Cramer/Söding/Zweckstetter

Molecular mechanisms of functional phase separation in eukaryotic gene transcription

Transcription of protein-coding genes by RNA polymerase II (Pol II) is highly regulated during cell differentiation and organismal development. In human cells, Pol II transcription is regulated by ~1,600 transcription factors, which bind specific DNA sequences in the vicinity of target genes and contain low-complexity regions that often function in transcription activation. Evidence for the involvement of liquid-liquid phase transitions in transcription initiation, pausing, and elongation has continued to accumulate. We showed, for instance, that the highly conserved C-terminal domain (CTD) of Pol II can phase separate and mediate the clustering of Pol II enzymes in human cells. These results provide a great starting point for analyzing how transcription factors interact with Pol II, using an integrated experimental-theoretical approach. Our efforts will elucidate the phenomenon of phase separation and its functional importance for gene transcription, and will address the enigmatic question of how the different transcription factors can interact with the same general transcription machinery.


Current State of Research

The Cramer lab purifies the transcription factors in a recombinant form and investigates their phase separation propensity as well as in vitro specificity regarding known transcriptional condensates (Cramer, 2019). To this end, they recently co-discovered a distinct, previously unknown transcriptional condensate that is essential for stress-induced transcriptional downregulation and cellular stress survival (Rawat, Boehning et al., 2021). Extending the analysis of the governing intermolecular interactions and in vitro specificity towards transcription factors will help to shed light on the sequence determinants that regulate condensate residency.

The Soeding lab has systematically analyzed data from an unbiased, high-throughput screen for transcriptional activation using a deep neural network. The analysis highlights which sequence features determine the potency of transcriptional activation (Erijman et al, Mol. Cell 2020). They are currently extending this analysis by training a machine learning classifier to predict condensate membership for transcription factors and other phase-separating proteins with intrinsically disordered domains (IDRs). They use representation learning with a pretrained transformer neural network to learn which sequence features predict the tendency to phase separate and the target condensates.  

The Zweckstetter lab analyzes residual structure in phase-separated CTD and transcription factor samples by nuclear magnetic resonance, aiming at the molecular basis of the interactions.

 


About

This is an integrative project involving complementary expertise in gene activation (Cramer lab), bioinformatics (Soeding lab) and NMR spectroscopy (Zweckstetter lab).

The Cramer lab investigates the process of eukaryotic gene transcription and its regulation in health and disease. For this, structural biology approaches are combined with system-wide functional techniques to derive molecular mechanistic models capable of describing the process of gene transcription on a holistic level in living human cells. 

Contact:
Patrick  Cramer
Max-Planck-Institut für biophysikalische Chemie
Am Faßberg 11
37077 Göttingen, Germany
Phone: +49 551 201-2800
Email

 

 


 

The Soeding lab for quantitative and computational biology has expertise in statistical and statistical physics modeling and software development for the analysis of high-throughput next generation sequencing experiments, and large data sets from systems medicine and metagenomics. 

Contact:
Johannes Söding
Max-Planck-Institut für biophysikalische Chemie
Am Faßberg 11
37077 Göttingen, Germany
Phone: +49 551 201-2890
Email

 

 


 

The Zweckstetter lab is working at the interface between biophysics and neuroscience. It uses NMR spectroscopy and complimentary biophysical tools to study conformational transitions and functional dynamics in intrinsically disordered proteins, membrane proteins and protein complexes.

Contact:
Markus Zweckstetter
Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)
Von-Siebold-Str. 3a
D-37075 Göttingen
Max-Planck-Institut für biophysikalische Chemie
Am Faßberg 11
37077 Göttingen, Germany
Phone: +49 551 201-2220
Email

 


Publications

Prashant Rawat, Marc Boehning, Barbara Hummel, Fernando Aprile-Garcia, Anwit S. Pandit, Nathalie Eisenhardt, Ashkan Khavaran, Einari Niskanen, Seychelle M. Vos, Jorma J. Palvimo, Andrea Pichler, Patrick Cramer, Ritwick Sawarkar. Stress-induced nuclear condensation of NELF drives transcriptional downregulation. Molecular Cell, 2021. https://doi.org/10.1016/j.molcel.2021.01.016.
 
Savastano, A.; Flores, D.; Kadavath, H.; Biernat, J.; Mandelkow, E.; Zweckstetter, M.: Disease-associated Tau Phosphorylation Hinders Tubulin Assembly within Tau Condensates. Angew. Chem. Int. Ed. Engl. (2021) 60 (2). DOI: https://doi.org/10.1002/anie.202011157
 
Erijman A, Kozlowski L, Sohrabi-Jahromi S, Noble WS, Söding J, Hahn S. A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning [published online ahead of print, 2020 May 12]. Mol Cell. 2020;S1097-2765(20)30262-8. doi:10.1016/j.molcel.2020.04.020 MolCell-2020-Erijman-Soding-Hahn-HT-screen-for-Transcription-activation-domains-reveals-seq-characteristics
 
Cramer, P. Organization and regulation of gene transcription. Nature 573, 45–54 (2019). https://doi.org/10.1038/s41586-019-1517-4
 
Sohrabi-Jahromi S, Hofmann KB, Boltendahl A, Roth C, Gressel S, Baejen C, Söding J, Cramer P. Transcriptome maps of general eukaryotic RNA degradation factors. Elife. 2019;8:e47040. Published 2019 May 28. doi:10.7554/eLife.47040Elife-2019-SohrabiJahromi-Cramer-Transcriptome-maps-of-general-euk-RNA degradation-factors
 

Söding J, Zwicker D, Sohrabi-Jahromi S, Boehning M, Kirschbaum J. Mechanisms of active regulation of biomolecular condensates. Trends Cell Biol. (2019) DOI: https://doi.org/10.1101/694406. TiCB-2019-Soding-et-al-Mechanisms-of-active-reg-of-biomol-condensates-Incl-SI

Ukmar-Godec, T.; Hutten, S.; Grieshop, M. P.; Rezaei-Ghaleh, N.; Cima-Omori, M. O.; Biernat, J.; Mandelkow, E.; Söding, J.; Dormann, D.; Zweckstetter, M.: Lysine/RNA-interactions drive and regulate biomolecular condensation. Nat. Commun. (2019) 10 (1). DOI: https://doi.org/10.1038/s41467-019-10792-y NatCommun-2019-UkmarGodec-Zweckstetter-Lysine-RNA-interactions-drive-and-reg-biomolecular-interactions