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Global role of RNA-binding proteins

Microarray analysis of a Rip-chip experiment RNAs enriched in the RNA-binding-protein immunoprecipitate are coloured red

Research Groupings: Structural and molecular cell biology | Functional genomics, systems biology and genetic medicine

Post-transcriptional control is carried out by RNA-binding proteins (RBPs) that bind to specific RNA molecules and control their processing, localisation, degradation and translation.  Although there are many examples of how specific RBPs control individual RNAs, little is known about the extent of this type of control, and about how cells co-ordinately regulate groups of genes at the posttranscriptional level. 

The systematic identification of all cellular targets of an RBP can provide information on its function at a ‘global’ level: An RBP can be purified together with its associated RNAs, and the RNAs can be identified using DNA microarrays.  This technique is known as Rip-chip (for RBP Immunoprecipitation analysed with a DNA chip). Several pioneering studies using this approach have revealed an unsuspected level of complexity: It appears that every RBP binds to specific RNA populations and that most RNAs in the cell are bound by one or more RBPs.  This network of RBP-RNA interactions regulates the fates of RNA molecules through every step of posttranscriptional regulation.  In the same way that the binding of different combinations of transcription factors to promoters coordinates the specific transcription of hundreds of target genes, combinatorial binding of RBPs to multiple RNAs would co-ordinately regulate their posttranscriptional processing. However, with hundreds of RBPs encoded in eukaryotic genomes, the regulatory networks created by the interactions between RBPs and their target genes remain largely unexplored.

Fission yeast cells undergoing differentiation

We are using the fission yeast Schizosaccharomyces pombe to understand the global role of RBPs.  Fission yeast is a relatively simple unicellular eukaryote that has been widely used as a model for diverse biological problems. To gain a systematic view of the structure of RNA-RBP networks, we have established the RIp-chip method for fission yeast, and we are applying it to a variety of proteins.  We are also developing methods to systematically identify all proteins bound to a specific RNA molecule.  We complement these experiments with a functional analysis of the RBPs, using cell biological and genomic methods.  The combination of these approaches will provide a unique view of the organisation of RNA-protein networks in fission yeast, from which we expect to extract general principles applicable to higher eukaryotes.

Lab members
Caia Duncan, Cristina Cotobal