Global investigations of gene regulation

2 PhD project proposals in the IPP summer call 2019 

Scientific Background:

Mass spectrometry is a powerful tool for studying proteins in an unbiased and global manner. The current improvements in identification accuracy, sample throughput, and data analysis allow the streamlined application of proteomics in answering diverse biological questions. Our group applies quantitative approaches, which enables us to directly compare thousands of proteins in complex mixtures. These technologies allow us to study changes in protein expression but are also applied in interactomics to identify specific interacting proteins within a vast number of background binders. The generic applicability of mass spectrometry allows to investigate model species for which antibodies are not readily available and can thus contribute to gain completely novel biological insight.

PhD project 1: Posttranslational gene regulation by RNA-binding proteins 

The nematode C. elegans is a classical model organism in development and ageing research. In this project, we aim to understand developmental posttranscriptional regulation in C.elegans using the combination of classical molecular biology techniques (cloning, protein expression) and proteomics to investigate the regulation of RNA-binding proteins during development. To this end, we will utilize our RNA-protein interactome approach to characterize the RBPome in C.elegans, expecting to uncover several new RNA-binding proteins. We will use quantitative mass spectrometry-based proteomics to identify the RNA-binding protein in an unbiased manner. In the second step, we will proceed to investigate the dynamic recruitment of RNA-binding proteins during the life span of the worm to uncover developmentally regulated proteins that will in a third step be studied for their functional influence in development and ageing. Here, we will closely collaborate with the Ketting group at IMB using transgenic strains, RNAi, gene-editing techniques, and other assays.

We are looking for a motivated student interested in working at the bench, but also keen to master the bioinformatics skills required by –omics approaches. Ability to work independently and experience in standard molecular biology techniques is necessary. Due to the collaborative nature of proteomics, the interest in collaborations beyond the direct research project is expected.

PhD project 2: Comparative systems biology

Working at the interface of transcriptomics and proteomics, we are currently exploring global gene regulation patterns at various levels. We have thus far studied developmental differentiation in trypanosomes, uncovering that mRNA levels in this parasite has only weak correlation to proteome levels due to polycistronic transcription units (Dejung et al., PLOS Pathog 2016). Furthermore, we generated a large-scale matched developmental transcriptome and proteome of Drosophila melanogaster (Casas Vila*, Bluhm*, Sayols* at al., Genome Res 2017) showing that for a subset of the proteome, proteins can be exceptionally stable long after transcription. We applied ordinary differential equations (ODE) as a mathematical framework to correlate transcriptome and proteome during embryogenesis and successfully predicted translational regulators (Becker et al., Nat Commun 2018). In the current project, we will compare transcriptome and proteome among different nematode species with an evolutionary angle. Comparative analysis based on quantitative RNA-Seq and mass spectrometry data will allow for example to globally investigate the effect of changes in the regulatory system across different species and/or to study the effect of dosage compensation on evolving paralogous proteins. Usually omics data at this scale provide groundwork for the investigation of many additional hypotheses and research questions.

This project bridges wet-lab and bioinformatics with a strong part constituting bioinformatics analysis of global transcriptomics, proteomics, interactomics data and evolutionary features. The lab has a strong track-record in these analyses as demonstrated by the recent publications and the applicant will be supported through-out the complete project (wet lab, omics and bioinformatics). Nevertheless some experience in computational biology with proficiency in a scripting languages (R, Python or similar) is highly advisable. Wet lab work will include worm maintenance, transcriptomics and proteomics sample preparation workflows and genetic alteration of C.elegans by transgenes and CRISPR-Cas tagging. 

At the end of the PhD, the applicant should be familiar with recent omics techniques and able to analyze and integrate large-scale data, important in nowadays data-driven science environment. Due to the collaborative nature of proteomics, collaborations beyond the direct research project are feasible and encouraged.


Publications relevant to this project

Becker K, Bluhm A*, Casas-Vila N*, Dinges N*, Dejung M, Sayols S, Roignant JY, Butter F# and Legewie S#. (2018) Quantifying post-transcriptional regulation in the development of D. melanogaster. Nat. Commun, 9: 4970.

Butter F, Scheibe M, Mörl M and Mann M. (2009) Unbiased RNA-protein interaction screen by quantitative proteomics. Proc. Natl. Acad. Sci. U S A, 106: 10626−10631.

Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F and Ketting RF. (2018) GTSF-1 is required for the formation of a functional RNA-dependent RNA Polymerase complex in C. elegans. EMBO J, 37: e99325.

Casas-Vila N*, Bluhm A*, Sayols S*, Dinges N, Dejung M., Altenhein T, Kappei D, Altenhein B, Roignant JY and Butter F. (2017) The developmental proteome of Drosophila melanogaster. Genome Res, 27: 1273-1285.

Dejung M, Subota I, Brucerius F, Dindar G, Freiwald A, Engstler M, Boshart M, Butter F# and Janzen CJ#. (2016) Quantitative proteomics uncovers novel factors involved in developmental differentiation of Trypanosoma brucei. PLOS Pathog, 12: e1005439.

(*indicates joint contribution, #indicates joint correspondence)


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