EU Framework Programme V

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EU Framework Programme V QLG2-CT-2001-01554 Qualit
y of Life and Management of Living
Resources             An Integrated Analysis of
Links between Pathways of RNA Metabolism in the
Post-genomic Era.     RNOMICS     Jean Beggs
David Tollervey U. Edinburgh Alain
Jacquier Micheline Fromont-Racine Institut
Pasteur Walter Keller U. Basel Maria
Carmo-Fonseca U. Lisbon Pierre Legrain
Hybrigenics
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WP1 (U Edinburgh) Objectives 1) To analyse
how 8 Lsm proteins assemble to form two distinct
complexes, one involved in nuclear RNA splicing,
the other in mRNA turnover in the cytoplasm. To
test requirements for correct localisation and
assembly. 2) To investigate observed
interactions between RNA poll II and splicing
factors.
WP2 (U Edinburgh) Objectives To investigate the
role of the nuclear cap-binding complex (CBC) in
integrating pre-mRNA metabolism with other
cellular processes.
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WP3 (U Basel) Objectives To further investigate
the yeast 3'-end processing apparatus and the
connections between 3'-end formation and other
processes such as transcription, splicing, RNA
export and RNA turnover.
WP4 (U Edinburgh) Objectives To determine how
and why individual pre-mRNA molecules are
committed to either productive or degradative
pre-mRNA processing pathways.
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WP5 (Institut Pasteur) Objectives To develop a
more efficient synthetic lethal screening
procedure. Complex yeast insertion mutant
libraries will be constructed to speed up the
identification of synthetic mutations. To
validate and use a new mating procedure allowing
these standardised libraries to be used in
distinct synthetic lethal screens (with different
bait mutant genes).
WP6 (U Edinburgh) Objectives To develop
microarray techniques for the analysis of RNA
metabolism.
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WP7 (U Lisbon) Objectives To develop novel
methods allowing the direct spatial and temporal
visualisation of macromolecular interactions
relevant to control RNA transcription, processing
and transport in vivo. 1) To develop a
fluorescence microscopy assay to visualise
intranuclear retention of abnormally processed
mRNAs in S. cerevisiae. This assay will be used
to perform genetic screens to investigate which
cellular factors may be involved. 2)
Fluorescence microscopy techniques will be
implemented to visualise how, when and where
specific proteins and RNAs associate with one
another in the yeast cell nucleus.
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WP8 (Hybrigenics) Objectives 1) To extend and
consolidate the protein interaction database
established during systematic two-hybrid analyses
performed in the TAPIR Program. The expected
result will be an extended protein interaction
map that will lead to the exploration of novel
functional pathways. 2) To improve a newly
described variation of these screens for the
identification of RNA-protein interactions and
adapt it for automation.
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WP9 (Hybrigenics) Objectives To build a
user-friendly database of protein interaction
maps and functional data that will combine
existing information in publicly available
databases with private information generated by
the members of the network. The bioinformatics
tools required for the analysis of the screens
and the interpretation and display of the
databases will be developed.
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Coordination and Project Management Coordinator
RP1
RP responsible partner
Functional Studies
WP5 SL screens RP2 Method
WP1 Splicing RP1
WP2 Capping RP1
WP7 Microscopy RP4 Method
WP6 Microarrays RP1 Method
WP8 2-H screens RP5
WP3 3 ends RP3
WP4 Turnover RP1
WP9 Bioinformatics RP5 Software Databases
Thin arrows flow of materials or other
deliverables between Workpackages Thick arrows
flow of data or data management software