Role of RNA-binding proteins in cellular differentiation: a global approach
Lead Research Organisation:
University of Cambridge
Department Name: Genetics
Abstract
Our bodies are made of very different types of cells: Skin cells are flat and protect our body, while brain cells have cables that pass messages around. Despite being so different, all our cells carry exactly the same information in their genes. What makes them special is what information they use, that is, which genes they switch on and off. Many diseases -such as cancer- appear when cells use the wrong genes.
The information on how to make a cell is stored in the form of a DNA molecule. However, this information cannot be read directly: it first needs to be copied into another molecule called RNA, from which it can be ?translated? into a protein. Proteins are the components that directly build the cell and make it function.
From the moment an RNA molecule is made in the cell different proteins attach to it, directing every step of its life. These proteins, called RNA-binding proteins, modify the RNA so that it can be translated into a protein, decide when it should be destroyed or to which part of the cell it should be transported.
RNA-binding proteins are important because they regulate the flow of information between DNA and proteins. When RNA-binding proteins do not function correctly, the cell loses control on the production of many proteins, and this may cause disease. For instance, defects in certain RNA-binding proteins lead to consequences such as muscular dystrophy or mental retardation.
My aim is to understand how RNA-binding proteins control the fate of RNA molecules. One way to study a complicated process of the human body is to use a model organism: this is a simpler creature, but similar enough to allow us to learn about ourselves. To study how RNA-binding proteins work I will use a simple yeast -made of a single cell- that can acquire different forms. I will remove RNA-binding proteins and see how this changes which genes are used by the cell, and I will study which RNAs are bound by different RNA-binding proteins. This will allow me to understand how cells control their genes in order to become different. I expect this information will be useful to understand how human cells behave and, eventually help us devise cures for disease.
The information on how to make a cell is stored in the form of a DNA molecule. However, this information cannot be read directly: it first needs to be copied into another molecule called RNA, from which it can be ?translated? into a protein. Proteins are the components that directly build the cell and make it function.
From the moment an RNA molecule is made in the cell different proteins attach to it, directing every step of its life. These proteins, called RNA-binding proteins, modify the RNA so that it can be translated into a protein, decide when it should be destroyed or to which part of the cell it should be transported.
RNA-binding proteins are important because they regulate the flow of information between DNA and proteins. When RNA-binding proteins do not function correctly, the cell loses control on the production of many proteins, and this may cause disease. For instance, defects in certain RNA-binding proteins lead to consequences such as muscular dystrophy or mental retardation.
My aim is to understand how RNA-binding proteins control the fate of RNA molecules. One way to study a complicated process of the human body is to use a model organism: this is a simpler creature, but similar enough to allow us to learn about ourselves. To study how RNA-binding proteins work I will use a simple yeast -made of a single cell- that can acquire different forms. I will remove RNA-binding proteins and see how this changes which genes are used by the cell, and I will study which RNAs are bound by different RNA-binding proteins. This will allow me to understand how cells control their genes in order to become different. I expect this information will be useful to understand how human cells behave and, eventually help us devise cures for disease.
Technical Summary
The fate of every cellular RNA is regulated by RNA-binding proteins (RBPs) that recognise and associate with specific RNA sequences. RBPs mediate and control every step of the life of an RNA molecule, including processing, splicing, nuclear export, subcellular localisation, degradation and translation (Keene, 2001; Hieronymus and Silver, 2004). A small number of systematic studies of the targets of RBPs have provided the basis for the hypothesis that the combinatorial binding of RBPs to groups of RNAs allows the cell to co-ordinately regulate posttranscriptional events of RNA populations. 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.
I plan to use sexual development of the fission yeast Schizosaccaromyces pombe as a model to study the global role of RBPs in controlling posttranscriptional regulation during cellular differentiation. Sexual differentiation is accompanied by a complex gene expression program (Mata et al. 2002) that is partly controlled at the posttranscriptional level.
I will systematically study the role of 14 RBPs that are specifically induced during this process. To identify RBP targets I will purify RBP-RNA complexes and identify the RNAs associated with the RBP using DNA microarrays. I will delete the genes encoding the RBPs and analyse their phenotypes using microscopy and their effect on gene expression using DNA microarrays. I will use the information on RBP targets and the phenotypic analysis of the RBP mutants to design additional experiments aimed at studying the molecular functions of the RBPs. The combination of the information from phenotypes, targets and functional studies will provide new insights into the global functions of RBPs in differentiating cells.
I plan to use sexual development of the fission yeast Schizosaccaromyces pombe as a model to study the global role of RBPs in controlling posttranscriptional regulation during cellular differentiation. Sexual differentiation is accompanied by a complex gene expression program (Mata et al. 2002) that is partly controlled at the posttranscriptional level.
I will systematically study the role of 14 RBPs that are specifically induced during this process. To identify RBP targets I will purify RBP-RNA complexes and identify the RNAs associated with the RBP using DNA microarrays. I will delete the genes encoding the RBPs and analyse their phenotypes using microscopy and their effect on gene expression using DNA microarrays. I will use the information on RBP targets and the phenotypic analysis of the RBP mutants to design additional experiments aimed at studying the molecular functions of the RBPs. The combination of the information from phenotypes, targets and functional studies will provide new insights into the global functions of RBPs in differentiating cells.
