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Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction

Nature Chemical Biology volume 7, pages 113–119 (2011)Cite this article

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Abstract

Regulation of chromatin structure involves histone posttranslational modifications that can modulate intrinsic properties of the chromatin fiber to change the chromatin state. We used chemically defined nucleosome arrays to demonstrate that H2B ubiquitylation (uH2B), a modification associated with transcription, interferes with chromatin compaction and leads to an open and biochemically accessible fiber conformation. Notably, these effects were specific for ubiquitin, as compaction of chromatin modified with a similar ubiquitin-sized protein, Hub1, was only weakly affected. Applying a fluorescence-based method, we found that uH2B acts through a mechanism distinct from H4 tail acetylation, a modification known to disrupt chromatin folding. Finally, incorporation of both uH2B and acetylated H4 resulted in synergistic inhibition of higher-order chromatin structure formation, possibly a result of their distinct modes of action.

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Figure 1: H2B ubiquitylation impairs fiber folding.
Figure 2: H2B ubiquitylation increases chromatin accessibility in vitro and in vivo.
Figure 3: A fluorescence method to monitor chromatin fiber folding reveals conformational heterogeneity at intermediate chromatin fiber compaction.
Figure 4: uH2B and acH4 have distinct effects on fiber compaction and higher-order structure formation.
Figure 5: Fiber decompaction is a specific property of the ubiquitin protein.

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Acknowledgements

We thank H. Deng and H. Yu (The Rockefeller University) for mass spectrometric analysis of histones, J. Kim and R. Subramanian for assistance with preparing hDot1L, K. Chiang for help with DNA preparation, H. Yang and D. Montiel for help with fluorescence lifetime measurements and A. Ruthenburg, R. Sadeh, P. Moyle and M. Vila-Perelló for assistance with cell experiments and discussions. This work was funded by the US National Institutes of Health (grant number RC2CA148354) and the Starr Cancer Consortium. B.F. was funded by the Swiss National Science Foundation (Nr. PBBSA-118839 and PA00P3_129130/1) and by the Novartis Foundation.

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  1. Champak Chatterjee

    Present address: Present address: Department of Chemistry, University of Washington, Seattle, Washington, USA,

Authors and Affiliations

  1. Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, New York, USA

    Beat Fierz, Champak Chatterjee, Robert K McGinty, Maya Bar-Dagan & Tom W Muir

  2. Department of Chemistry, State University of New York Stony Brook, Stony Brook, New York, USA

    Daniel P Raleigh

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Contributions

B.F. and T.W.M. designed the experiments. B.F. performed the biophysical chromatin experiments. B.F. and C.C. performed the methyltransferase assays and cell experiments. B.F., C.C., R.K.M. and M.B.-D. prepared new reagents. B.F., D.P.R. and T.W.M. analyzed the experimental data, and B.F. and T.W.M. wrote the paper.

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Correspondence to Tom W Muir.

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Fierz, B., Chatterjee, C., McGinty, R. et al. Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nat Chem Biol 7, 113–119 (2011). https://doi.org/10.1038/nchembio.501

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