NSF-BSF: Circular RNAs as a primate-specific mechanism to create proteome diversity

University Of Kentucky Research Foundation, Lexington KY

Investigators

Abstract

Although proteins that make up the body are almost identical between mice and humans, humans have a superior brain. This conundrum raises the question: What is the molecular basis that makes human brains superior to the brains of other species? The major genomic differences between humans and other species are outside the DNA sequences containing the instructions to make proteins. Human DNA has been ‘invaded’ by short fragments, called Alu-elements that now comprise about 10% of our genome. Alu-elements do not contain instructions to make proteins. The Alu element invasion started in primitive monkeys and is most pronounced in humans, chimpanzees and gorillas. The number of Alu elements correlates with brain function via an unclear molecular mechanism. To make proteins, DNA is made into RNA, which is made into proteins. Alu elements promote the formation of a new class of RNAs, called circular RNAs, where the RNA is not linear with a beginning and an end, but circular like a record. Unexpectedly, circular RNAs can be made into proteins. Thus, by promoting circular RNAs, Alu elements could generate new human-specific proteins. These proteins will be identified and their effect on human nerve cells will be tested. The project is a collaboration with an Israeli group. To train the next generation of molecular biologists, undergraduate students will be taught in a two-week RNA biology course that involves theoretical lessons and hands-on experiments at Hebrew University in Jerusalem. The theoretical lessons will be published as free internet videos and as a book. Circular RNAs are a novel class of RNA generated through backsplicing from pre-mRNAs that are strongly expressed in brain. Despite their lack of a cap or ribosomal entry sites, circRNAs can be translated after adenosine to inosine editing in cell culture. Backsplicing is promoted by Alu elements that expanded in the primate lineage. It is possible that the observed correlation between Alu elements and cognitive abilities is due to the formation of Alu-element dependent, primate-specific circular RNAs. The project will test the overall hypothesis that Alu-dependent circular RNAs are translated after A>I editing emanating from ADAR enzymes and that the circRNAs encode novel, undiscovered proteins. The project will (a) investigate the molecular mechanism of circRNA translation after adenosine to inosine editing, hypothesizing that inosines promote ribosomal entry. The formation of circRNAs will be (b) mechanistically characterized by determining the factors that influence the competition between linear and circular RNA splicing in the endogenous spliceosome, and by characterizing associated proteins. The functionality of selected circRNAs will be (c) tested in biochemical and cell-based assays, postulating that proteins made from circular RNAs interfere with the multimerization of their linear counterparts. For broader impacts, the USA-Israeli team will organize annual RNA summer schools with theoretical lectures and practical courses at Hebrew University in Jerusalem. The graduate level English RNA lectures will be recorded, subtitled with Spanish, Hebrew and Arabic and posted on YouTube. They will be accompanied by a book: ‘RNA biology: A practical approach’ to train the next generation of RNA biologists. This collaborative US/Israel project is supported by the US National Science Foundation and the Israeli Binational Science Foundation. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.