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Post-transcriptional regulation of germ cell apoptosis in C. elegans

Applicant Allain Frédéric
Number 127454
Funding scheme Sinergia
Research institution Institut für Molekularbiologie und Biophysik ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Molecular Biology
Start/End 01.11.2009 - 31.10.2012
Approved amount 2'200'000.00
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All Disciplines (3)

Discipline
Molecular Biology
Biophysics
Embryology, Developmental Biology

Keywords (15)

C. elegans; apoptosis; Protein-RNA interactions; RNA binding proteins; microRNA; structural biology; oligonucleotide synthesis; NMR spectroscopy; bioinformatics; High-throughput sequencing; microarrays; translation regulation; cross-linker; surface plasmon resonance; germ cell

Lay Summary (English)

Lead
Lay summary
Gene expression in eukaryotes is regulated at multiple levels. Whereas the mechanisms that regulate the early and late steps in this cascade - transcription and post-translational modifications - are well characterized, much less is known about the intervening steps. The regulatory processes controlling the fate of mRNAs in the cytosol are still poorly understood. It has become recently apparent that mRNA metabolism is heavily and dynamically regulated by RNA-binding proteins (RBPs) and the microRNAs (miRNAs). In this grant application, we propose to use a multi-disciplinary approach to construct a comprehensive view of the involvement of RBPs and miRNAs in the regulation of a physiologically relevant process: germ cell apoptosis (programmed cell death) in the nematode C. elegans. We chose this system for the following reasons. First, previous studies have shown that RBPs and miRNAs can regulate apoptosis in C. elegans. Second, C. elegans is a model organism that is easily amenable to genetic and reverse genetic studies. Third, translational control is particularly prevalent in the C. elegans germ line, controlling nearly every single fate decision and differentiation step. In order to construct a comprehensive view of this translational regulatory network, we have assembled a team of five research groups that covers a broad range of technical expertises. Our team includes a developmental geneticist (M. Hengartner) who will screen for novel RBPs and miRNAs involved in germ line apoptosis and perform in vivo functional characterization of novel targets. We will apply genomics tools to identify the in vivo targets of known and novel RBPs/miRNAs that regulate apoptosis (A. Gerber) and through computational analyses will define common structural and functional features among the specific mRNAs targeted by the RBPs/miRNAs (M. Zavolan). Studies in vivo will be complemented by quantitative in vitro approaches to define the chemical determinants behind functional RBP/miRNA-mRNA interactions (J. Hall), and by the structural elucidation of several RNA-protein complexes (F. Allain). Within granting period, we will strengthen our understanding of the interactions of RBPs/miRNAs with mRNAs, decipher the molecular mechanism of know RBPs and identify and dissect the function of additional RBPs and miRNAs which control apoptosis in C. elegans. This multidisciplinary approach could become a 'landmark' attempt that may guide similar studies on other important biological processes. Finally, since many of the core components of the apoptosis network are evolutionarily conserved, our findings in C. elegans may be relevant for further investigations of human diseases.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
The expression levels of microRNA-361-5p and its target VEGFA are inversely correlated in human cutaneous squamous cell carcinoma.
Kanitz Alexander, Imig Jochen, Dziunycz Piotr J, Primorac Adriana, Galgano Alessia, Hofbauer Günther F L, Gerber André P, Detmar Michael (2012), The expression levels of microRNA-361-5p and its target VEGFA are inversely correlated in human cutaneous squamous cell carcinoma., in PloS one, 7(11), 49568-49568.
Systematic screens of proteins binding to synthetic microRNA precursors.
Towbin Harry, Wenter Philipp, Guennewig Boris, Imig Jochen, Zagalak Julian A, Gerber André P, Hall Jonathan (2012), Systematic screens of proteins binding to synthetic microRNA precursors., in Nucleic acids research, 1-11.
RNA regulons and the RNA-protein interaction network
Imig Jochen, Kanitz Alexander, Gerber Andre P (2012), RNA regulons and the RNA-protein interaction network, in Biomolecular Concepts, 3(5), 403-414.
Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28.
Loughlin Fionna E, Gebert Luca F R, Towbin Harry, Brunschweiger Andreas, Hall Jonathan, Allain Frédéric H-T (2011), Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28., in Nature structural & molecular biology, 19(1), 84-9.
A Decade of the Human Genome Sequence-How Does the Medicinal Chemist Benefit?
Brunschweiger Andreas, Hall Jonathan (2011), A Decade of the Human Genome Sequence-How Does the Medicinal Chemist Benefit?, in ChemMedChem, 1-11.

Associated projects

Number Title Start Funding scheme
139221 New electronics for 900MHz NMR spectrometer 01.12.2011 R'EQUIP
133134 NMR structure determination of protein-RNA complexes involved in pre-mRNA editing and translation regulation 01.10.2010 Project funding
139230 High-performance IT Infrastructure for Computational Biology 01.02.2012 R'EQUIP
141942 Post-transcriptional regulation of germ cell apoptosis in C. elegans 01.11.2012 Sinergia

Abstract

Gene expression in eukaryotes is regulated at multiple levels. Whereas the mechanisms that regulate the early and late steps in this cascade - transcription and post-translational modifications - have been studied in great detail, much less is known about the intervening steps. In particular, the regulatory processes controlling the fate of mRNAs in the cytosol (mRNA stability, subcellular localization, translation) are still poorly understood. In the last few years, it has become apparent that mRNA metabolism is heavily and dynamically regulated by RNA-binding proteins (RBPs) and the microRNAs (miRNAs). Hundreds of RBPs and miRNAs are present in metazoan organisms, rivaling in number other classes of regulatory molecules such as transcription factors and kinases. Moreover, both RBPs and miRNAs appear to have on average between dozens and hundreds of targets. Consequently, it is estimated that at least two thirds of all human genes are regulated at the mRNA level by RBPs and miRNAs. miRNAs preferentially regulate transcription factors and the RBPs frequently regulate their own mRNAs, suggesting that RBPs and miRNAs might be used to modulate coordinately almost every aspect of a cell's life. Aberrations in RBP or miRNA expression can readily lead to human diseases, further underscoring the importance of these regulatory molecules for proper development and homeostasis. As the significance of RBPs and miRNAs in the regulation of gene expression is increasingly recognized, the interest in characterizing their mode of action, the targets that they regulate, and how RBP and miRNA systems interact with each other is rising. In this Sinergia grant application, we propose to use a multi-disciplinary approach to construct a comprehensive view of the involvement of RBPs and miRNAs in the regulation of a physiologically relevant process: germ cell apoptosis in the invertebrate nematode C. elegans. We chose this system for the following three reasons. First, previous studies have shown that RBPs and miRNAs can regulate apoptosis in a variety of species, including C. elegans. Second, C. elegans is a model organism that is easily amenable to genetic and reverse genetic studies. Third, translational control is particularly prevalent in the C. elegans germ line, controlling nearly every single fate decision and differentiation step. In order to construct a comprehensive view of the translational regulatory network that controls germ line apoptosis, we have assembled a team of five research groups that covers a broad range of technical expertises from chemistry to physiology and computational modeling. Our team includes a developmental geneticist (M. Hengartner) who will screen for novel RBPs and miRNAs involved in germ line apoptosis and who will perform in vivo functional characterization of novel targets. We will apply genomics tools to identify the in vivo targets of known and novel RBPs/miRNAs that regulate apoptosis (A. Gerber) and through computational analyses we will define common structural and functional features among the specific mRNAs targeted by the RBPs/miRNAs (M. Zavolan). Studies in vivo will be complemented by quantitative in vitro approaches to define the chemical determinants behind functional RBP/miRNA-mRNA interactions. To date, genetics, bioinformatics, biology and biochemistry are the disciplines which have contributed most in this field. Chemistry has played a relatively minor role, yet, understanding the physiochemical nature of the interactions between mRNAs and RBPs/miRNAs which is one cornerstone of this Sinergia proposal, is essentially a chemical problem. We will bring chemistry to bear during this collaboration in three synergistic ways: investigation of protein-RNA interactions at the atomic level (NMR structure: F. Allain), and generation of high quality libraries to enable new bioinformatics methods and development of chemical tools which will allow us to isolate miRNA-mRNA interactions in the cell (J. Hall). Within a three-year period, we will strengthen our understanding of the interactions of RBPs/miRNAs with mRNAs, we will decipher the molecular mechanism of GLD-1 and GLA-3 and we will identify and dissect the function of additional RBPs and miRNAs which control apoptosis in C. elegans. We will know to what extent, and how, various RBPs and miRNAs combine to regulate common target mRNAs, and we will build an understanding of how specific alterations in these regulatory networks can affect the apoptotic outcome of a cell. Since RBP/miRNAs play important roles in a plethora of physiological processes, this multidisciplinary approach could become a 'landmark' attempt that may guide similar studies on other important biological processes. Finally, since many of the core components of the apoptosis network are evolutionarily conserved, the characterization of regulatory pathways in C. elegans may be relevant for further investigations of human diseases.
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