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Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin

Nature Cell Biology volume 7, pages 1007–1013 (2005)Cite this article

Abstract

In eukaryotes, heterochromatin mediates diverse processes including gene silencing and regulation of long-range chromatin interactions1,2. The formation of heterochromatin involves a conserved array of histone modifications; in particular, methylation of histone H3 at Lys 9 (H3K9me) is essential for recruiting HP1/Swi6 proteins3. In fission yeast, the Clr4 methyltransferase is responsible for H3K9me across all heterochromatic domains4,5. However, the mechanism of Clr4 recruitment to these loci is poorly understood. We show that Clr4 associates with Cul4, a cullin family protein that serves as a scaffold for assembling ubiquitin ligases. Mutations in Cul4 result in defective localization of Clr4 and loss of silencing at heterochromatic loci. This is accompanied by a severe reduction in H3K9me and Swi6 levels, and accumulation of transcripts corresponding to naturally silenced repeat elements within heterochromatic domains. Moreover, heterochromatin defects in Cul4 mutants could not be rescued by expression of Cul4 protein lacking Nedd8 modification, which is essential for its ubiquitin ligase activity. Rik1, a protein related to DNA damage binding protein DDB1 and required for H3K9me4,6, also interacts with Cul4, the association of which might serve to target Clr4 to heterochromatic loci. These analyses uncover a role for Cul4-based protein ubiquitination in regulating H3K9me and heterochromatin formation.

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Figure 1: Cul4 associates with Clr4 and Rik1.
Figure 2: Cul4 is required for heterochromatin formation.
Figure 3: Mutation in Cul4 affects chromosome segregation and mating-type switching.
Figure 4: The ubiquitin ligase activity of Cul4 is required for heterochromatin formation.
Figure 5: Cul4 recruits Clr4 to heterochromatic loci.

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Acknowledgements

We thank G. Mizuguchi and C. Wu for purification protocol. We thank O. Nielsen for allowing us to cite their work before publication, and J. Zerillo and A. Zuniga for mass spectrometry analyses. We also thank H. Cam for help in manuscript preparation, A. Guhathakurta and T. Sugiyama for critical reading of the manuscript, and E. Chen and other members of the Grewal laboratory for help and discussions. This research was supported by the National Cancer Institute intramural research programme.

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Authors and Affiliations

  1. Laboratory of Molecular Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, 20892, MD, USA

    Songtao Jia & Shiv I. S. Grewal

  2. Department of Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA

    Ryuji Kobayashi

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Correspondence to Shiv I. S. Grewal.

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Jia, S., Kobayashi, R. & Grewal, S. Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat Cell Biol 7, 1007–1013 (2005). https://doi.org/10.1038/ncb1300

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