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DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation

Nature Structural & Molecular Biology volume 24, pages 1039–1047 (2017)Cite this article

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Abstract

Polycomb repressive complex 2 (PRC2) trimethylates histone H3 at lysine 27 to mark genes for repression. We measured the dynamics of PRC2 binding on recombinant chromatin and free DNA at the single-molecule level using total internal reflection fluorescence (TIRF) microscopy. PRC2 preferentially binds free DNA with multisecond residence time and midnanomolar affinity. PHF1, a PRC2 accessory protein of the Polycomblike family, extends PRC2 residence time on DNA and chromatin. Crystallographic and functional studies reveal that Polycomblike proteins contain a winged-helix domain that binds DNA in a sequence-nonspecific fashion. DNA binding by this winged-helix domain accounts for the prolonged residence time of PHF1–PRC2 on chromatin and makes it a more efficient H3K27 methyltranferase than PRC2 alone. Together, these studies establish that interactions with DNA provide the predominant binding affinity of PRC2 for chromatin. Moreover, they reveal the molecular basis for how Polycomblike proteins stabilize PRC2 on chromatin and stimulate its activity.

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Figure 1: PHF1 prolongs the residence time of PRC2 on chromatin and DNA.
Figure 2: High-affinity binding of PRC2 to DNA is enhanced by PHF1.
Figure 3: Structure of the Pcl PHD2 WH domain.
Figure 4: The Pcl and PHF1 WH domains bind dsDNA.
Figure 5: DNA binding by PHF1 extends PRC2 residence time on chromatin and permits more efficient H3K27 methylation.

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Acknowledgements

We thank the MPI Biochemistry Facility and the Crystallization Facility for support with the biophysical and structural experiments and the beamline scientists at the Swiss Light Source for excellent assistance with data collection. We thank T. Cech and his lab members X. Wang and R.D. Paucek (University of Colorado Boulder) for sharing unpublished data and discussions. We thank S. Kilic and M. Tobler for reagents. This work was supported by the European Commission Seventh Framework Program 4DCellFate (grant number 277899), the Max Planck Society (J.M.), the Swiss National Science Foundation (grant number 31003A_173169) and EPFL (B.F.).

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  1. Jeongyoon Choi and Andreas Linus Bachmann: These authors contributed equally to this work.

Authors and Affiliations

  1. Max Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Martinsried, Germany

    Jeongyoon Choi, Katharina Tauscher & Jürg Müller

  2. Ecole Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering (ISIC), Laboratory of Biophysical Chemistry of Macromolecules, Lausanne, Switzerland

    Andreas Linus Bachmann & Beat Fierz

  3. Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany

    Christian Benda

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Contributions

J.C. and J.M. conceived the project. J.C., C.B., B.F. and J.M. designed the experiments. J.C. performed protein purification, biophysical experiments, crystallization and HMTase assays. J.C. and A.L.B. performed smTIRFM. J.C., A.L.B., C.B., B.F. and J.M. discussed and interpreted the data. J.C., B.F. and J.M. wrote the manuscript. K.T. provided technical support.

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Correspondence to Beat Fierz or Jürg Müller.

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Integrated supplementary information

Supplementary Figure 1 Quality assessment of reagents and conditions used for smTIRFM

(a) Gel filtration profile of PHF1-PRC2 on a Superose6 column with absorption at 280 nm (A280) and at 260 nm (A260). Below, elution fractions from the gel filtration peak, separated on a 12% polyacrylamide-SDS gel and visualized by coomassie staining.

(b) DY-547 labelling efficiency (%) of PRC2 complexes

(c) Left: scheme of chromatin array construct. Right: 12-mer chromatin arrays where digested with ScaI, separated on a 5% native TBE polyacrylamide gel and analysed by GelRed staining (left) and detection of Atto647N fluorescence emission (right). Numbers in parentheses: nucleosome positions, MN: mononucleosomes, DNA: free DNA released from array digestion, buffer DNA/buffer MNs: octamer buffer DNA and MNs formed on buffer DNA. Note that MN(1) carries an extended DNA linker and is labeled with a Atto647N dye. Full chromatin occupancy is judged by the absence of free DNA after ScaI digestion.

(d) Photobleaching kinetics of DY-547-labelled PRC2 during laser irradiation at different intensities (10 W/cm2, 20 W/cm2, 40 W/cm2 and 70 W/cm2). At 40 W/cm2 (experimental conditions), the fluorophore bleaching time constant (τbleach) is 18 s.

(e) Left: cumulative histogram of tdark for PRC2, an exponential fit yields λon, from which kon is calculated. Right: association rate constants kon for indicated PRC2 complexes on chromatin arrays. Symbols: Individual experimental results, N = 3 replicates for all PRC2 complexes (independent experiments), error bars: s.d., For the fit values, see Table 1.

Supplementary Figure 2 Quality assessment of PRC2 preparations and DNA binding analysis of PRC2 by MST

(a) PRC2, PHF1-PRC2, PHF1C-PRC2, PHF1WH>A-PRC2 and PHF1WH>E-PRC2 separated on a 13% polyacrylamide-SDS gel and visualized by coomassie staining. M: Molecular weight marker.

(b) Mononucleosomes used for EMSAs in Figure 2a, analyzed on a 0.7 % agarose gel and visualized by GelRed staining. M: DNA size marker.

(c) Binding of PRC2, PHF1-PRC2 and PHF1C -PRC2 to Flc-labelled PRE 11L probe (45nM), measured by MST. N = 3, error bars: s.d.. Curve fitting was performed using the Hill function; Kd values ± s.d. are indicated.

(d) MST analysis as in (c) but on a dsDNA probe PRE F5.

Supplementary Figure 3 The PHD2-WH domain is a conserved unit in Drosophila and human Polycomblike proteins

Alignment of PHD2-WH domain sequences of the proteins shown in Figure 3a. Secondary structure elements based on the PclPHD2-WH structure are indicated above the alignment. Blue boxes label the Zn-coordinating residues. Blue asterisks mark the residues Y514, M527 and W536 in PHD2 that are predicted to form an aromatic cage, but we note that Y514 in our crystal structure is not oriented correctly for cage formation, and F523 (also marked by a blue asterisk) is oriented in a way to obstruct access to the cage. Blue or orange circles show residues involved in the interaction between PHD2 and WH domain shown in Figure 3c; orange triangles mark residues mutated in PclPHD2-WHWH>A and in PHF1PHD2-WHWH>A/E.

Supplementary Figure 4 The PHD2-WH domain of Drosophila Pcl binds PRE DNA in a sequence non-specific fashion

(a) Schematic representation of the bxd PRE and the DNA probes, PRE01 to PRE21, used for binding assays with PclPHD2-WH protein in (c), that cover 210 bp of the bxd PRE core region. Lollipops indicate location of Pho protein binding sites that are required for normal PRC2 recruitment (Frey et al, 2016).

(b) DNA sequences of PRE01 to PRE20 probes.

(c) Binding of wild-type PclPHD2-WH to Flc-labelled PRE01 to PRE21 DNA probes (45 nM), measured by using fluorescence polarization assays. Kd values of the binding interaction of PclPHD2-WH with the different PRE probes are indicated in parentheses; binding assays with probes PRE12 and PRE13 were omitted from the analysis because these oligos failed to form stable DNA duplexes by annealing reaction.

Supplementary Figure 5 DNA binding by the PHF1 WH domain extends PRC2 residence time on DNA and mononucleosomes

(a) Time constants of the fast (τoff,1) and slow (τoff,2) dissociation process of indicated PRC2 complexes from the 601-DNA template. Numbers indicate % amplitude. Symbols: Individual experimental results, N = 3 replicates for PRC2 (independent experiments), N = 5 replicates for PRC2-PHF1 (independent experiments), N = 4 replicates for PRC2-PHF1C (independent experiments), N = 4 replicates for PRC2-PHF1WH>E (independent experiments), error bars: s.d., *: p<0.05, two-tailed student's t-test. For the fit values, see Table 1.

(b) Mononucleosomes used for smTIRFM analysis were run on a 5% native TBE polyacrylamide gel and analysed by GelRed staining (left) and detection of Atto647N fluorescence emission (right).

(c) τoff,1 and τoff,2 of PRC2 complexes on mononucleosomes. Numbers indicate % amplitude. Symbols: Individual experimental results, N = 3 replicates for PRC2 (independent experiments), N = 5 replicates for PRC2-PHF1 (independent experiments), N = 4 replicates for PRC2-PHF1C (independent experiments), N = 4 replicates for PRC2-PHF1WH>E (independent experiments), error bars: s.d., *: p<0.05, two-tailed student's t-test. For the fit values, see Table 1.

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Choi, J., Bachmann, A., Tauscher, K. et al. DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation. Nat Struct Mol Biol 24, 1039–1047 (2017). https://doi.org/10.1038/nsmb.3488

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