Regulation of R-loops for transcriptional control

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The Dean group study the control of flowering time in the reference plant, thalecress (Arabidopsis thaliana). Several flowering pathways converge to regulate a gene called FLC and variation in expression of this gene contributes enormously to natural variation in flowering time of Arabidopsis types collected from around the world. One pathway regulating FLC involves so called non-coding RNAs - for FLC this is the RNA encoded from the opposite strand to the protein. This RNA has been called COOLAIR because it is up regulated by cold temperature. Analysis of the regulation of COOLAIR has recently led to the identification of a novel regulatory mechanism that involves an opening up of the DNA duplex, invasion by RNA and stabilization of this structure by a protein called AtNDX. This structure is called an R-loop and it inhibits production of RNA initiating in that region of the gene. This proposal aims to further dissect this mechanism and identify other proteins that play a role. In the last few years similar non-coding RNAs have been found in many organisms but their regulation and function is generally not known. Advancing our understanding from a study such as this can provide concepts important to gene regulation across many genomes.