Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference

Nature volume 548, pages 607–611 (2017)Cite this article

Subjects

Abstract

ATP-dependent chromatin remodellers regulate access to genetic information by controlling nucleosome positions in vivo1. However, the mechanism by which remodellers discriminate between different nucleosome substrates is poorly understood. Many chromatin remodelling proteins possess conserved protein domains that interact with nucleosomal features2. Here we used a quantitative high-throughput approach, based on the use of a DNA-barcoded mononucleosome library, to profile the biochemical activity of human ISWI family remodellers in response to a diverse set of nucleosome modifications. We show that accessory (non-ATPase) subunits of ISWI remodellers can distinguish between differentially modified nucleosomes, directing remodelling activity towards specific nucleosome substrates according to their modification state. Unexpectedly, we show that the nucleosome acidic patch3 is necessary for maximum activity of all ISWI remodellers evaluated. This dependence also extends to CHD and SWI/SNF family remodellers, suggesting that the acidic patch may be generally required for chromatin remodelling. Critically, remodelling activity can be regulated by modifications neighbouring the acidic patch, signifying that it may act as a tunable interaction hotspot for ATP-dependent chromatin remodellers and, by extension, many other chromatin effectors that engage this region of the nucleosome surface4,5,6,7,8,9.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: A diverse library of modified nucleosomes.
Figure 2: A high-throughput nucleosome remodelling assay for ISWI family chromatin remodellers.
Figure 3: Specialization of ISWI remodellers for diverse nucleosome modifications.
Figure 4: The nucleosome acidic patch is crucial for remodelling and regulatable by histone PTMs.

Similar content being viewed by others

References

  1. Jiang, C. & Pugh, B. F. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10, 161–172 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273–304 (2009)

    Article  CAS  PubMed  Google Scholar 

  3. Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997)

    Article  ADS  CAS  PubMed  Google Scholar 

  4. Morgan, M. T. et al. Structural basis for histone H2B deubiquitination by the SAGA DUB module. Science 351, 725–728 (2016)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  5. Makde, R. D., England, J. R., Yennawar, H. P. & Tan, S. Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature 467, 562–566 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  6. Armache, K. J., Garlick, J. D., Canzio, D., Narlikar, G. J. & Kingston, R. E. Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 Å resolution. Science 334, 977–982 (2011)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  7. McGinty, R. K., Henrici, R. C. & Tan, S. Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature 514, 591–596 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  8. Barbera, A. J. et al. The nucleosomal surface as a docking station for Kaposi’s sarcoma herpesvirus LANA. Science 311, 856–861 (2006)

    Article  ADS  CAS  PubMed  Google Scholar 

  9. Kato, H. et al. A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Science 340, 1110–1113 (2013)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  10. Tan, M. et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146, 1016–1028 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Ferreira, H., Flaus, A. & Owen-Hughes, T. Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms. J. Mol. Biol. 374, 563–579 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Neumann, H. et al. A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation. Mol. Cell 36, 153–163 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. North, J. A. et al. Phosphorylation of histone H3(T118) alters nucleosome dynamics and remodeling. Nucleic Acids Res. 39, 6465–6474 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Chatterjee, N. et al. Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms. Nucleic Acids Res. 39, 8378–8391 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Shogren-Knaak, M. et al. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311, 844–847 (2006)

    Article  ADS  CAS  PubMed  Google Scholar 

  16. Chatterjee, N. et al. Histone acetylation near the nucleosome dyad axis enhances nucleosome disassembly by RSC and SWI/SNF. Mol. Cell. Biol. 35, 4083–4092 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Goldman, J. A., Garlick, J. D. & Kingston, R. E. Chromatin remodeling by imitation switch (ISWI) class ATP-dependent remodelers is stimulated by histone variant H2A.Z. J. Biol. Chem. 285, 4645–4651 (2010)

    Article  CAS  PubMed  Google Scholar 

  18. Nguyen, U. T. et al. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Nat. Methods 11, 834–840 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. He, X., Fan, H. Y., Narlikar, G. J. & Kingston, R. E. Human ACF1 alters the remodeling strategy of SNF2h. J. Biol. Chem. 281, 28636–28647 (2006)

    Article  CAS  PubMed  Google Scholar 

  20. Clapier, C. R., Nightingale, K. P. & Becker, P. B. A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res. 30, 649–655 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Tropberger, P. & Schneider, R. Scratching the (lateral) surface of chromatin regulation by histone modifications. Nat. Struct. Mol. Biol. 20, 657–661 (2013)

    Article  CAS  PubMed  Google Scholar 

  22. Tallant, C. et al. Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC. Structure 23, 80–92 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Filippakopoulos, P. et al. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 149, 214–231 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Ruthenburg, A. J. et al. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell 145, 692–706 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Müller, M. M. & Muir, T. W. Histones: at the crossroads of peptide and protein chemistry. Chem. Rev. 115, 2296–2349 (2015)

    Article  PubMed  CAS  Google Scholar 

  26. Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D. & Patel, D. J. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14, 1025–1040 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. McGinty, R. K. & Tan, S. Nucleosome structure and function. Chem. Rev. 115, 2255–2273 (2015)

    Article  CAS  PubMed  Google Scholar 

  28. Fujiki, R. et al. GlcNAcylation of histone H2B facilitates its monoubiquitination. Nature 480, 557–560 (2011)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. Clapier, C. R. & Cairns, B. R. Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature 492, 280–284 (2012)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhao, S. et al. Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial-mesenchymal transition. Proc. Natl Acad. Sci. USA 113, 12238–12243 (2016)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Casadio, F. et al. H3R42me2a is a histone modification with positive transcriptional effects. Proc. Natl Acad. Sci. USA 110, 14894–14899 (2013)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  32. McGinty, R. K. et al. Structure-activity analysis of semisynthetic nucleosomes: mechanistic insights into the stimulation of Dot1L by ubiquitylated histone H2B. ACS Chem. Biol. 4, 958–968 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Biron, E., Chatterjee, J. & Kessler, H. Optimized selective N-methylation of peptides on solid support. J. Pept. Sci. 12, 213–219 (2006)

    Article  CAS  PubMed  Google Scholar 

  34. Brown, Z. Z. et al. Strategy for “detoxification” of a cancer-derived histone mutant based on mapping its interaction with the methyltransferase PRC2. J. Am. Chem. Soc. 136, 13498–13501 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Hackeng, T. M., Griffin, J. H. & Dawson, P. E. Protein synthesis by native chemical ligation: expanded scope by using straightforward methodology. Proc. Natl Acad. Sci. USA 96, 10068–10073 (1999)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  36. Li, X. Q., Kawakami, T. & Aimoto, S. Direct preparation of peptide thioesters using an Fmoc solid-phase method. Tetrahedr. Lett. 39, 8669–8672 (1998)

    CAS  Google Scholar 

  37. Mitchell, S. A., Pratt, M. R., Hruby, V. J. & Polt, R. Solid-phase synthesis of O-linked glycopeptide analogues of enkephalin. J. Org. Chem. 66, 2327–2342 (2001)

    Article  CAS  PubMed  Google Scholar 

  38. Thompson, R. E. et al. Trifluoroethanethiol: an additive for efficient one-pot peptide ligation-desulfurization chemistry. J. Am. Chem. Soc. 136, 8161–8164 (2014)

    Article  CAS  PubMed  Google Scholar 

  39. Li, Y. et al. Molecular coupling of histone crotonylation and active transcription by AF9 YEATS domain. Mol. Cell 62, 181–193 (2016)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Xiong, X. et al. Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2. Nat. Chem. Biol. 12, 1111–1118 (2016)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Batjargal, S., Walters, C. R. & Petersson, E. J. Inteins as traceless purification tags for unnatural amino acid proteins. J. Am. Chem. Soc. 137, 1734–1737 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Barak, O., Lazzaro, M. A., Cooch, N. S., Picketts, D. J. & Shiekhattar, R. A tissue-specific, naturally occurring human SNF2L variant inactivates chromatin remodeling. J. Biol. Chem. 279, 45130–45138 (2004)

    Article  CAS  PubMed  Google Scholar 

  43. Phelan, M. L., Sif, S., Narlikar, G. J. & Kingston, R. E. Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol. Cell 3, 247–253 (1999)

    Article  CAS  PubMed  Google Scholar 

  44. Dyer, P. N. et al. Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol. 375, 23–44 (2004)

    Article  CAS  PubMed  Google Scholar 

  45. Flaus, A. & Richmond, T. J. Positioning and stability of nucleosomes on MMTV 3′LTR sequences. J. Mol. Biol. 275, 427–441 (1998)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank current and former members of the Muir laboratory for discussions and comments; W. Wang and J. Wiggins from the Princeton Sequencing Core Facility; C. Hannon and S. Blythe for writing a custom R script for managing sequencing data; and L. Guerra and L. Beh for advice with data analysis. The SNF2h, ACF1, WSTF, CHRAC-15, and CHRAC-17 coding sequences were a gift from R. Kingston; the RSF1 coding sequence was a gift from D. Reinberg; the BPTF coding sequence was a gift from C. D. Allis; F.W. was funded by a postdoctoral fellowship from the German Research Foundation (DFG); T.P. was funded by a postdoctoral fellowship from the US National Institutes of Health (GM112365); and this research was supported by the US National Institutes of Health grants P01 CA196539, R37 GM086868 and R01 GM107047.

Author information

Author notes

  1. Manuel M. Müller

    Present address: Department of Chemistry, King’s College London, 7 Trinity Street, London, SE1 1DB, UK

  2. Uyen T. T. Nguyen

    Present address: Bayer Pharma AG, Berlin, Germany

  3. Tatyana Panchenko

    Present address: Perlmutter Cancer Center, New York University Langone Medical Center, Alexandria Center for Life Sciences West Tower, Suite 625, 430 East 29th Street, New York, New York, 10016, USA

  4. Rasmus Pihl

    Present address: Department of Biomedicine, Aarhus University, Aarhus, Denmark

  5. Samuel B. Pollock

    Present address: University of California, San Francisco, 505 Parnassus Avenue, San Francisco, California, 94143, USA

Authors and Affiliations

  1. Department of Chemistry, Princeton University, Frick Laboratory, Princeton, 08544, New Jersey, USA

    Geoffrey P. Dann, Glen P. Liszczak, John D. Bagert, Manuel M. Müller, Uyen T. T. Nguyen, Felix Wojcik, Zachary Z. Brown, Jeffrey Bos, Rasmus Pihl, Samuel B. Pollock, Katharine L. Diehl & Tom W. Muir

  2. Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, 10065, USA

    Tatyana Panchenko & C. David Allis

Authors
  1. Geoffrey P. Dann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Glen P. Liszczak
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John D. Bagert
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Manuel M. Müller
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Uyen T. T. Nguyen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Felix Wojcik
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zachary Z. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jeffrey Bos
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Tatyana Panchenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Rasmus Pihl
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Samuel B. Pollock
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Katharine L. Diehl
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. C. David Allis
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Tom W. Muir
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

G.P.D. purified all remodellers, performed all remodelling and nucleosome library experiments, and processed all sequencing data; G.P.D prepared the nucleosome library with contributions from G.P.L., M.M.M., U.T.T.N., T.P., Z.Z.B., F.W., J.B., R.P. and S.B.P.; G.P.D. and G.P.L. purified RCC1 and Sir3 constructs for nucleosome library binding experiments; G.P.L. performed the qPCR analysis; G.P.D. and K.L.D. synthesized and purified the LANA peptides; J.D.B. performed the PCA analysis; C.D.A. oversaw the preparation of crotonylated histones; G.P.D, J.D.B. and T.W.M. analysed the data; G.P.D., M.M.M. and T.W.M. conceived the project; T.W.M. supervised the study; G.P.D. and T.W.M. wrote the manuscript.

Corresponding author

Correspondence to Tom W. Muir.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

Reviewer Information Nature thanks B. Cairns, F. Pugh and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Figure 1 Characterization of barcoded 601 (BC-601) DNA.

a, BC-601 DNA prepared for all 115 nucleosome library members as described in Methods (Barcoded 601 (BC-601) DNA preparation). Ligation products are 192 bp in size and were visualized by polyacrylamide gel electrophoresis (5% acrylamide, 0.5× TBE, 200 V, 40 min) and staining with SYBR Safe DNA gel stain. A faint band corresponding to unligated 601 DNA (601) is slightly visible in certain cases. b, BC-601 DNA for nucleosome 99 (Supplementary Table 1) was CpG methylated by the M.SssI methyltransferase (NEB) according to the manufacturer’s instructions and characterized by digestion with the RsaI restriction enzyme, which is sensitive to CpG methylation, and PstI, which is not. For gel source data, see Supplementary Fig. 1.

Extended Data Figure 2 Analysis of the quality and integrity of the nucleosome library.

a, b, Analysis of individual nucleosome preparations (a) and the final library after pooling of nucleosomes (b) by native gel electrophoresis and staining with ethidium bromide. c, Antibody pull-down of library members using an anti-H3K4me3 antibody. Every nucleosome member containing an H3K4me3 mark (red) was efficiently isolated relative to other library members (black). Notably, the antibody was also able to pull down a nucleosome possessing solely the H3K4me2 mark (blue), indicating a lack of antibody specificity in this case. This experiment was performed once. For gel source data, see Supplementary Fig. 1.

Extended Data Figure 3 Characterization of recombinant ISWI chromatin remodellers.

a, Purified chromatin remodellers were run a 4–20% Mini-PROTEAN TGX gel (Bio-Rad) and for 35 min at 180 V. Proteins were stained with Coomassie. The composition of each remodeller–remodelling complex is depicted above each respective lane on the gel. Expected molecular weights: SNF2h: 122 kDa, ACF1: 179 kDa, CHRAC-15: 14.7 kDa, CHRAC-17: 16.9 kDa, WSTF: 171 kDa, TIP5: 208 kDa, RSF1: 164 kDa; migrates at higher apparent molecular weight, SNF2L: 121 kDa, BPTF: 338 kDa, RbAp46: 47.8 kDa. b, All remodellers display ATP-dependent nucleosome remodelling activity as detected by a restriction enzyme accessibility assay. For gel source data, see Supplementary Fig. 1.

Extended Data Figure 4 Nucleosome remodelling activity is negligible in the absence of ATP.

Bar graphs show individual DNA cleavage rates (kMN, remodelling rates in the case of nucleosomes; see Supplementary Table 3) from library remodelling experiments for each member of the library in the presence of the indicated chromatin remodeller with and without ATP. Rate values were rank ordered and are displayed from low to high. The dashed red line represents the rate of remodelling of unmodified nucleosomes. The related graphs for the ACF complex can be found in Fig. 2d. Data are represented as the mean of experimental replicates ± s.e.m. (n = 3).

Extended Data Figure 5 Principal component (PC) analysis of library remodelling data.

Percentages show the fractions of the variance accounted for by each PC. Individual nucleosomes are shown in light blue, and PC weight values for each remodeller are shown in either orange or black. Weights are scaled by a factor of 2 for visibility. a, PC1 vs. PC2 and PC1 vs. PC3 are plotted. b, PC2 vs. PC3 are plotted as in Fig. 3a. Nucleosomes driving differences in remodeller activity were numbered as in Supplementary Table 1 and grouped by their location in PC space (Supplementary Table 4).

Extended Data Figure 6 Alteration of histone–DNA contacts affects remodelling activity.

a, Modified histone residues in the nucleosome library that lie under the DNA (tan) are highlighted on the nucleosome (PDB: 1KX5) in red. PTMs are numbered and labelled on the nucleosome structure. Values were capped at −2 and 2 for display purposes. b, Histone mutants present in the nucleosome library that lie under the DNA (tan) are highlighted on the nucleosome (PDB: 1KX5) in red. The heatmap is displayed as in a. Locations of each mutation are individually labelled on the nucleosome structure. Values were capped at −3 and 3 for display purposes. All histones are unmodified unless otherwise specified.

Extended Data Figure 7 Remodelling of nucleosomes containing modifications preferred by histone recognition domains.

Library remodelling data generated by the NoRC (a), WICH (b), and NURF (c) complexes for nucleosomes containing residues known to interact with histone binding modules in accessory subunits of each complex (NoRC: TIP5; WICH: WSTF; NURF: BPTF). Literature binding specificities are displayed in corresponding tables on the right. Bar graphs display log2 values of the rate of remodelling of individual nucleosome library members (kMN) relative to unmodified nucleosomes (kunmod.). Data are represented as the ratio of the mean of experimental replicates ± s.e.m. (n = 3). Note that H3KpolyAc includes the H3K14ac modification (Supplementary Table 1). All histones are unmodified unless otherwise specified. BRD, bromodomain; PHD, PHD-finger; PHD–BRD, tandem PHD-finger–bromodomain module; ND, not determined.

Extended Data Figure 8 Remodelling assays carried out on individual nucleosomes measured via standard gel-based read-out to validate library data.

a, Activity of the NURF complex towards H3K4me3+H4K16ac relative to unmodified nucleosomes as measured in the context of the nucleosome library (library) or individual assays (individual). b, Activity of the ACF complex on unmodified and acidic patch mutant nucleosomes. c, Remodelling of unmodified nucleosomes is inhibited by the presence of the LANA peptide when compared to a LANA peptide with key binding residues mutated (LRS to AAA). d, Activity of the ACF complex towards nucleosomes modified near the acidic patch (H2BK108ac and H2BS112GlcNac) relative to unmodified nucleosomes as measured in the context of the nucleosome library (library) or individual assays (individual). Gel images of example replicates used to generate densitometry measurements in each subpanel are shown above respective graphs. a, c, and d use a restriction enzyme accessibility assay. b uses a nucleosome repositioning electrophoretic mobility shift assay. All histones are unmodified unless otherwise specified. All data are represented as the mean of experimental replicates ± s.e.m. (n = 3). For gel source data, see Supplementary Fig. 1.

Extended Data Figure 9 High-throughput chromatin remodelling and binding data.

a, Heat-map displaying ISWI remodelling data (as in Fig. 2b) against the nucleosome library with CHD4 data for comparison. Rows were sorted on the basis of values for SNF2h (low to high). b, Heat map displaying binding of chromatin factors RCC1 and Sir3 against the nucleosome library relative to unmodified nucleosomes. Values were capped at −4 and 4 for display purposes. All data are represented as the mean of experimental replicates (n = 3).

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1–6. (PDF 11328 kb)

Reporting Summary (PDF 363 kb)

Supplementary Table 1

Histone Composition of Nucleosome Library Members. Individual histone composition of each member of the nucleosome library. Modifications include lysine acetylation (Kac), lysine mono, di, and trimethylation (Kme, Kme2, Kme3), arginine mono, asymmetric and symmetric dimethylation (Rme, Rme2a and Rme2s, respectively), lysine ubiquitylation (Kub), serine and tyrosine phosphorylation (Sph and Yph, respectively), serine modified with N-acetylglucosamine (SGlcNAc), and lysine crotonylation (Kcr). * = CpG methylation of nucleosomal DNA. (XLSX 33 kb)

Supplementary Table 2

Normalized Sequencing Reads Used to Calculate Nucleosome Remodeling Rate Constants. This table contains sequencing read counts that have been sorted by both a nucleosome identifier and multiplexing barcodes. This includes reads corresponding all 28,224 kinetic measurements to measure ISWI nucleosome remodeling as well as those for DNA Standard 2 and CHD4. The reads have already been normalized to DNA Standard 1, and are organized by enzyme, time point, with or without ATP, and by nucleosome (experimental triplicate measurements) as in Supplementary Table 1. (XLSX 371 kb)

Supplementary Table 3

Calculated Nucleosome Remodeling Rate Data. Raw rate values calculated by averaging experimental triplicate measurements from data in Supplementary Table 2 as described in the methods section of this study. Rows are organized by nucleosome number as in Supplementary Table 1. Per remodeler, the average of remodeling rate of all unmodified nucleosomes and corresponding error (considering error propagation) as well as the low threshold for measurement and corresponding error (considering error propagation) were calculated (bottom of table; see methods). Columns correspond to raw average measured rates (kslow ± ATP), standard error of the rates (kslow ± ATP SEM), final nucleosome remodeling rates used to calculate fold changes relative to unmodified nucleosomes (Final kslow +ATP, “kMN„; values are adjusting considering the calculated low threshold rate; note that these values for conditions –ATP were calculated to be negligible and thus ignored), fold change of remodeling rate relative to unmodified nucleosomes (log2k_MN/k_unmod.), and the corresponding error (considering error propagation). (XLSX 163 kb)

Supplementary Table 4

Nucleosome Library Members Contributing to Variation in Remodeler Behavior. This table contains nucleosomes grouped (by color) according to Extended Data Fig. 5b. Per remodeler, values in each column correspond to log2 values of the ratio of the rate of remodeling for a particular nucleosome to that of unmodified nucleosomes (as in Supplementary Table 3). Nucleosome modifications per histone are specified and nucleosomes are numbered as in Supplementary Table 1. (XLSX 16 kb)

Supplementary Table 5

Unique hexanucleotide nucleosome identifier barcodes. This table contains a list of unique hexanucleotide nucleosome identifier barcodes used in this study. Barcodes are numbered corresponding to the nucleosome (as in Supplementary Table 1) they are associated with. (XLSX 35 kb)

Supplementary Table 6

Unique multiplexing barcodes. This table contains a list of unique multiplexing barcodes used in this study. Barcodes are numbered arbitrarily. Typically, no more than 72 samples were sequenced in a single sequencing run. (XLSX 34 kb)

Supplementary Table 7

Raw Sequencing Reads and Calculation of Relative Binding Measurements for RCC1 and Sir3 Using the Nucleosome Library. This contains raw sequencing read counts used to calculate relative binding measurements for RCC1 and Sir3 using the nucleosome library as described in methods section ‘Processing of sequencing data for binding experiments using the nucleosome library’. (XLSX 132 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Dann, G., Liszczak, G., Bagert, J. et al. ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference. Nature 548, 607–611 (2017). https://doi.org/10.1038/nature23671

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature23671

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing