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Regulation of R-loops for transcriptional control

Reference	BBS/E/J/000CA543
Principal Investigator / Supervisor	Professor Dame Caroline Dean
Co-Investigators / Co-Supervisors
Institution	John Innes Centre
Department	John Innes Centre Department
Funding type	Research
Value (£)	202,945
Status	Completed
Type	Institute Project
Start date	01/01/2014
End date	31/03/2017
Duration	38 months

Abstract

We are exploring different pathways involving RNA-mediated chromatin regulation of gene expression. The importance of these mechanisms has emerged through our work determining natural variation in flowering, an important adaptive trait in native plants and many crops. Multiple pathways regulate the Arabidopsis floral repressor FLC and these converge on cotranscriptional mechanisms involving antisense transcripts (named COOLAIR) and chromatin pathways. Regulation of COOLAIR transcription has been monitored using a COOLAIR:LUC reporter system. This enabled identification of a repressor of COOLAIR transcription that encoded an atypical homeodomain protein, which bound single-stranded DNA. Investigation of where single-stranded DNA might occur in vivo revealed the existence of an R-loop over the COOLAIR promoter. We intend to exploit this finding to identify and functionally analyse proteins that modulate the R-loop, which in turn influences transcription. We will build on preliminary data that identifies in vivo interactors of the homeodomain protein AtNDX and functionally analyse their action on the R-loop. We will also identify other regulators that repress COOLAIR transcription and investigate how their function intersects with R-loop formation, stabilization and resolution. The project will have two overall objectives. The goal of the first will be the effective combination of genetic, molecular and proteomic approaches to define in vivo interactors of AtNDX and to understand how their function modulates the R-loop formation/stabilization/resolution thus influencing COOLAIR transcription. The goal of the second will be to clone four additional COOLAIR repressors and fully integrate their activities into the mechanism detailed in Objective 1. A mechanistic understanding generated from this study will detail the links between transcript processing, R-loop stabilization and RNA decay and is likely to be widely relevant.

Summary

unavailable

Committee	Not funded via Committee
Research Topics	Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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