Role of RNA-binding proteins in the control of RNA turnover: a genome-wide approach

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.

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.

The amount of each RNA molecule in a cell has to be carefully controlled. For example, many diseases -such as cancer- appear when cells contain the wrong amounts of certain RNAs. The levels of all RNAs are set by the balance between how quickly they are made and how fast they are destroyed. Although both aspects are equally important, we know much less about how cells control the destruction of RNAs.

From the moment an RNA molecule is made, different proteins attach to it. These proteins, called RNA-binding proteins, decide when the RNA should be destroyed. When RNA-binding proteins do not function correctly, the cell loses control of 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.

Our aim is to understand how RNA-binding proteins control the destruction 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 we will use a simple yeast -made of a single cell- that can acquire different forms. We will remove RNA-binding proteins to see how this changes the way in which RNAs are destroyed, and we will study which RNAs are bound by different RNA-binding proteins. This will allow us to understand how cells control their genes in order to become different. We expect this information will be useful to understand how human cells behave and, eventually, help us devise cures for disease.

mRNA abundance is determined by the balance between transcription and mRNA degradation. mRNA stability is a transcript-specific property, with mRNA half-lives in eukaryotic cells varying over a range of more than a hundred-fold. mRNA turnover is performed by several well-conserved protein complexes. This degradation machinery can directly recognise mRNAs; in other cases, its recruitment to mRNAs is modulated by RNA-binding proteins (RBPs) that recognise specific sequence motifs on their targets.

mRNA turnover is actively regulated during stress, aging and immune responses, highlighting its importance for human health. Moreover, some cancers and many inherited diseases are linked to defects in RBPs.

Little is known about how mRNA half-lives are determined for specific transcripts, and about how cells coordinate the turnover of groups of mRNAs. Dissecting the principles that underlie the specificity and coordination of mRNA turnover will require the systematic characterisation of the genome-wide roles of RBPs in mRNA turnover. We will use mitotically growing cells of the fission yeast Schizosaccharomyces pombe to study these questions.

We will generate and characterise a collection of mutants in all essential RBP genes to identify those involved in mRNA turnover. We will focus on essential genes, as our preliminary results suggest that these RBPs perform most of the regulation of this process. Mutants identified in this screen will be characterised in detail by determining global mRNA decay rates and by identifying their direct targets (RBP-associated RNAs). These data will provide a complete view of the regulatory network that controls mRNA decay in mitotically growing cells. We will mine these data to identify general principles of how mRNA turnover is regulated at the level of the whole cell. It is expected that many of the principles will be applicable to human cells.

This project will contribute to the training of researchers in key areas of research, and will result in knowledge that may have long-term implications in various areas of medical research and biotechnology described below.

The biotechnology and pharmaceutical industries are potential beneficiaries of this project, both through the training of highly qualified researchers (point 1) and the knowledge and expertise it will generate (points 2-4). In addition, the project will contribute to fighting human disease (points 2 and 3). The impact plan discusses in more detail how we will ensure that the potential beneficiaries of this project will be reached.

[1] Training and capacity building in functional genomics / systems biology. This project will provide an excellent opportunity for the training of the postdoctoral researcher in advanced functional genomics methods, analysis of large scale datasets and complex networks. This will be done through the work carried out in the laboratory, as well as through interactions with members of the Cambridge Systems Biology Centre and our collaborators. The provision of scientists trained in these multidisciplinary approaches will be beneficial for the UK industry, especially the biotechnology and pharmaceutical sectors.

[2] General understanding of human disease: The regulation of mRNA decay is essential in processes of medical importance, such as inflammation, hypoxia and cancer. In many cases the mRNAs whose stability is controlled encode proteins with important regulatory functions, including oncogenes, cytokines and growth factors. Deregulation of RNA-binding proteins (RBPs) that control RNA stability or mutations in RNA signals recognised by these proteins can lead to disease. For example, some symptoms of type I myotonic dystrophy are caused by inactivation of an RBP that regulates decay, while the stability of oncogenes is often altered by translocations or mutations that affect RNA regulatory regions. This proposal aims at identifying general principles of how RBPs control RNA decay, which may be applicable to human cells.

[3] As described in more detail in the 'Academic Beneficiaries' section, recent work has shown similarities between pathogens of the Pneumocystis genus and fission yeast (in particular, in their meiotic pathways). These organisms cause pneumonia in patients with weakened immune systems (premature babies, AIDS and cancer patients). As Pneumocystis cannot be cultured in vitro, there is a need for model systems that allow the study of their basic biology. Therefore, our results on individual RNA binding proteins might be useful to understand the biology of these pathogens and develop treatments against their infection. To make sure this information reaches the Pneumocystis research community, we will highlight these similarities in peer-reviewed publications, our website and relevant scientific conferences.

[4] Synthetic biology aims at building artificial biological systems for practical applications. Many of these applications are based on the constructions of simple gene circuits, in which DNA, RNAs and protein interact with each other to produce specific behaviours (for example, the detection of a specific compound in the environment). This project will help understand how gene circuits (specifically, those belonging to the understudied types that include RNA-binding proteins) are organised. This information will be useful for the construction of artificial circuits.