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Ubiquitin utilizes an acidic surface patch to alter chromatin structure

Nature Chemical Biology volume 13, pages 105–110 (2017)Cite this article

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Abstract

Ubiquitylation of histone H2B, associated with gene activation, leads to chromatin decompaction through an unknown mechanism. We used a hydrogen–deuterium exchange strategy coupled with NMR spectroscopy to map the ubiquitin surface responsible for its structural effects on chromatin. Our studies revealed that a previously uncharacterized acidic patch on ubiquitin comprising residues Glu16 and Glu18 is essential for decompaction. These residues mediate promiscuous electrostatic interactions with the basic histone proteins, potentially positioning the ubiquitin moiety as a dynamic 'wedge' that prevents the intimate association of neighboring nucleosomes. Using two independent crosslinking strategies and an oligomerization assay, we also showed that ubiquitin–ubiquitin contacts occur in the chromatin environment and are important for the solubilization of the chromatin polymers. Our work highlights a novel, chromatin-related aspect of the 'ubiquitin code' and sheds light on how the information-rich ubiquitin modification can orchestrate different biochemical outcomes using distinct surface features.

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Figure 1: Experimental strategy for detecting ubiquitin interaction surfaces in nucleosome arrays.
Figure 2: Ubiquitin residues protected from backbone H/D exchange in nucleosome arrays.
Figure 3: Effect of ubiquitin mutations on intra- and inter-fiber compaction.
Figure 4: Ubiquitin–chromatin interactions probed with crosslinking experiments.
Figure 5: Intra-array ubiquitin–ubiquitin interactions impede oligomerization.
Figure 6: Mechanism of chromatin decompaction induced by H2B ubiquitylation.

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Acknowledgements

We thank M. Müller, I. Pelczer, B. Fierz, L. Guerra, N. Shah, S. Kilic, M. Holt, U. Nguyen, J. Bos and K. Jani for stimulating discussions and help regarding the preparation of materials. This work was funded by US National Institutes of Health grant R01-GM107047 to T.W.M.

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Authors and Affiliations

  1. Department of Chemistry, Princeton University, Princeton, New Jersey, USA

    Galia T Debelouchina, Karola Gerecht & Tom W Muir

  2. Department of Chemistry, Technical University Munich, Garching, Germany

    Karola Gerecht

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  1. Galia T Debelouchina
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Contributions

G.T.D. designed experiments, prepared materials, performed H/D exchange and NMR experiments, compaction assays and crosslinking experiments, analyzed data and wrote the manuscript; K.G. prepared materials, performed compaction assays and analyzed data; T.W.M. designed experiments, analyzed data and wrote the manuscript.

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Correspondence to Tom W Muir.

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Debelouchina, G., Gerecht, K. & Muir, T. Ubiquitin utilizes an acidic surface patch to alter chromatin structure. Nat Chem Biol 13, 105–110 (2017). https://doi.org/10.1038/nchembio.2235

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