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Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex

Nature Structural & Molecular Biology volume 13, pages 704–712 (2006)Cite this article

Abstract

WDR5 is a core component of SET1-family complexes that achieve transcriptional activation via methylation of histone H3 on Nζ of Lys4 (H3K4). The role of WDR5 in the MLL1 complex has recently been described as specific recognition of dimethyl-K4 in the context of a histone H3 amino terminus; WDR5 is essential for vertebrate development, Hox gene activation and global H3K4 trimethylation. We report the high-resolution X-ray structures of WDR5 in the unliganded form and complexed with histone H3 peptides having unmodified and mono-, di- and trimethylated K4, which together provide the first comprehensive analysis of methylated histone recognition by the ubiquitous WD40-repeat fold. Contrary to predictions, the structures reveal that WDR5 does not read out the methylation state of K4 directly, but instead serves to present the K4 side chain for further methylation by SET1-family complexes.

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Figure 1: The overall structure of WDR5 complexes with histone H3.
Figure 2: Bound histone H3 peptide electron density and conformation.
Figure 3: Peptide recognition by WDR5 and conformational changes upon peptide binding.
Figure 4: Peptide binding by WDR5.
Figure 5: Differences in K4 conformation in the different methylation states.

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Acknowledgements

We are grateful to the staff of National Synchrotron Light Source (NSLS) beamline X-29, in particular W. Shi and H. Robinson, as well as the staff of Advanced Light Source beamline 5.02, especially C. Trame, and the staff of Advanced Photon Source (APS) beamline 24-ID, importantly I. Kourinov and K. Rajashankar, for assistance in X-ray data collection. Financial support for NSLS px group beamlines comes principally from the Offices of Biological and Environmental Research and of Basic Energy Sciences of the US Department of Energy and from the National Center for Research Resources of the US National Institutes of Health (NIH). This work is based upon research conducted at the Northeastern Collaborative Access Team beamlines of the APS, which is supported by the National Center for Research Resources at the NIH. We thank the Dana Farber Cancer Research Center, F. Bernal and L. Walensky for amino acid analysis and peptide synthesis advice; S.S. Yi (Memorial Sloan-Kettering Cancer Center) for synthesis of H3K4me2 complex II and the unmodified peptides, the Dana Farber Cancer Research Center and the Harvard Center for Genomics Research for use of their Biacore instruments, and F. Bernal, Y. Dou, K. Herlihy, Y. Inuzuka, D. Pakotiprapha, T.A. Milne, R.G. Roeder, S.D. Taverna and J. Wysocka for valuable discussions and scientific input. This work was supported by an NIH grant to G.L.V.; D.J.P. is supported by funds from the Abby Rockefeller Mauze Trust and the Dewitt Wallace and Maloris Foundations; and C.D.A. is supported by an NIH MERIT award and funds from Rockefeller University.

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Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, 02138, Massachusetts, USA

    Alexander J Ruthenburg, Daina M Graybosch & Gregory L Verdine

  2. Laboratory of Chromatin Biology, The Rockefeller University, 1230 York Avenue, New York, 10021, New York, USA

    Alexander J Ruthenburg & C David Allis

  3. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, 10021, New York, USA

    Wooikoon Wang, Haitao Li & Dinshaw J Patel

  4. Department of Molecular and Cellular Biology, Harvard University, 12 Oxford Street, Cambridge, 02138, Massachusetts, USA

    Gregory L Verdine

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Contributions

A.J.R. is responsible for the X-ray studies of the apo structure and the H3K4me1, H3K4me2 and H3K4me3 structures, W.-K.W. and H.L. are responsible for the unmodified peptide structure and an additional H3K4me2 structure (complex II), and D.M.G. performed the binding studies with some assistance from A.J.R. and W.-K.W. G.L.V., D.J.P. and C.D.A. supervised the structural and biochemical aspects of the project and take overall responsibility for their joint research. All authors discussed the results and commented on the manuscript.

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Correspondence to Gregory L Verdine.

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Supplementary information

Supplementary Fig. 1

Superpositions of WDR5 structures. (PDF 1218 kb)

Supplementary Fig. 2

Stereo view of Arg2 and Lys4 electron density. (PDF 560 kb)

Supplementary Fig. 3

Fluorescence anisotropy measurment of peptide binding to WDR5 (Y191F). (PDF 83 kb)

Supplementary Methods (PDF 100 kb)

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Ruthenburg, A., Wang, W., Graybosch, D. et al. Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nat Struct Mol Biol 13, 704–712 (2006). https://doi.org/10.1038/nsmb1119

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