Publications – Molecular Mechanisms of Functional Phase Separation

Lara Gruijs da Silva, Francesca Simonetti, Saskia Hutten, Henrick Riemenschneider, Erin L. Sternburg, Lisa M. Pietrek, Jakob Gebel, Volker Dötsch, Dieter Edbauer, Gerhard Hummer, Lukas S. Stelzl, Dorothee Dormann. Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. bioRxiv 2021.04.30.442163; doi: https://doi.org/10.1101/2021.04.30.442163

Hutten S, Dormann D. A Quantitative Assay to Measure Stress Granule Association of Proteins and Peptidesin Semi-permeabilized Human Cells. Bio Protoc. 2020 Dec 20;10(24):e3846. doi: 10.21769/BioProtoc.3846. PMID: 33659496; PMCID: PMC7842520.

Baade I, Hutten S, Sternburg EL, Pörschke M, Hofweber M, Dormann D, Kehlenbach RH. The RNA-binding protein FUS is chaperoned and imported into the nucleus by a network of import receptors. J Biol Chem. 2021 Apr 12:100659. doi: 10.1016/j.jbc.2021.100659. Epub ahead of print. PMID: 33857479.

Hutten S, Usluer S, Bourgeois B, Simonetti F, Odeh HM, Fare CM, Czuppa M, Hruska-Plochan M, Hofweber M, Polymenidou M, Shorter J, Edbauer D, Madl T, Dormann D. Nuclear Import Receptors Directly Bind to Arginine-Rich Dipeptide Repeat Proteins and Suppress Their Pathological Interactions. Cell Rep. 2020 Dec 22;33(12):108538. doi: 10.1016/j.celrep.2020.108538. PMID: 33357437

Noa A, Kuan HS, Aschmann V, Zaburdaev V, Hilbert L (2021) The hierarchical packing of euchromatin domains can be described as multiplicative cascades. PLOS Computational Biology 17(5): e1008974. https://doi.org/10.1371/journal.pcbi.1008974

B.W. Hoogenboom, L.E. Hough, E.A. Lemke et al., Physics of the nuclear pore complex: Theory, modeling and experiment, Physics Reports (2021), doi:
https://doi.org/10.1016/j.physrep.2021.03.003.

Lennart Hilbert, Yuko Sato, Hiroshi Kimura, Frank Jülicher, Alf Honigmann, Vasily Zaburdaev, Nadine L. Vastenhouw. Transcription organizes euchromatin similar to an active microemulsion. bioRxiv. 234112; doi:https://doi.org/10.1101/234112

Agnieszka Pancholi, Tim Klingberg, Weichun Zhang, Roshan Prizak, Irina Mamontova, Amra Noa, Andrei Yu Kobitski, Gerd Ulrich Nienhaus, Vasily Zaburdaev, Lennart Hilbert. RNA polymerase II clusters form in line with liquid phase wetting of chromatin. bioRxiv 2021.02.03.429626; doi:https://doi.org/10.1101/2021.02.03.429626

Klosin, A., Oltsch, F., Harmon, T., Honigmann, A., Jülicher, F., Hyman, A. A., & Zechner, C. (2020). Phase separation provides a mechanism to reduce noise in cells. Science, 367 (6476), 464-468. DOI: 10.1126/science.aav6691

Donau, C.; Späth, F.; Sosson, M.; Kriebisch, B. A. K.; Schnitter, F.; Tena-Solsona, M.; Kang, H.-S.; Salibi, E.; Sattler, M.; Mutschler, H.; Boekhoven, J. Active Coacervate Droplets as a Model for Membraneless Organelles and Protocells. Nat. Commun.2020, 11 (1), 5167. https://doi.org/10.1038/s41467-020-18815-9.

Amra Noa, Hui-Shun Kuan, Vera Aschmann, Vasily Zaburdaev, Lennart Hilbert. The domain-within-domain packing of euchromatin can be described as multiplicative cascades. bioRxiv 2020.10.20.346882; doi:https://doi.org/10.1101/2020.10.20.346882

Peter E. A. Ash, Shuwen Lei, Jenifer Shattuck, Samantha Boudeau, Yari Carlomagno, Maria Medalla, Bryce L. Mashimo, Guillermo Socorro, Louloua F. A. Al-Mohanna, Lulu Jiang, Muhammet M. Öztürk, Mark Knobel, Pavel Ivanov, Leonard Petrucelli, Susanne Wegmann, Nicholas M. Kanaan, and Benjamin Wolozin. TIA1 potentiates tau phase separation and promotes generation of toxic oligomeric tau. PNAS March 2, 2021 118 (9) e2014188118; https://doi.org/10.1073/pnas.2014188118

Trojanowski J, Frank L, Rademacher A, Grigaitis P, Rippe K (2021) Transcription activation is enhanced by multivalent interactions independent of liquid-liquid phase separation. bioRxiv. doi:https://doi.org/10.1101/2021.01.27.428421

Lukacs A, Thomae AW, Krueger P, Schauer T, Venkatasubramani AV, Kochanova NY, Aftab W, Choudhury R, Forne I, Imhof A (2021) The Integrity of the Speciation Core Complex is necessary for centromeric binding and reproductive isolation in Drosophila. bioRxiv. doi:https://doi.org/10.1101/2021.02.05.429932

Frank L, Weinmann R, Erdel F, Trojanowski J, Rippe K (2021) Transcriptional activation of heterochromatin by recruitment of dCas9 activators. In Enhancers and Promoters: Methods and Protocols, Borggrefe T, Giaimo BD (eds), in press. New York: Springer Nature

Kochanova NY, Schauer T, Mathias GP, Lukacs A, Schmidt A, Flatley A, Schepers A, Thomae AW, Imhof A (2020) A multi-layered structure of the interphase chromocenter revealed by proximity-based biotinylation. Nucleic Acids Res 48: 4161-4178. DOI: 10.1093/nar/gkaa145

Frank L, Rippe K (2020) Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation. J Mol Biol 432: 4270-4286. DOI: 10.1016/j.jmb.2020.04.015

Erdel F, Rademacher A, Vlijm R, Tunnermann J, Frank L, Weinmann R, Schweigert E, Yserentant K, Hummert J, Bauer C, Schumacher S, Al Alwash A, Normand C, Herten DP, Engelhardt J, Rippe K (2020) Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation. Mol Cell 78: 236-249 e237. DOI: 10.1016/j.molcel.2020.02.005

Nike Heinß, Mikhail Sushkin, Miao Yu, Edward A. Lemke; Multifunctionality of F-rich nucleoporins. Biochem Soc Trans 18 December 2020; 48 (6): 2603–2614. doi: https://doi.org/10.1042/BST20200357

Ariel Erijman, Lukasz Kozlowski, Salma Sohrabi-Jahromi, James Fishburn, Linda Warfield, Jacob Schreiber, William S. Noble, Johannes Söding, Steven Hahn. A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning. Mol Cell. 2020;S1097-2765(20)30262-8. doi:10.1016/j.molcel.2020.04.020

Majewski, J., Jones, E.M., Vander Zanden, C.M., Biernat, J., Mandelkow, E., Chi, E.Y.: Lipid membrane templated misfolding and self-assembly of intrinsically disordered tau protein. Sci Rep 10, 13324 (2020). https://doi.org/10.1038/s41598-020-70208-6

Giorgia Celetti, Giulia Paci, Joana Caria, Virginia VanDelinder, George Bachand, Edward A. Lemke; The liquid state of FG-nucleoporins mimics permeability barrier properties of nuclear pore complexes. J Cell Biol 6 January 2020; 219 (1): e201907157. doi: https://doi.org/10.1083/jcb.201907157

Ukmar-Godec, T.; Wegmann, S.; Zweckstetter, M.: Biomolecular condensation of the microtubule-associated protein tau. Semin Cell Dev Biol. (2019) Jul 4. pii: S1084-9521(18)30199-X. DOI: 10.1016/j.semcdb.2019.06.007.

Hofweber M, Dormann D. Friend or foe-Post-translational modifications as regulators of phase separation and RNP granule dynamics. J Biol Chem. 2019 May 3;294(18):7137-7150. doi: 10.1074/jbc.TM118.001189. Epub 2018 Dec 26.

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.

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

Ribeiro, S. S.; Samanta, N.; Ebbinghaus, S.; Marcos, J. C.: The synergic effect of water and biomolecules in intracellular phase separation. Nat. Rev. Chem. (2019) 3, pages 552–561. DOI: https://doi.org/10.1038/s41570-019-0120-4

Ribeiro, S.; Ebbinghaus, S.; Marcos, J. C.: Protein folding and quinary interactions: Creating cellular organization through functional disorder. FEBS Lett. (2018) 592.18, 3040-3053 2018. DOI: https://doi.org/10.1002/1873-3468.13211

Tants, J. N.; Fesser, S.; Kern, T.; Stehle, R.; Geerlof, A.; Wunderlich, C.; Juen, M.; Hartlmüller, C.; Böttcher, R.; Kunzelmann, S.; Lange, O.; Kreutz, C.; Förstemann, K.; Sattler, M.: Molecular basis for asymmetry sensing of siRNAs by the Drosophila Loqs-PD/Dcr-2 complex in RNA interference. Nucleic Acids Res. (2017) Dec 1;45(21):12536-12550. DOI: https://doi.org/10.1093/nar/gkx886