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A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing

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Abstract

Recent studies have implicated the nucleosome acidic patch in the activity of ATP-dependent chromatin remodeling machines. We used a photocrosslinking-based nucleosome profiling technology (photoscanning) to identify a conserved basic motif within the catalytic subunit of ISWI remodelers, SNF2h, which engages this nucleosomal epitope. This region of SNF2h is essential for chromatin remodeling activity in a reconstituted biochemical system and in cells. Our studies suggest that the basic motif in SNF2h plays a critical role in anchoring the remodeler to the nucleosomal surface. We also examine the functional consequences of several cancer-associated histone mutations that map to the nucleosome acidic patch. Kinetic studies using physiologically relevant heterotypic nucleosomal substrates (‘Janus’ nucleosomes) indicate that these cancer-associated mutations can disrupt regularly spaced chromatin structure by inducing ISWI-mediated unidirectional nucleosome sliding. These results indicate a potential mechanistic link between oncogenic histones and alterations to the chromatin landscape.

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Fig. 1: Site-directed photocrosslinking strategy used to explore SNF2h engagement with the nucleosome acidic patch.
Fig. 2: Photoscanning of SNF2h reveals a conserved basic motif that interacts with the nucleosome acidic patch.
Fig. 3: The APB motif is required for SNF2h-mediated nucleosome remodeling.
Fig. 4: The APB motif is essential for ACF remodeling activity, and yeast viability.
Fig. 5: Nucleosome desymmetrization leads to altered ISWI activity.

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Data availability

The authors declare that data supporting the finding of this study are available within the article and its Supplementary Information. Additional data are available from the corresponding author upon reasonable request.

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Acknowledgements

We thank R. E. Thompson, K. Diehl, J. D. Bagert, K. Jani and other members of the Muir laboratory for valuable discussions. We thank S. Tharan from the Proteomics and Mass Spectrometry core. Yeast strains (YTT 227, YTT 420-424) were a gift from T. Tsukiyama. H.T.D. was funded by a postdoctoral fellowship from the Jane Coffin Childs Memorial fund. This work was supported by the US National Institutes of Health (NIH grant nos. R37-GM086868 and P01-CA196539).

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Author notes

  1. Geoffrey P. Dann

    Present address: Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA

  2. Glen P. Liszczak

    Present address: Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA

Authors and Affiliations

  1. Department of Chemistry, Princeton University, Princeton, NJ, USA

    Hai T. Dao, Barbara E. Dul, Geoffrey P. Dann, Glen P. Liszczak & Tom W. Muir

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Contributions

H.T.D. synthesized the probe and all photoactivable nucleosomes, heterotypic nucleosomes, dinucleosomes, expressed and purified all remodelers, and performed all biochemical experiments. H.T.D. and B.E.D. performed yeast experiments. G.P.D. expressed and purified the Sir3-BAH domain, and assisted with the expression and purification of the ACF complex. G.P.L. expressed and purified RCC1 and mRCC1. H.T.D. and T.W.M. analyzed all data and wrote the manuscript.

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Correspondence to Tom W. Muir.

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Supplementary Tables 3 and 4, Figs. 1–39 and Notes 1 and 2

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Dao, H.T., Dul, B.E., Dann, G.P. et al. A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing. Nat Chem Biol 16, 134–142 (2020). https://doi.org/10.1038/s41589-019-0413-4

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