Integrated analysis of cis-acting translocated RNAs (INTACTRNA)

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A sub-family of long intergenic non-coding RNAs, referred to herein as ict (in cis translocated) RNAs have evolved the capability to spread from their site of synthesis to inactivate genes within large chromosomal domains or entire chromosomes. Whilst there has been good progress towards defining how ictRNAs silence genes, the basis for their accumulation and spread in cis is poorly understood. Based on evidence that different ictRNAs share common origins and pathways of action, INTACTRNA will use an integrated approach to compare and contrast the activity of Xist and Rsx, ictRNAs that have evolved to silence the X chromosome in mammals, and Knq1ot1 and Airn, ictRNAs that silence genes within smaller domains of around 15-20 Mb. INTACTRNA comprises three interlinked work packages: First, we will investigate how ictRNAs evade nuclear export and become anchored to their chromosome of origin, applying advanced genomics, genome engineering and protein degron strategies. Second, we will probe how ictRNAs spread from their site of synthesis and investigate the feedback mechanisms that regulate their abundance. Here we will optimise and apply Nuc-BRITE, a new method that we have developed, for live-cell imaging and tracking of nuclear RNAs. Thirdly, we will investigate what defines the chromosomal sites to which ictRNAs translocate, and building on prior work, the role of chromosome topology in this process. For these experiments, we will develop and apply another new methodology, sRNA-DamID, for mapping association sites at high resolution and at the single-cell level. In addition we will implement advanced imaging approaches to consecutively analyse both chromosome interactions and ictRNA translocations.INTACTRNA will lead to ground-breaking advances in our understanding of processes controlling gene expression and will further catalyse the development and application of new state-of-the-art methodologies/technologies in genomics and advanced cellular imaging.