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meltRBP SIGNED

Tracking interactions between RNA and RNA-binding proteins by thermal profiling of the proteome

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

meltRBP project word cloud

Explore the words cloud of the meltRBP project. It provides you a very rough idea of what is the project "meltRBP" about.

relies protein ligand expression rbps relying unbiased tags benchmarked ad asos throughput mass profiling proteolysis disease hybridisation post antisense rna beta identification global gene peptides rbp regulation prone abundant endogenous biologically aggregation methodology generates amyloid binding meltrbp specificity thermal players individual secondly ire proteins alzheimer summary alternatively characterised mutant stabilisation oligonucleotides benchmarking lysis app transcriptional encompasses innovative insertion spliced proteome hallmark interactions function bound mrnas iron confined manner regulatory techniques tpp spectrometry treatment scope versus unravelling critical technique screen precursor cellular mrna interaction normal proteomic wild first enrichment neurodegenerative reveal limits

Project "meltRBP" data sheet

The following table provides information about the project.

Coordinator	EUROPEAN MOLECULAR BIOLOGY LABORATORY Organization address address: Meyerhofstrasse 1 city: HEIDELBERG postcode: 69117 website: http://www.embl.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	Germany [DE]
Total cost	171˙460 €
EC max contribution	171˙460 € (100%)
Programme	1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
Code Call	H2020-MSCA-IF-2016
Funding Scheme	MSCA-IF-EF-ST
Starting year	2017
Duration (year-month-day)	from 2017-04-01 to 2019-03-31

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	EUROPEAN MOLECULAR BIOLOGY LABORATORY EUROPEAN MOLECULAR BIOLOGY LABORATORY Organization address address: Meyerhofstrasse 1 city: HEIDELBERG postcode: 69117 website: http://www.embl.de contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	DE (HEIDELBERG)	coordinator	171˙460.00

Map

Project objective

RNA-binding proteins (RBPs) are among the key players in post-transcriptional gene regulation. A detailed knowledge of the RBPs bound to a specific RNA target is critical to the unravelling of the regulatory steps of RNA expression under normal and disease conditions. However, the study of these interactions is complex and requires methodologies that go beyond the scope of individual RBPs. So far, the techniques have been confined to post-lysis protein or RNA enrichment, which limits the identification of non-abundant targets and often relies on the insertion of tags. To solve these issues, thermal proteome profiling (TPP)—relying on the stabilisation of the endogenous protein through the binding of its ligand—will be applied in this project. Here, using mass spectrometry, TPP will be applied to investigate complex RBP-RNA interactions on a proteome-wide level in an unbiased manner ('meltRBP'). First, the methodology will be benchmarked with the help of a well-characterised interaction: the iron regulatory proteins and their RNA target, the iron response element (IRE). Secondly, TPP will be applied to a biologically relevant system, namely the mRNA of the Amyloid Beta Precursor Protein (APP). The proteolysis of mutant APP proteins, which are generated from alternatively spliced mRNAs, generates highly aggregation-prone β-amyloid peptides, a hallmark of Alzheimer’s disease (AD). The application of TPP to identify RBPs bound to the wild-type versus mutant APP mRNA will reveal new potential targets for AD treatment. Finally, TPP will be used to determine the specificity of the hybridisation of antisense oligonucleotides (ASOs), currently of great interest to the field of neurodegenerative disease treatment and whose global cellular effects have thus far not been investigated in a high-throughput manner. In summary, this proposal encompasses the benchmarking and application of an innovative proteomic technique, that has the potential to function as a screen for ASOs.

Publications

List of publications.
year	authors and title	journal	last update
2019	Amy Cooke, Thomas Schwarzl, Ina Huppertz, Gertjan Kramer, Panagiotis Mantas, Anne-Marie Alleaume, Wolfgang Huber, Jeroen Krijgsveld, Matthias W. Hentze The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance published pages: 3097-3106.e5, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2019.05.039	Cell Reports 27/11	2019-08-05

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