Co-condensation of proteins with single- and double-stranded DNA

Renger, Roman; Morín, José A.; Lemaitre, Regis; Ruer, Martine; Jülicher, Frank; Hermann, Andreas; Grill, Stephan W.

doi:10.1101/2021.03.17.435834

Cited by 10 publications

(12 citation statements)

References 65 publications

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“…The causal relevance of Pol II phosphorylation is supported by chemical perturbation of Pol II recruitment and pause release, which induces changes in cluster morphology and cluster number that are in line with results from our lattice simulations. In combination with previous work on Pol II liquid‐phase behavior (Cho et al , 2018; Sabari et al , 2018) and studies showing surface condensation of transcription factors on DNA in vitro (preprint: Morin et al , 2020; Quail et al , 2021; preprint: Renger et al , 2021), our findings in zebrafish, an embryonic model system, suggest that a similar surface condensation on regulatory chromatin might occur in vivo as well.…”

Section: Introductionsupporting

confidence: 86%

“…Formation of macromolecular clusters at genomic target regions has recently been described using a model of liquid‐phase condensation on microscopic surfaces provided by polymers (Cho et al , 2018; Sabari et al , 2018; Shin et al , 2018; Li et al , 2020; preprint: Morin et al , 2020; Quail et al , 2021; preprint: Renger et al , 2021). To test whether such a model can reproduce the different cluster morphologies seen in our experiments, we implemented corresponding lattice kinetic Monte Carlo (LKMC) simulations (Larson et al , 1985; Miermans & Broedersz, 2020) (for details, see Materials and Methods and Appendix Fig S9A–F).…”

Section: Resultsmentioning

confidence: 99%

“…Our findings indicate that formation of these clusters can be understood as the condensation of a liquid on surfaces provided by regulatory chromatin regions. Based on recent in vitro experiments, surface condensation can serve as a model for the formation of a liquid film on microscopic condensation surfaces provided by DNA (preprint: Morin et al , 2020; Quail et al , 2021; preprint: Renger et al , 2021). Surface condensation has been extensively characterized outside of biology as a process in which affinity for a surface allows formation of growth‐limited condensates from a sub‐saturated liquid phase (Cahn, 1977; Ebner & Saam, 1977; Pandit et al , 1982).…”

Section: Discussionmentioning

confidence: 99%

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RNA polymerase II clusters form in line with surface condensation on regulatory chromatin

Pancholi

Klingberg

Zhang

et al. 2021

Molecular Systems Biology

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It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state, and subsequent pause release toward transcription. Pol II recruitment and pause release occur in association with macromolecular clusters, which were proposed to be formed by a liquid–liquid phase separation mechanism. How such a phase separation mechanism relates to the interaction of Pol II with DNA during recruitment and transcription, however, remains poorly understood. Here, we use live and super‐resolution microscopy in zebrafish embryos to reveal Pol II clusters with a large variety of shapes, which can be explained by a theoretical model in which regulatory chromatin regions provide surfaces for liquid‐phase condensation at concentrations that are too low for canonical liquid–liquid phase separation. Model simulations and chemical perturbation experiments indicate that recruited Pol II contributes to the formation of these surface‐associated condensates, whereas elongating Pol II is excluded from these condensates and thereby drives their unfolding.

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Section: Introductionsupporting

confidence: 86%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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RNA polymerase II clusters form in line with surface condensation on regulatory chromatin

Pancholi

Klingberg

Zhang

et al. 2021

Molecular Systems Biology

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“…4A,B). This was also reported for other DNA binding proteins, like HP1α (Keenen et al, 2020), FUS (Renger et al, 2021) or the transcription factor Klf4 (Morin et al, 2020) as well as for ParB (T. G. W. Graham et al, 2014) and can be explained by a preference of these proteins to bridge where tension is lowest and DNA is highly flexible (Baumann et al, 2000;H. Kim & Loparo, 2016).…”

Section: Bridging Vs Bendingsupporting

confidence: 63%

The loader complex Scc2/4 forms co-condensates with DNA as loading sites for cohesin

Zernia

Kamp

Stigler

2021

Preprint

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The genome is organized by diverse packaging mechanisms like nucleosome formation, loop extrusion and phase separation, which all compact DNA in a dynamic manner. Phase separation additionally drives protein recruitment to condensed DNA sites and thus regulates gene transcription. The cohesin complex is a key player in chromosomal organization that extrudes loops to connect distant regions of the genome and ensures sister chromatid cohesion after S-phase. For stable loading onto the DNA and for activation, cohesin requires the loading complex Scc2/4. As the precise loading mechanism remains unclear, we investigated whether phase separation might be the initializer of the cohesin recruitment process. We found that, in absence of cohesin, budding yeast Scc2/4 forms phase separated co-condensates with DNA, which comprise liquid-like properties shown by droplet shape, fusion ability and reversibility. We reveal in DNA curtain and optical tweezer experiments that these condensates are built by DNA bridging and bending through Scc2/4. Importantly, Scc2/4-mediated condensates recruit cohesin efficiently and increase the stability of the cohesin complex. We conclude that phase separation properties of Scc2/4 enhance cohesin loading by molecular crowding, which might then provide a starting point for the recruitment of additional factors and proteins.

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“…Our results discussed above suggest that the PLD of FUS enables phase separation of the oncogenic FUS‐DDIT3 transcription factor. Transcription factors can interact with the surface of DNA and such interactions can contribute to their phase separation at specific genomic loci 19,57,58 . To test if FUS‐DDIT3 can form condensates on DNA, we tethered a single double‐stranded (ds) λ‐phage genomic DNA between two optically‐trapped polystyrene beads using laminar‐flow in a microfluidic glass chamber (see Materials & Methods for further details and Figure 4a, Figure S8).…”

Section: Resultsmentioning

confidence: 99%

FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion‐like domains

et al. 2021

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Fusion transcription factors generated by genomic translocations are common drivers of several types of cancers including sarcomas and leukemias. Oncofusions of the FET (FUS, EWSR1, and TAF15) family proteins result from the fusion of the prion‐like domain (PLD) of FET proteins to the DNA‐binding domain (DBD) of certain transcription regulators and are implicated in aberrant transcriptional programs through interactions with chromatin remodelers. Here, we show that FUS‐DDIT3, a FET oncofusion protein, undergoes PLD‐mediated phase separation into liquid‐like condensates. Nuclear FUS‐DDIT3 condensates can recruit essential components of the global transcriptional machinery such as the chromatin remodeler SWI/SNF. The recruitment of mammalian SWI/SNF (mSWI/SNF) is driven by heterotypic PLD‐PLD interactions between FUS‐DDIT3 and core subunits of SWI/SNF, such as the catalytic component BRG1. Further experiments with single‐molecule correlative force‐fluorescence microscopy support a model wherein the fusion protein forms condensates on DNA surface and enrich BRG1 to activate transcription by ectopic chromatin remodeling. Similar PLD‐driven co‐condensation of mSWI/SNF with transcription factors can be employed by other oncogenic fusion proteins with a generic PLD‐DBD domain architecture for global transcriptional reprogramming.

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Co-condensation of proteins with single- and double-stranded DNA

Cited by 10 publications

References 65 publications

RNA polymerase II clusters form in line with surface condensation on regulatory chromatin

RNA polymerase II clusters form in line with surface condensation on regulatory chromatin

The loader complex Scc2/4 forms co-condensates with DNA as loading sites for cohesin

FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion‐like domains

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