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Intracellular production of hydrogels and synthetic RNA granules by multivalent enhancers

Hideki Nakamura, Albert A. Lee, Ali Sobhi Afshar, Shigeki Watanabe, Elmer Rho, Shiva Razavi, Allison Suarez, Yu-Chun Lin, Makoto Tanigawa, Brian Huang, Robert DeRose, Diana Bobb, William Hong, Sandra B. Gabelli, John Goutsias, Takanari Inoue
doi: https://doi.org/10.1101/117572
Hideki Nakamura
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
2Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 2120
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Albert A. Lee
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
2Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 2120
8Current address: Department of Chemistry, National Taiwan University, Taiwan
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Ali Sobhi Afshar
3Center for Imaging Science, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD, 2121
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  • For correspondence: aas.afshar@gmail.com
Shigeki Watanabe
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
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Elmer Rho
2Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 2120
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Shiva Razavi
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
4Department of Biomedical Engineering, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 2121
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Allison Suarez
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
2Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 2120
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Yu-Chun Lin
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
2Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 2120
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Makoto Tanigawa
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
4Department of Biomedical Engineering, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 2121
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Brian Huang
2Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 2120
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Robert DeRose
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
2Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 2120
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Diana Bobb
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
2Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 2120
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William Hong
5Department of Biophysics and Biophysical Chemistry, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
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Sandra B. Gabelli
5Department of Biophysics and Biophysical Chemistry, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
6Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, 2120
7Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, 2120
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John Goutsias
3Center for Imaging Science, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD, 2121
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Takanari Inoue
1Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, MD, 2120
2Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, MD, 2120
4Department of Biomedical Engineering, Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 2121
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  • For correspondence: ictinoue@ihmi.edu
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Abstract

Non-membrane bound, hydrogel-like entities, such as RNA granules, nucleate essential cellular functions through their unique physico-chemical properties. However, these intracellular hydrogels have not been as extensively studied as their extracellular counterparts, primarily due to technical challenges in probing these materials in situ. Here, by taking advantage of a chemically inducible dimerization paradigm, we developed iPOLYMER, a strategy for rapid induction of protein-based hydrogels inside living cells. A series of biochemical and biophysical characterizations, in conjunction with computational modeling, revealed that the polymer network formed in the cytosol resembles a physiological hydrogel-like entity that behaves as a size-dependent molecular sieve. We studied several properties of the gel and functionalized it with RNA binding motifs that sequester polyadenine-containing nucleotides to synthetically mimic RNA granules. Therefore, we here demonstrate that iPOLYMER presents a unique and powerful approach to synthetically reconstitute hydrogel-like structures including RNA granules in intact cells.

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Posted March 16, 2017.
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Intracellular production of hydrogels and synthetic RNA granules by multivalent enhancers
Hideki Nakamura, Albert A. Lee, Ali Sobhi Afshar, Shigeki Watanabe, Elmer Rho, Shiva Razavi, Allison Suarez, Yu-Chun Lin, Makoto Tanigawa, Brian Huang, Robert DeRose, Diana Bobb, William Hong, Sandra B. Gabelli, John Goutsias, Takanari Inoue
bioRxiv 117572; doi: https://doi.org/10.1101/117572
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Intracellular production of hydrogels and synthetic RNA granules by multivalent enhancers
Hideki Nakamura, Albert A. Lee, Ali Sobhi Afshar, Shigeki Watanabe, Elmer Rho, Shiva Razavi, Allison Suarez, Yu-Chun Lin, Makoto Tanigawa, Brian Huang, Robert DeRose, Diana Bobb, William Hong, Sandra B. Gabelli, John Goutsias, Takanari Inoue
bioRxiv 117572; doi: https://doi.org/10.1101/117572

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