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Dynamics and function of compact nucleosome arrays

Nature Structural & Molecular Biology volume 16, pages 938–944 (2009)Cite this article

Abstract

The packaging of eukaryotic DNA into chromatin sterically occludes polymerases, recombinases and repair enzymes. How chromatin structure changes to allow their actions is unknown. We constructed defined fluorescently labeled trinucleosome arrays, allowing analysis of chromatin conformational dynamics via fluorescence resonance energy transfer (FRET). The arrays undergo reversible Mg2+-dependent folding similar to that of longer arrays studied previously. We define two intermediate conformational states in the reversible folding of the nucleosome arrays and characterize the microscopic rate constants. Nucleosome arrays are highly dynamic even when compact, undergoing conformational fluctuations on timescales in the second to microsecond range. Compact states of the arrays allow binding to DNA within the central nucleosome via site exposure. Protein binding can also drive decompaction of the arrays. Thus, our results reveal multiple modes by which spontaneous chromatin fiber dynamics allow for the invasion and action of DNA-processing protein complexes.

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Figure 1: FRET analyses of nucleosome array compaction induced by Mg2+.
Figure 2: FRET analyses of site exposure in mononucleosomes and in nucleosome arrays in the absence of Mg2+.
Figure 3: FRET analyses of site exposure and decompaction for nucleosome arrays in 1 mM Mg2+.
Figure 4: Conformational dynamics of nucleosome arrays.
Figure 5: Minimal kinetic scheme for nucleosome array dynamics in 1 mM Mg2+.

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Acknowledgements

We thank E. Elson (Washington University) and E. Matayoshi (Abbott Laboratories) for access to Zeiss Confocor 2 instruments, on which preliminary FCS experiments were carried out. We thank J. Little (University of Arizona) for the LexA expression plasmid. We thank E. Elson and E. Matayoshi and members of the Widom laboratory for discussions, K. Swinger (Northwestern University) for help with the trinucleosome structure figures and the Keck Biophysics and Biological Imaging Facilities at Northwestern University for the use of instruments. M.G.P. acknowledges support from US National Institutes of Health postdoctoral fellowship F32 GM072306 and a Career Award in the Biomedical Sciences from the Burroughs-Wellcome Fund. J.W. acknowledges research support from US National Institutes of Health grants R01 GM54692 and R01 GM58617.

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  1. Michael G Poirier

    Present address: Present address: Department of Physics, The Ohio State University, Columbus, Ohio, USA.,

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  1. Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois, USA

    Michael G Poirier, Eugene Oh, Hannah S Tims & Jonathan Widom

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M.G.P. designed, executed and interpreted experiments and wrote some of the paper; E.O. designed, executed and interpreted experiments; H.S.T. designed, executed and interpreted experiments; J.W. designed and interpreted experiments and wrote some of the paper.

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Correspondence to Michael G Poirier or Jonathan Widom.

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Poirier, M., Oh, E., Tims, H. et al. Dynamics and function of compact nucleosome arrays. Nat Struct Mol Biol 16, 938–944 (2009). https://doi.org/10.1038/nsmb.1650

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