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SPP1935 -- Deciphering the mRNP code :
RNA-bound Determinants of Post-transcriptional Gene Regulation

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laboratoriesProf. Dr. Cramer

Patrick Cramer Center
Max Planck Institute for Biophysical Chemistry
Department of Molecular Biology

Adress
Am Fassberg 11 37077 Göttingen Germany

Phone
00495512012800


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High-resolution mapping and quantitative modeling of cooperative RNA binding in mRNPs

Colaboration with Dr. Johannes Söding



Lab InfoPROJECT INFORMATION :

We have previously developed and optimized methods to map mRNP components and other RNA-binding factors onto the transcriptome in vivo (Schulz et al., Cell 2013; Baejen et al., Mol. Cell 2014). These methods enabled the first global mapping of proteins recognizing pre-mRNA and shortlived RNAs, and demonstrated that RNA recognition cannot be described by standard methods that are used to describe DNA recognition such as position weight matrices (PWMs). Here we propose an integrated experimental-theoretical approach to contribute to two major goals of the new Schwerpunktprogramm (SPP). First, we will systematically identify cellular binding sites for mRNA-binding proteins with the use of PAR-CLIP (photoactivateble ribonucleoside-enhanced crosslinking and immunoprecipitation), to study formation and function of mRNPs in the budding yeast S. cerevisiae. Second, we will develop new techniques enabling a quantitative description of RNA recognition by cooperative RNA binding of multiple factors that will allow us to predict RNA sequence-binding preferences. The aim of this work is to understand mRNP formation in vivo and to understand the biogenesis and fate of different RNA classes based on their association with cellular factors. The derived technology and bioinformatic tools will be provided to SPP teams.


Focus of the group :
- Structural biology of transcription complexes
- Functional genomics and computational biology of genome regulation



Lab techsKEY TECHNOLOGIES :

- Protein biochemistry
- X-ray crystallography
- Cryo-electron microscopy
- Functional genomics
- Computational biology



PublicationsPUBLICATIONS :

B. Schwalb, M. Michel, B. Zacher, K. Frühauf, C. Demel, A. Tresch, J. Gagneur, and P. Cramer.
TT-Seq maps the human transient transcriptome.
Science 352, 1225-1228 (2016).

C. Plaschka, M. Hantsche, C. Dienemann, C. Burzinski, J. Plitzko, and P. Cramer.
Transcription initiation complex structures elucidate DNA opening.
Nature 533, 353-358 (2016).

C. Bernecky, F. Herzog, W. Baumeister, J. Plitzko, P. Cramer.
Structure of transcribing mammalian RNA polymerase II.
Nature 529, 551-554 (2016).

P. Cramer.
A tale of chromatin and transcription in 100 structures.
Cell 159, 985–994 (2014).

D. Schulz, B. Schwalb, A. Kiesel, C. Baejen, P. Torkler, J. Gagneur, J. Soeding, P. Cramer.
Transcriptome surveillance by selective termination of noncoding RNA synthesis.
Cell 2013, 155, 1075-1087.