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CUL4–DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation

Nature Cell Biology volume 8, pages 1277–1283 (2006)Cite this article

Abstract

The CUL4–DDB1–ROC1 ubiquitin E3 ligase regulates cell-cycle progression, replication and DNA damage response1,2,3,4. However, the substrate-specific adaptors of this ligase remain uncharacterized. Here, we show that CUL4–DDB1 complexes interact with multiple WD40-repeat proteins (WDRs) including TLE1-3, WDR5, L2DTL (also known as CDT2) and the Polycomb-group protein EED (also known as ESC). WDR5 and EED are core components of histone methylation complexes that are essential for histone H3 methylation and epigenetic control at K4 or K9 and K27, respectively5,6,7, whereas L2DTL regulates CDT1 proteolysis after DNA damage through CUL4–DDB1 (ref. 8). We found that CUL4A–DDB1 interacts with H3 methylated mononucleosomes and peptides. Inactivation of either CUL4 or DDB1 impairs these histone modifications. However, loss of WDR5 specifically affects histone H3 methylation at K4 but not CDT1 degradation, whereas inactivation of L2DTL prevents CDT1 degradation but not histone methylation. Our studies suggest that CUL4–DDB1 ligases use WDR proteins as molecular adaptors for substrate recognition, and modulate multiple biological processes through ubiquitin-dependent proteolysis.

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Figure 1: Isolation of various WDR proteins that interact with CUL4B.
Figure 2: WDR proteins interact with the CUL4–DDB1 complexes.
Figure 3: Endogenous WDR proteins interact with the CUL4–DDB1 complexes.
Figure 4: L2DTL, but not other WDR proteins, specifically targets CDT1 for proteolysis in response to DNA damage.
Figure 5: CUL4–DDB1 associates with histone H3 methylated at K4, K9 and K27 and regulates H3 methylation in vivo.

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Acknowledgements

This work was supported by the grants from National Institutes of Health to H.S. (CA77695) and H.Z. (CA72878 and CA98955). H.Z. was also supported in part by an US Army grant (W81XWH-04-1-0230). H.S. and H.Z. would like to thank the members of the Sun and Zhang laboratories for discussions, R.K. for mass spectrometry, and T.Y and J. Guan for sequence alignments. The 293 suspension cells were from the Cell Culture Centre (Cellex Sciences, Minneapolis, MN).

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  1. Leigh Ann Higa and Min Wu: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, 06520, Connecticut, USA

    Leigh Ann Higa, Min Wu, Hong Sun & Hui Zhang

  2. Laboratory of Chemical Genomics, The Shenzhen Graduate School of Peking University, Shenzhen, 518055, China

    Tao Ye & Hui Zhang

  3. Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China

    Tao Ye

  4. Department of Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030, TX, USA

    Ryuji Kobayashi

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  1. Leigh Ann Higa
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Correspondence to Hui Zhang.

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Higa, L., Wu, M., Ye, T. et al. CUL4–DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat Cell Biol 8, 1277–1283 (2006). https://doi.org/10.1038/ncb1490

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