The neuropsychiatric disorders schizophrenia and autism together affect over 15% of children in the United States, representing a significant public health concern. Development of effective therapeutics and diagnostic tools for these disorders has been hindered by our incomplete understanding of their complex neurodevelopmental etiologies. Gene expression variation is a common attribute of these disorders, thought to arise from developmental stage- and tissue-specific RNA regulation during neurodevelopment. New genome- wide mapping strategies have identified a connection between R-loops (a three-stranded nucleic acid structure containing a DNA/RNA hybrid) and transcriptional regulation, suggesting a possible link between R-loops and gene expression variation. However, R-loops have never before been characterized on a genome-wide scale in the human brain, precluding research studying their role in neurodevelopmental illnesses. Our research has showed that R-loops may poise developmental genes for transcription during neural differentiation, and our immediate goal is to test this hypothesis by leveraging human induced pluripotent stem cell (hiPSC)-based models to functionally manipulate R-loop levels. Specifically, we aim to reduce R-loop levels in hiPSC-derived neural progenitor cells and measure the effect this has on transcription, differentiation, and ability of neural cells to form functional synapses.
We aim to identify a causal mechanism of this R-loop-mediated transcriptional poising by exploring the hypothesis that R-loops stall RNA polymerase II, as stalled RNA polymerase II is thought to keep developmental genes transcriptionally inactive but ready for expression upon developmental cues. Importantly, we will map R-loops genome-wide for the first time in the developing human brain, and link R-loop distributional shifts during human neurogenesis with neurodevelopmental disease-associated gene expression signatures. Here, we will use cutting-edge techniques, including DNA/RNA immunoprecipitation followed by next- generation sequencing, to achieve these goals. These first steps toward understanding R-loop function in neural cells will facilitate our long-term objective to uncover the epigenetic mechanisms of aberrant RNA regulation in neuropsychiatric illness, in order to improve diagnostics and identify novel therapeutic targets for these illnesses.
Neurodevelopmental illnesses such as schizophrenia and autism are highly prevalent in the United States and are thought to arise, in part, from altered gene expression patterns in the brain during development. This proposal is aimed at identifying a causal link between R-loops (a three-stranded nucleic acid structure) and gene expression during neural development, with the overall objective to promote more effective approaches to diagnosing and treating neurodevelopmental disorders.