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RNA polymerase II clustering through carboxy-terminal domain phase separation

Nature Structural & Molecular Biology volume 25, pages 833–840 (2018)Cite this article

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Abstract

The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is an intrinsically disordered low-complexity region that is critical for pre-mRNA transcription and processing. The CTD consists of hepta-amino acid repeats varying in number from 52 in humans to 26 in yeast. Here we report that human and yeast CTDs undergo cooperative liquid phase separation, with the shorter yeast CTD forming less-stable droplets. In human cells, truncation of the CTD to the length of the yeast CTD decreases Pol II clustering and chromatin association, whereas CTD extension has the opposite effect. CTD droplets can incorporate intact Pol II and are dissolved by CTD phosphorylation with the transcription initiation factor IIH kinase CDK7. Together with published data, our results suggest that Pol II forms clusters or hubs at active genes through interactions between CTDs and with activators and that CTD phosphorylation liberates Pol II enzymes from hubs for promoter escape and transcription elongation.

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Fig. 1: Phase separation of Pol II CTD into liquid-like droplets.
Fig. 2: Physicochemical properties of hCTD phase separation.
Fig. 3: Human Dendra2-RPB1 cell lines for imaging CTD-dependent Pol II clustering.
Fig. 4: CTD-dependent Pol II clustering in human cells.
Fig. 5: CTD-dependent Pol II dynamics in human cells.
Fig. 6: Liberation through initiation-coupled CTD phosphorylation.
Fig. 7: Model for the role of CTD-driven phase separation in activated transcription.

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Acknowledgements

We thank S.M. Vos for the MBP-hCTD expression plasmid and advice on purification, S. Schilbach for the yeast TFIIH kinase module, and A. Boltendahl and C. Burzinski for help with cloning and purification. We are grateful to S. Ambadipudi for help with initial microscopy measurements and discussions about LLPS. Microscopic analysis of phase separation was conducted at the Facility for Innovative Light Microscopy at the MPI for Biophysical Chemistry. We thank L. Lavis for generously providing JF dyes. We thank A. Robles, C. Inouye, S. Zheng, M. Haggart, and J. Lim for technical and administrative assistance. In vivo FRAP experiments were conducted at the CRL Molecular Imaging Center, supported by the Gordon and Betty Moore Foundation. We thank all current members of the Cramer, Zweckstetter, and Tjian–Darzacq labs for discussions and R. Tjian for critical reading of the manuscript. M.Z. was supported by the Deutsche Forschungsgemeinschaft (SFB860; project B02), by the Cluster of Excellence and DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, and the advanced grant ‘787679-LLPS-NMR’ from the European Research Council. P.C. was supported by the Deutsche Forschungsgemeinschaft (SFB860; project A13), the advanced grant ‘TRANSREGULON’ from the European Research Council, and the Volkswagen Foundation. X.D. was supported by NIH grant UO1-EB021236 and the California Institute of Regenerative Medicine grant LA1-08013.

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  1. These authors contributed equally and are listed alphabetically: Marc Boehning, Claire Dugast-Darzacq, Marija Rankovic.

Authors and Affiliations

  1. Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany

    Marc Boehning, Goran Kokic & Patrick Cramer

  2. Department of Molecular and Cell Biology, University of California, Berkeley, California, USA

    Claire Dugast-Darzacq, Anders S. Hansen, Herve Marie-Nelly, David T. McSwiggen, Gina M. Dailey & Xavier Darzacq

  3. CIRM Center of Excellence, University of California, Berkeley, California, USA

    Claire Dugast-Darzacq, Anders S. Hansen, Herve Marie-Nelly, David T. McSwiggen, Gina M. Dailey & Xavier Darzacq

  4. Max Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology, Göttingen, Germany

    Marija Rankovic & Markus Zweckstetter

  5. German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany

    Taekyung Yu & Markus Zweckstetter

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Contributions

M.B. designed experiments, generated constructs, and prepared proteins unless otherwise noted. C.D.-D. designed experiments, established and characterized the RPB1 cell lines, and performed and analyzed the in vivo FRAP and SPT experiments. M.R. designed experiments, performed all phase separation assays, DIC and fluorescence microscopy, in vitro FRAP measurements and data analysis. A.S.H. designed, performed, and analyzed SPT experiments and helped with the in vivo FRAP analysis. H.M.-N. designed, performed, and analyzed 3D-PALM experiments. D.T.McS. performed cell-viability experiments and helped in performing 3D-PALM experiments. G.M.D. designed and cloned the different RPB1 expression vectors. G.K. prepared human TFIIH kinase complex. T.Y. performed CD and NMR experiments. C.D.-D., X.D., P.C., and M.Z. designed and supervised research. M.B., M.R., C.D.-D., P.C., X.D., and M.Z. prepared the manuscript with input from all authors.

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Correspondence to Patrick Cramer, Xavier Darzacq or Markus Zweckstetter.

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Integrated supplementary information

Supplementary Figure 1 Low-complexity nature of CTD sequences.

(a) Comparison of the CTD sequences from human (blue) and yeast (red). Consisting of 52 heptad repeats, the human CTD is twice the length of the yeast CTD. It can be divided in a N-terminal part, which is almost exclusively composed of consensus repeats (Y1S2P3T4S5P6S7) and is highly similar to the yeast CTD (highlighted are identical regions between the two species), and a C-terminal part that is more degenerate (Hsin, J.P. & Manley, J.L., Genes Dev. 26, 2119-37, 2012). Deviations from the consensus sequence are indicated in black. (b) Absolute (black bars) and relative (green line) abundance of tyrosine residues within the CTD sequences of various distantly related species (from left to right): Trichomonas vaginalis (Nucleotide ID: TVU20501, Protein ID: AAB50025), Trypanosoma brucei (Nucleotide ID: X13492, Protein ID: P17545), Leishmania donovani (Nucleotide ID: AF126254, Protein ID: AAF36438), Monoblepharis macrandra (Nucleotide ID: AF315822, Protein ID: AAK00312), Acanthamoeba castellanii (Nucleotide ID: ACU90211, Protein ID: AAC18417), Plasmodium falciparum 3D7 (Nucleotide ID: XM_001351216, Protein ID: XP_001351252), Vairimorpha necatrix (Nucleotide ID: AF060234, Protein ID: AAD12604), Glaucosphaera vacuolata (Nucleotide ID: AF315820, Protein ID: AAK00310), Dictyostelium discoideum AX4 (Nucleotide ID: XM_636643, Protein ID: XP_641735), Nosema ceranae (Nucleotide ID: ACOL01000247, Protein ID: EEQ81731), Breviata anathema (Nucleotide ID: AF083338, Protein ID: AAC62246), Saccharomyces cerevisiae (Nucleotide ID: X96876, Protein ID: CAA65619), Schizosaccharomyces pombe (Nucleotide ID: NM_001021568, Protein ID: NP_595673), Monosiga brevicollis (Nucleotide ID: AF315821, Protein ID: AAK00311), Arabidopsis thaliana (Nucleotide ID: X52954, Protein ID: CAA37130), Caenorhabditis elegans (Nucleotide ID: CELPOLII, Protein ID: AAA28126.1), Drosophila melanogaster (Nucleotide ID: NM_078569, Protein ID: NP_511124), Culex quinquefasciatus (Nucleotide ID: XM_001866696, Protein ID: XP_001866731), Branchiostoma floridae (Nucleotide ID: XM_002593172, Protein ID: XP_002593218), Strongylocentrotus purpuratus (Nucleotide ID: XM_001175967, Protein ID: XP_001175967), Ixodes scapularis (Nucleotide ID: XM_002407458, Protein ID: XP_002407502), Tribolium castaneum (Nucleotide ID: XM_968377, Protein ID: XP_973470), Danio rerio (Nucleotide ID: XM_677590, Protein ID: XP_682682), Mus musculus (Nucleotide ID: MMU37500, Protein ID: AAB58418), Homo sapiens (Nucleotide ID: NM_000937.3, Protein ID: NP_000928) and Hydra magnipapillata (Nucleotide ID: XM_002164318, Protein ID: XP_002164354). Although the number of repeats greatly differs among species, the tyrosine content is well conserved. Bars corresponding to S. cerevisiae und H. sapiens are highlighted in red and blue, respectively. The number/definition of repeats was taken from Simonti, C.N. et al., BMC Evol Biol. 15, 35, 2015. (c) Circular dichroism difference spectra of MBP-hCTD and MBP (upper panel), and MBP-yCTD and MBP (lower panel) show a minimum at ~194 nm that is characteristic for a random coil, confirming that the CTD is intrinsically disordered.

Supplementary Figure 2 Physicochemical properties of yCTD phase separation.

(a) GST alone (10 µM) did not undergo phase separation in 16% dextran. (b) Concentration-dependent phase separation of GST-yCTD in the presence of 150 mg/ml Ficoll. (c- upper panels) Recruitment of Alexa 488-labeled MBP-hCTD (green; right) to preformed droplets of GST-yCTD that were visualized by DIC microscopy (left) and by recruitment of a TMR-labeled YSPTSPS peptide (red; middle). (c –lower panels) Recruitment of Alexa 488-labeled GST-yCTD (green; right) to preformed droplets of MBP-hCTD. Preformed hCTD droplets were visualized by DIC microscopy (left) and by recruitment of the TMR-labeled YSPTSPS peptide (red; middle). (d, e) LLPS of MBP-yCTD in 16% dextran is not sensitive to ionic strength changes (d) or incubation of the sample for one hour at the indicated temperatures (e). All experiments were performed two times with similar outcome and representative images are shown. Scale bars correspond to 10 µm in all panels.

Supplementary Figure 3 Influence of aliphatic alcohols and solubility tags on CTD phase separation.

(a, b) Influence of aliphatic alcohols on CTD LLPS. 1,6-hexanediol (1,6-hex) and 2,5-hexanediol (2,5-hex) counteract LLPS of hCTD (a) or yCTD (b) in a concentration-dependent manner. Images from ≥ 5 representative images taken for each condition are shown. (c) The solubilizing effect of a N-terminal MBP-tag inhibits droplet formation of yCTD at low protein concentrations. Concentration-dependent LLPS of MBP-hCTD, MBP-yCTD and GST-yCTD in 16% dextran. MBP-hCTD undergoes liquid phase separation already at a concentration of 5 µM (top), while a ≥ 4-fold higher concentration of MBP-yCTD is required for droplet formation (middle). Replacement of MBP by a GST-tag decreases the critical concentration for yCTD phase separation to approximately 5 µM (bottom). Shown images are representative of two independent experiments. Scale bars correspond to 10 µm in all panels.

Supplementary Figure 4 Characterization of Halo-RPB1 cell lines.

(a) Confocal image of RPB1-25R (left), RPB1-52R (middle) and RPB1-70R (right) cell lines showing the nuclear localization of Halo-RPB1. Before fixation the cells were labeled for 30 min with HALO-TMR ligand (500 nM final concentration). Scale bars correspond to 5 µm. (b) Western blot analysis of the Halo-RPB1-25R, -52R and -70R expression level for the different cell lines. (c) FACS analysis to evaluate Halo-RPB1 expression levels of the different cell lines. (d) Growth curve analysis of the Halo-tagged Pol II cell lines. The growth rate of the three cell lines is overall similar albeit the RPB1-25R (red) and RPB1-70R (grey) cell lines grew slightly slower than the U2OS WT (purple) and RPB1-52R (blue) cell lines. Once treated with alpha-amanitin, the WT cells (black) die while the growth rate of the other lines is unaffected. Growth curves show mean across n = 6 independent samples and error bars show the standard deviation. Growth curves of a representative experiment performed independently five times are shown. (e) Doubling time analysis of the Halo-tagged Pol II cell lines. The three cell lines have relatively similar doubling times. The mean across n = 3 independent replicates is shown and error bars show the standard deviation.

Supplementary Figure 5 spaSPT and FRAP.

(a) Overview of the 2-state model used in fitting the displacement data from spaSPT (Spot-On) (Hansen, A.S. et al., Elife 7, 2018). Diffusion is modeled as Brownian and arising from a bound/immobile population and a freely diffusing population assuming no state transitions at the short time-scale of observation. A correction is applied to the free population to correct for “defocalization”: since the 2D imaging only captures a ~700 nm axial slice of the nucleus, the free population rapidly moves out of focus at later time points. (b) Cumulative distribution functions (CDF) for displacements. The CDF of displacements for the representative time-lag Δτ = 22.5 ms is shown for Halo-RPB1-25R, Halo-RPB1-52R and Halo-RPB1-70R. The data shown is merged from three independent replicates (n = 29, 30, 26 cells in total for Halo-RPB1-25R, -52R, -70R, respectively). (c) Model fit to displacement histograms. Raw displacements from spaSPT data for six different time-lags are shown for Halo-RPB1-25R, Halo-RPB1-52R and Halo-RPB1-70R. Model-fitting from a two-state (bound vs. free) model is overlaid, from which the diffusion constants and subpopulation sizes were calculated. The data shown is merged from three independent replicates (n = 29, 30, 26 cells in total for Halo-RPB1-25R, -52R, -70R, respectively). (d-f) FRAP data of Halo-RPB1-25R (d), Halo-RPB1-52R (e) and Halo-RPB1-70R (f) were fitted to a reaction dominant two-state model (Sprague, B.L. et al., Biophys J. 86, 3473-95, 2004; Hansen, A.S. et al., Elife 6, 2017). We performed 50 iterations using 50% of the data in each to estimate the error (standard deviation of the subsampling) on the bound fraction.

Supplementary Figure 6 Effect of flavopiridol treatment on RNA Pol II dynamics.

(a) Cumulative distribution functions (CDF) for displacements. The CDF of displacements for the representative time-lags Δτ = 22.5 ms and Δτ = 30.0 ms are shown for Halo-RPB1-25R, Halo-RPB1-52R and Halo-RPB1-70R after treatment with flavopiridol. The data shown is merged from three independent replicates. (b) Model fit to displacement histograms. Raw displacements from spaSPT data for six different time-lags are shown for Halo-RPB1-25R, Halo-RPB1-52R and Halo-RPB1-70R. Model-fitting from a two-state (bound vs. free) model is overlaid, from which the diffusion constants and subpopulation sizes were calculated. The data shown is merged from three independent replicates (n = 13, 15, 28 cells in total for Halo-RPB1-25R, -52R, -70R, respectively). (c) Bound fractions of Halo-RPB1-25R, -52R and -70R after flavopiridol treatment. The bound fraction was inferred from two-state model-fitting to the spaSPT displacement data using Spot-On (Hansen, A.S. et al., Elife 7, 2018). Each of three independent replicates was fitted separately and bar graphs show the mean and standard error. (d) Diffusion coefficients of the free population of Halo-RPB1-25R, -52R and -70R. Free diffusion coefficients were inferred from two-state model-fitting to the spaSPT displacement data using Spot-On (Hansen, A.S. et al., Elife 7, 2018). Each of three independent replicates was fitted separately and bar graphs show the mean and standard error. (e) FRAP data of Halo-RPB1-25R (red), Halo-RPB1-52R (blue) and Halo-RPB1-70R (grey) after flavopiridol treatment. The data were fitted to a reaction dominant two-state model (Sprague, B.L. et al., Biophys J. 86, 3473-95, 2004; Hansen, A.S. et al., Elife 6, 2017). FRAP curves represent the mean across n = 5 independent measurements for each cell line and error bars show the standard error. We performed 50 iterations using 50% of the data in each to estimate the error (standard deviation of the subsampling) on the bound fraction. For comparison purposes, the FRAP curves of untreated cells (presented in Fig. 5f) are overlaid (light grey).

Supplementary Figure 7 CTD phosphorylation by recombinant yeast TFIIK complex (Kin28–Ccl1–Tfb3).

(a) Superposition of 1H-15N heteronuclear single quantum coherence (HSQC) spectra of a 21-residue peptide comprising three consecutive YSPTSPS repeats in its non-phosphorylated form (black) and after phosphorylation by recombinant yeast TFIIK complex (red). Sequence-specific resonance assignments were achieved by a combination of two-dimensional NOESY and TOCSY spectra. Unambiguous assignments were obtained for all residues of the non-phosphorylated peptide and most of the residues of the phosphorylated peptide. The NMR signals of phosphorylated S12 (p-S12) and phosphorylated S19 (p-S19) can be assigned to either the cross-peaks at 8.28 or 8.34 ppm 1H frequency, respectively. The shift of the three NMR signals of S5, S12 and S19 from its non-phosphorylated positions to the region from approximately 8.2 to 8.6 ppm (shown in grey) demonstrates that the three Ser5-positions in the YSPTSPS hepta-repeats were fully phosphorylated. In addition, the NMR data show that no other residue in this 21-residue peptide was phosphorylated by TFIIK. (b) Sodium dodecyl sulfate polyacrylamide gel electrophoresis and western blot analysis of phosphorylated GST-yCTD fusion protein. GST-yCTD was treated with recombinant yeast TFIIK. The CTD substrate became highly phosphorylated, resulting in a pronounced mobility change during polyacrylamide gel electrophoresis in comparison to the non-phosphorylated substrate (–ATP and –kinase control reactions). Western blotting confirms phosphorylation of heptad position Ser5. Corresponding loading controls are shown to correct for potential differences in blotting efficiency. Western blot analysis of Ser5-phosphorylation was performed in duplicate. (c) Phosphorylation of GST-yCTD by recombinant TFIIK inhibits phase separation. GST-yCTD was pre-incubated with TFIIK and ATP leading to its phosphorylation. A 10 µM solution of TFIIK-phosphorylated GST-yCTD does not undergo phase separation in 16 % dextran. This effect is neither caused by hydrotropic properties of ATP nor the pure presence of the kinase, since GST-yCTD readily forms droplets in control reactions containing ATP or the kinase alone. Images from ≥ 5 representative images taken for each condition are shown. Scale bars correspond to 10 µm.

Supplementary information

Supplementary Figures 1–7

Reporting Summary

Supplementary Note

Supplementary Dataset 1

Source data

Supplementary Video 1

yCTD droplet fusion. Real-time DIC recording of yCTD droplet fusion. Two droplets fuse upon contact into one droplet that readily returns to spherical shape. Experiments were performed with 25 µM GST-yCTD in the presence of 16% dextran. Scale bar, 2.5 µm.

Supplementary Video 2

hCTD droplet fusion. Real-time DIC recording of hCTD droplet fusion. Two droplets fuse upon contact into one droplet that readily returns to spherical shape. Experiments were performed with 20 µM MBP-hCTD in the presence of 16% dextran. Scale bar, 2.5 µm.

Supplementary Video 3

spaSPT of Halo-RPB1-25R. U2OS cells expressing Halo-RPB1- 25R were cultured with alpha-amanitin, labeled with PA-JF549 and single-particle tracking performed as described in Hansen, A.S. et al., eLife 7, 2018 at 133 Hz. Pixel size, 160 nm.

Supplementary Video 4

spaSPT of Halo-RPB1-52R. U2OS cells expressing Halo-RPB1- 52R were cultured with alpha-amanitin, labeled with PA-JF549 and single-particle tracking performed as described in Hansen, A.S. et al., eLife 7, 2018 at 133 Hz. Pixel size, 160 nm.

Supplementary Video 5

spaSPT of Halo-RPB1-70R. U2OS cells expressing Halo-RPB1- 70R were cultured with alpha-amanitin, labeled with PA-JF549 and single-particle tracking performed as described in Hansen, A.S. et al., eLife 7, 2018 at 133 Hz. Pixel size, 160 nm.

Supplementary Video 6

CDK7-mediated phosphorylation dissolves CTD droplets. CTD phosphorylation by the human CDK7 kinase complex caused gradual shrinking and ultimately disappearance of human CTD droplets. The time-lapse movie was created from cropped DIC micrographs of a single droplet recorded every minute within a 12 min time frame. Scale bar, 2.5 µm.

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Boehning, M., Dugast-Darzacq, C., Rankovic, M. et al. RNA polymerase II clustering through carboxy-terminal domain phase separation. Nat Struct Mol Biol 25, 833–840 (2018). https://doi.org/10.1038/s41594-018-0112-y

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