Proteomics and RNA-protein interactomics

1 PhD project in the IPP summer call 2021

Scientific background

We use mass spectrometry based proteomics to study diverse biological questions making use of powerful quantitative techniques. Our group covers all aspects from molecular biology and biochemical approaches, different mass spectrometry sample preparation workflows and bioinformatics analysis to study changes of the proteome and to identify and characterize new biological relevant interactions. One of our research areas is to identify and characterize RNA-binding proteins by RNA-protein interactomics screens. Pioneering the use of SILAC for RNA-protein interactomics (Butter et al., 2009), we have just recently performed a large scale screen for mRNA-binding proteins in yeast identifying new translational regulators (Casas-Vila et al., 2020). Our technique can also be used to identify RNA-binding proteins for long non-coding RNAs, like telomeric repeat containing RNA (TERRA) involved in cellular regulation (Scheibe et al., 2013) or MALAT1 (Scherer et al., 2020), which is linked to cancer prognosis.

PhD project: Studying RNA-protein interactions by quantitative proteomics

We are looking for a PhD student interested to develop and apply quantitative proteomics and interactomics techniques. In detail, the PhD candidate will perform RNA pulldowns in combination with either reductive demethylation labeling or label-free quantitative proteomics workflows. The project will bridge cell culture, molecular biology techniques, mass spectrometry and some data analysis. The ideal candidate has a background in molecular biology or related fields. Good English communication skills are required to interact within our multi-disciplinary team. Experience in computational analysis of omics data is a plus.

Furthermore, we offer the opportunity to contribute to the scientific community by assisting collaboration partners within the IMB and around the world in data analysis of joint projects for which our group generates quantitative proteomics data.

Publications relevant to this project

Casas-Vila N, Sayols S, Pérez-Martínez L, Scheibe M and Butter F (2020) The RNA fold interactome of evolutionary conserved RNA structures in S. cerevisiaeNat Commun, 11:2789 Link

Scherer M, Levin M, Butter F and Scheibe M (2020) Quantitative proteomics to identify nuclear RNA-binding proteins of Malat1Int J Mol Sci, 21:E1166 Link

Scheibe M, Arnoult N, Kappei D, Buchholz F, Decottignies A, Butter F# and Mann M# (2013) Quantitative interaction screen of telomeric repeatcontaining RNA reveals novel TERRA regulatorsGenome Res, 23:2149–2157 (#indicates joint correspondence) Link

Scheibe M, Butter F, Hafner M, Tuschl T and Mann M (2012) Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactionsNucleic Acids Res, 40:9897–9902 Link

Butter F, Scheibe M, Mörl M and Mann M (2009) Unbiased RNA-protein interaction screen by quantitative proteomicsProc Natl Acad Sci USA, 106:10626–10631 Link

 

Contact

Dr Falk Butter

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