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Light-induced nuclear export reveals rapid dynamics of epigenetic modifications

Abstract

We engineered a photoactivatable system for rapidly and reversibly exporting proteins from the nucleus by embedding a nuclear export signal in the LOV2 domain from phototropin 1. Fusing the chromatin modifier Bre1 to the photoswitch, we achieved light-dependent control of histone H2B monoubiquitylation in yeast, revealing fast turnover of the ubiquitin mark. Moreover, this inducible system allowed us to dynamically monitor the status of epigenetic modifications dependent on H2B ubiquitylation.

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Figure 1: Design of the light-inducible nuclear exporter (LINX) and its use with the improved light-inducible dimer (iLID).
Figure 2: Control of gene transcription and histone modifications with LINX.

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Acknowledgements

We would like to thank D. Dickinson for help with C. elegans injections, H. Meriesh for providing a plasmid containing BRE1, and R. Dronamraju and Z.-W. Sun for helpful discussions. Funding: J.E.B. (NIH GM111557), B.K., K.H., B.S. (NIH DA036877), K.H. (GM102924).

Author information

Affiliations

Authors

Contributions

H.Y. and B.K. conceived the project and designed the experiments. H.Y., A.M.L. and S.P.Z. performed the experiments. H.Y., A.M.L., S.P.Z., B.D.S. and B.K. analyzed the results. K.H. and J.E.B. provided reagents and equipment. H.Y. and B.K. wrote the manuscript with input from all authors.

Corresponding author

Correspondence to Brian Kuhlman.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–13, Supplementary Tables 1–4 and Supplementary Note. (PDF 19788 kb)

LINXa3 blue light single activation and reversion in mouse fibroblast cells (IA32)

The appearance and disappearance of a square indicate the area and the time of blue light activation. Scale bar is 50 μm. (MOV 6347 kb)

LINXb3 blue light single activation and reversion in mouse fibroblast cells (IA32)

The appearance and disappearance of a square indicate the area and the time of blue light activation. Scale bar is 50 μm. (MOV 8240 kb)

Two cycles of blue light activation and reversion of LINXa3 in mouse fibroblast cells (IA32)

The appearance and disappearance of a square indicate the area and the time of blue light activation. Scale bar is 100 μm. (MOV 9768 kb)

Two cycles of blue light activation and reversion of LINXb3 in mouse fibroblast cells (IA32)

The appearance and disappearance of a square indicate the area and the time of blue light activation. Scale bar is 50 μm. (MOV 22837 kb)

Activation and reversion of LINXa3 in the C. elegans embryo

Activation is performed on the entire field of view and is indicated with words at the upper left corner. Scale bar is 10 μm. (MOV 14408 kb)

Two cycles of blue light activation and reversion of LINXa3-nano (red color) and iLID-Mito (green color) in mouse fibroblast cells (IA32)

The appearance and disappearance of a square indicate the area and the time of blue light activation. Scale bar is 50 μm. (MOV 28412 kb)

Activation and reversion of LINXa4-Bre1 (green color) in an H2B-mCherry (labels the nucleus in red) yeast strain (Supplementary Table 3)

The appearance and disappearance of a square indicate the area and the time of blue light activation. Scale bar is 10 μm. (MOV 9449 kb)

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Yumerefendi, H., Lerner, A., Zimmerman, S. et al. Light-induced nuclear export reveals rapid dynamics of epigenetic modifications. Nat Chem Biol 12, 399–401 (2016). https://doi.org/10.1038/nchembio.2068

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