremely challenging due to limited biomass from low-efficiency immunoprecipitations, loss of transient and weak interactors, or isolation of promiscuous RNA binding proteins. We are beginning to define lncRNA-dependent interactomes through development of a lncRNA-based yeast three hybrid (Y3H) platform.
Projects are available to systematically define lncRNA-protein interactomes for a set of cancer-promoting lncRNAs through implementation of RATA and Y3H systems.
More broadly, the Novina lab is attempting to understand lncRNA biology and its roles in oncogenesis by systematically identifying lncRNA-associated proteins. It is virtually impossible to bioinformatically predict lncRNA function (or interacting proteins) by sequence analysis because (1) lncRNAs are poorly conserved and (2) proteins bind to RNAs by a poorly understood combination of RNA sequence and secondary structure. Traditional methods to define lncRNA-protein interactions focus on immunoprecipitating one candidate RNA with an RNA tag or antisense DNA oligos, or incubating cell lysates with biotinylated in vitro transcribed RNAs followed by mass spectrometry or western blotting. Not only are these methods low throughput, but the protein identification step is extremely challenging due to limited biomass from low-efficiency immunoprecipitations, loss of transient and weak interactors, or isolation of promiscuous RNA binding proteins. We are beginning to define lncRNA-dependent interactomes through development of a lncRNA-based yeast three hybrid (Y3H) platform.
Projects are available to systematically define lncRNA-protein interactomes for a set of cancer-promoting lncRNAs through implementation of RATA and Y3H systems.
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