1
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Gustavsson AK, Ghosh RP, Petrov PN, Liphardt JT, Moerner WE. Fast and parallel nanoscale 3D tracking of heterogeneous mammalian chromatin dynamics. Mol Biol Cell 2022; 33:ar47. [PMID: 35352962 PMCID: PMC9265149 DOI: 10.1091/mbc.e21-10-0514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Chromatin organization and dynamics are critical for gene regulation. In this work we present a methodology for fast and parallel three-dimensional (3D) tracking of multiple chromosomal loci of choice over many thousands of frames on various timescales. We achieved this by developing and combining fluorogenic and replenishable nanobody arrays, engineered point spread functions, and light sheet illumination. The result is gentle live-cell 3D tracking with excellent spatiotemporal resolution throughout the mammalian cell nucleus. Correction for both sample drift and nuclear translation facilitated accurate long-term tracking of the chromatin dynamics. We demonstrate tracking both of fast dynamics (50 Hz) and over timescales extending to several hours, and we find both large heterogeneity between cells and apparent anisotropy in the dynamics in the axial direction. We further quantify the effect of inhibiting actin polymerization on the dynamics and find an overall increase in both the apparent diffusion coefficient D* and anomalous diffusion exponent α and a transition to more-isotropic dynamics in 3D after such treatment. We think that in the future our methodology will allow researchers to obtain a better fundamental understanding of chromatin dynamics and how it is altered during disease progression and after perturbations of cellular function.
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Affiliation(s)
- Anna-Karin Gustavsson
- Department of Chemistry, Stanford University, Stanford, CA, USA.,Department of Chemistry, Rice University, Houston, TX, USA.,Department of Biosciences, Rice University, Houston, TX, USA.,Smalley-Curl Institute, Rice University, Houston, TX, USA.,Institute of Biosciences and Bioengineering, Rice University, Houston, TX, USA
| | - Rajarshi P Ghosh
- Bioengineering, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Petar N Petrov
- Department of Chemistry, Stanford University, Stanford, CA, USA.,Department of Physics, University of California, Berkeley, CA, USA
| | | | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
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2
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Ruijgrok PV, Ghosh RP, Zemsky S, Nakamura M, Gong R, Ning L, Chen R, Vachharajani VT, Chu AE, Anand N, Eguchi RR, Huang PS, Lin MZ, Alushin GM, Liphardt JT, Bryant Z. Optical control of fast and processive engineered myosins in vitro and in living cells. Nat Chem Biol 2021; 17:540-548. [PMID: 33603247 PMCID: PMC10807509 DOI: 10.1038/s41589-021-00740-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. Direct optical control of motor speed and direction is one promising approach, but it remains a challenge to engineer controllable motors with desirable properties such as the speed and processivity required for transport applications in living cells. Here, we develop engineered myosin motors that combine large optical modulation depths with high velocities, and create processive myosin motors with optically controllable directionality. We characterize the performance of the motors using in vitro motility assays, single-molecule tracking and live-cell imaging. Bidirectional processive motors move efficiently toward the tips of cellular protrusions in the presence of blue light, and can transport molecular cargo in cells. Robust gearshifting myosins will further enable programmable transport in contexts ranging from in vitro active matter reconstitutions to microfabricated systems that harness molecular propulsion.
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Affiliation(s)
- Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rajarshi P Ghosh
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
- Howard Hughes Medical Institute, and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sasha Zemsky
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rui Gong
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Lin Ning
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Robert Chen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Vipul T Vachharajani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Alexander E Chu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Namrata Anand
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Raphael R Eguchi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Gregory M Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Jan T Liphardt
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Bio-X Institute, Stanford University, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Northey JJ, Barrett AS, Acerbi I, Hayward MK, Talamantes S, Dean IS, Mouw JK, Ponik SM, Lakins JN, Huang PJ, Wu J, Shi Q, Samson S, Keely PJ, Mukhtar RA, Liphardt JT, Shepherd JA, Hwang ES, Chen YY, Hansen KC, Littlepage LE, Weaver VM. Stiff stroma increases breast cancer risk by inducing the oncogene ZNF217. J Clin Invest 2021; 130:5721-5737. [PMID: 32721948 DOI: 10.1172/jci129249] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/14/2020] [Indexed: 12/14/2022] Open
Abstract
Women with dense breasts have an increased lifetime risk of malignancy that has been attributed to a higher epithelial density. Quantitative proteomics, collagen analysis, and mechanical measurements in normal tissue revealed that stroma in the high-density breast contains more oriented, fibrillar collagen that is stiffer and correlates with higher epithelial cell density. microRNA (miR) profiling of breast tissue identified miR-203 as a matrix stiffness-repressed transcript that is downregulated by collagen density and reduced in the breast epithelium of women with high mammographic density. Culture studies demonstrated that ZNF217 mediates a matrix stiffness- and collagen density-induced increase in Akt activity and mammary epithelial cell proliferation. Manipulation of the epithelium in a mouse model of mammographic density supported a causal relationship between stromal stiffness, reduced miR-203, higher levels of the murine homolog Zfp217, and increased Akt activity and mammary epithelial proliferation. ZNF217 was also increased in the normal breast epithelium of women with high mammographic density, correlated positively with epithelial proliferation and density, and inversely with miR-203. The findings identify ZNF217 as a potential target toward which preexisting therapies, such as the Akt inhibitor triciribine, could be used as a chemopreventive agent to reduce cancer risk in women with high mammographic density.
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Affiliation(s)
- Jason J Northey
- Department of Surgery.,Center for Bioengineering and Tissue Regeneration, UCSF, San Francisco, California, USA
| | - Alexander S Barrett
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Irene Acerbi
- Department of Surgery.,Center for Bioengineering and Tissue Regeneration, UCSF, San Francisco, California, USA
| | - Mary-Kate Hayward
- Department of Surgery.,Center for Bioengineering and Tissue Regeneration, UCSF, San Francisco, California, USA
| | - Stephanie Talamantes
- Department of Surgery.,Center for Bioengineering and Tissue Regeneration, UCSF, San Francisco, California, USA
| | - Ivory S Dean
- Department of Surgery.,Center for Bioengineering and Tissue Regeneration, UCSF, San Francisco, California, USA
| | - Janna K Mouw
- Department of Surgery.,Center for Bioengineering and Tissue Regeneration, UCSF, San Francisco, California, USA
| | - Suzanne M Ponik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jonathon N Lakins
- Department of Surgery.,Center for Bioengineering and Tissue Regeneration, UCSF, San Francisco, California, USA
| | - Po-Jui Huang
- Department of Surgery.,Center for Bioengineering and Tissue Regeneration, UCSF, San Francisco, California, USA
| | - Junmin Wu
- Harper Cancer Research Institute, Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, Indiana, USA
| | - Quanming Shi
- Department of Bioengineering, Stanford University, Palo Alto, California, USA
| | - Susan Samson
- Helen Diller Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Patricia J Keely
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Jan T Liphardt
- Department of Bioengineering, Stanford University, Palo Alto, California, USA
| | - John A Shepherd
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, University of Hawaii at Manoa, Manoa, Hawaii, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Yunn-Yi Chen
- Department of Pathology, UCSF, San Francisco, California, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA.,Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Laurie E Littlepage
- Harper Cancer Research Institute, Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, Indiana, USA
| | - Valerie M Weaver
- Department of Surgery.,Center for Bioengineering and Tissue Regeneration, UCSF, San Francisco, California, USA.,Helen Diller Comprehensive Cancer Center, UCSF, San Francisco, California, USA.,Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, University of Hawaii at Manoa, Manoa, Hawaii, USA.,Radiation Oncology, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
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4
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Abstract
Yes-associated protein 1 (YAP) is a transcriptional regulator with critical roles in mechanotransduction, organ size control, and regeneration. Here, using advanced tools for real-time visualization of native YAP and target gene transcription dynamics, we show that a cycle of fast exodus of nuclear YAP to the cytoplasm followed by fast reentry to the nucleus ("localization-resets") activates YAP target genes. These "resets" are induced by calcium signaling, modulation of actomyosin contractility, or mitosis. Using nascent-transcription reporter knock-ins of YAP target genes, we show a strict association between these resets and downstream transcription. Oncogenically-transformed cell lines lack localization-resets and instead show dramatically elevated rates of nucleocytoplasmic shuttling of YAP, suggesting an escape from compartmentalization-based control. The single-cell localization and transcription traces suggest that YAP activity is not a simple linear function of nuclear enrichment and point to a model of transcriptional activation based on nucleocytoplasmic exchange properties of YAP.
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Affiliation(s)
- J Matthew Franklin
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
- Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Rajarshi P Ghosh
- Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- BioX Institute, Stanford University, Stanford, CA, 94305, USA.
- ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA.
| | - Quanming Shi
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Michael P Reddick
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
- Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Jan T Liphardt
- Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- BioX Institute, Stanford University, Stanford, CA, 94305, USA.
- ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA.
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5
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Yang L, Ghosh RP, Franklin JM, Chen S, You C, Narayan RR, Melcher ML, Liphardt JT. NuSeT: A deep learning tool for reliably separating and analyzing crowded cells. PLoS Comput Biol 2020; 16:e1008193. [PMID: 32925919 PMCID: PMC7515182 DOI: 10.1371/journal.pcbi.1008193] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 09/24/2020] [Accepted: 07/25/2020] [Indexed: 01/30/2023] Open
Abstract
Segmenting cell nuclei within microscopy images is a ubiquitous task in biological research and clinical applications. Unfortunately, segmenting low-contrast overlapping objects that may be tightly packed is a major bottleneck in standard deep learning-based models. We report a Nuclear Segmentation Tool (NuSeT) based on deep learning that accurately segments nuclei across multiple types of fluorescence imaging data. Using a hybrid network consisting of U-Net and Region Proposal Networks (RPN), followed by a watershed step, we have achieved superior performance in detecting and delineating nuclear boundaries in 2D and 3D images of varying complexities. By using foreground normalization and additional training on synthetic images containing non-cellular artifacts, NuSeT improves nuclear detection and reduces false positives. NuSeT addresses common challenges in nuclear segmentation such as variability in nuclear signal and shape, limited training sample size, and sample preparation artifacts. Compared to other segmentation models, NuSeT consistently fares better in generating accurate segmentation masks and assigning boundaries for touching nuclei.
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Affiliation(s)
- Linfeng Yang
- Bioengineering, Stanford University, Stanford, CA, United States of America
- BioX Institute, Stanford University, Stanford, CA, United States of America
- ChEM-H, Stanford University, Stanford, CA, United States of America
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, United States of America
| | - Rajarshi P. Ghosh
- Bioengineering, Stanford University, Stanford, CA, United States of America
- BioX Institute, Stanford University, Stanford, CA, United States of America
- ChEM-H, Stanford University, Stanford, CA, United States of America
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, United States of America
| | - J. Matthew Franklin
- Bioengineering, Stanford University, Stanford, CA, United States of America
- BioX Institute, Stanford University, Stanford, CA, United States of America
- ChEM-H, Stanford University, Stanford, CA, United States of America
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, United States of America
- Chemical Engineering, Stanford University, Stanford, CA, United States of America
| | - Simon Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Chenyu You
- Electrical Engineering, Stanford University, Stanford, CA, United States of America
| | - Raja R. Narayan
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Marc L. Melcher
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Jan T. Liphardt
- Bioengineering, Stanford University, Stanford, CA, United States of America
- BioX Institute, Stanford University, Stanford, CA, United States of America
- ChEM-H, Stanford University, Stanford, CA, United States of America
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, United States of America
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6
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Ghosh RP, Shi Q, Yang L, Reddick MP, Nikitina T, Zhurkin VB, Fordyce P, Stasevich TJ, Chang HY, Greenleaf WJ, Liphardt JT. Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions. Nat Commun 2019; 10:3221. [PMID: 31324780 PMCID: PMC6642133 DOI: 10.1038/s41467-019-11118-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 06/20/2019] [Indexed: 01/12/2023] Open
Abstract
The Satb1 genome organizer regulates multiple cellular and developmental processes. It is not yet clear how Satb1 selects different sets of targets throughout the genome. Here we have used live-cell single molecule imaging and deep sequencing to assess determinants of Satb1 binding-site selectivity. We have found that Satb1 preferentially targets nucleosome-dense regions and can directly bind consensus motifs within nucleosomes. Some genomic regions harbor multiple, regularly spaced Satb1 binding motifs (typical separation ~1 turn of the DNA helix) characterized by highly cooperative binding. The Satb1 homeodomain is dispensable for high affinity binding but is essential for specificity. Finally, we find that Satb1-DNA interactions are mechanosensitive. Increasing negative torsional stress in DNA enhances Satb1 binding and Satb1 stabilizes base unpairing regions against melting by molecular machines. The ability of Satb1 to control diverse biological programs may reflect its ability to combinatorially use multiple site selection criteria.
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Affiliation(s)
- Rajarshi P Ghosh
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Quanming Shi
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Linfeng Yang
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
| | - Michael P Reddick
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- BioX Institute, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA
- Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Tatiana Nikitina
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Polly Fordyce
- Bioengineering, Stanford University, Stanford, CA, 94305, USA
- ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology and the Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Applied Physics, Stanford University, Stanford, United States
| | - Jan T Liphardt
- Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- BioX Institute, Stanford University, Stanford, CA, 94305, USA.
- ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, 94305, USA.
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7
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Ban E, Wang H, Franklin JM, Liphardt JT, Janmey PA, Shenoy VB. Strong triaxial coupling and anomalous Poisson effect in collagen networks. Proc Natl Acad Sci U S A 2019; 116:6790-6799. [PMID: 30894480 PMCID: PMC6452734 DOI: 10.1073/pnas.1815659116] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
While cells within tissues generate and sense 3D states of strain, the current understanding of the mechanics of fibrous extracellular matrices (ECMs) stems mainly from uniaxial, biaxial, and shear tests. Here, we demonstrate that the multiaxial deformations of fiber networks in 3D cannot be inferred solely based on these tests. The interdependence of the three principal strains gives rise to anomalous ratios of biaxial to uniaxial stiffness between 8 and 9 and apparent Poisson's ratios larger than 1. These observations are explained using a microstructural network model and a coarse-grained constitutive framework that predicts the network Poisson effect and stress-strain responses in uniaxial, biaxial, and triaxial modes of deformation as a function of the microstructural properties of the network, including fiber mechanics and pore size of the network. Using this theoretical approach, we found that accounting for the Poisson effect leads to a 100-fold increase in the perceived elastic stiffness of thin collagen samples in extension tests, reconciling the seemingly disparate measurements of the stiffness of collagen networks using different methods. We applied our framework to study the formation of fiber tracts induced by cellular forces. In vitro experiments with low-density networks showed that the anomalous Poisson effect facilitates higher densification of fibrous tracts, associated with the invasion of cancerous acinar cells. The approach developed here can be used to model the evolving mechanics of ECM during cancer invasion and fibrosis.
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Affiliation(s)
- Ehsan Ban
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA 19104
- Department of Materials Science and Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104
| | - Hailong Wang
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA 19104
- Department of Materials Science and Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104
- Department of Modern Mechanics, Chinese Academy of Sciences Key Laboratory of Mechanical Behavior and Design of Materials, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - J Matthew Franklin
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
| | - Jan T Liphardt
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
| | - Paul A Janmey
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA 19104
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104
| | - Vivek B Shenoy
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Materials Science and Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104
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8
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Ghosh RP, Franklin JM, Draper WE, Shi Q, Beltran B, Spakowitz AJ, Liphardt JT. A fluorogenic array for temporally unlimited single-molecule tracking. Nat Chem Biol 2019; 15:401-409. [PMID: 30858596 DOI: 10.1038/s41589-019-0241-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/29/2019] [Indexed: 12/15/2022]
Abstract
We describe three optical tags, ArrayG, ArrayD and ArrayG/N, for intracellular tracking of single molecules over milliseconds to hours. ArrayG is a fluorogenic tag composed of a green fluorescent protein-nanobody array and monomeric wild-type green fluorescent protein binders that are initially dim but brighten ~26-fold on binding with the array. By balancing the rates of binder production, photobleaching and stochastic binder exchange, we achieve temporally unlimited tracking of single molecules. High-speed tracking of ArrayG-tagged kinesins and integrins for thousands of frames reveals novel dynamical features. Tracking of single histones at 0.5 Hz for >1 hour with the import competent ArrayG/N tag shows that chromosomal loci behave as Rouse polymers with visco-elastic memory and exhibit a non-Gaussian displacement distribution. ArrayD, based on a dihydrofolate reductase nanobody array and dihydrofolate reductase-fluorophore binder, enables dual-color imaging. The arrays combine brightness, fluorogenicity, fluorescence replenishment and extended fluorophore choice, opening new avenues for tracking single molecules in living cells.
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Affiliation(s)
- Rajarshi P Ghosh
- Bioengineering, Stanford University, Stanford, CA, USA.,BioX Institute, Stanford University, Stanford, CA, USA.,ChEM-H, Stanford University, Stanford, CA, USA.,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | - J Matthew Franklin
- Bioengineering, Stanford University, Stanford, CA, USA.,BioX Institute, Stanford University, Stanford, CA, USA.,ChEM-H, Stanford University, Stanford, CA, USA.,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA.,Biophysics, Stanford University, Stanford, CA, USA
| | - Will E Draper
- Bioengineering, Stanford University, Stanford, CA, USA.,BioX Institute, Stanford University, Stanford, CA, USA.,ChEM-H, Stanford University, Stanford, CA, USA.,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | - Quanming Shi
- Bioengineering, Stanford University, Stanford, CA, USA.,BioX Institute, Stanford University, Stanford, CA, USA.,ChEM-H, Stanford University, Stanford, CA, USA.,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | | | - Andrew J Spakowitz
- BioX Institute, Stanford University, Stanford, CA, USA.,Chemical Engineering, Stanford University, Stanford, CA, USA.,Applied Physics, Stanford University, Stanford, CA, USA.,Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Jan T Liphardt
- Bioengineering, Stanford University, Stanford, CA, USA. .,BioX Institute, Stanford University, Stanford, CA, USA. .,ChEM-H, Stanford University, Stanford, CA, USA. .,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA.
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9
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Ruijgrok PV, Ghosh RP, Nakamura M, Zemsky S, Chen R, Vachharajani V, Liphardt JT, Bryant Z. Optical Control of Fast and Processive Engineered Myosins In Vitro and in Living Cells. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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10
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Ban E, Franklin JM, Nam S, Smith LR, Wang H, Wells RG, Chaudhuri O, Liphardt JT, Shenoy VB. Mechanisms of Plastic Deformation in Collagen Networks Induced by Cellular Forces. Biophys J 2018; 114:450-461. [PMID: 29401442 PMCID: PMC5984980 DOI: 10.1016/j.bpj.2017.11.3739] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/11/2017] [Accepted: 11/20/2017] [Indexed: 12/19/2022] Open
Abstract
Contractile cells can reorganize fibrous extracellular matrices and form dense tracts of fibers between neighboring cells. These tracts guide the development of tubular tissue structures and provide paths for the invasion of cancer cells. Here, we studied the mechanisms of the mechanical plasticity of collagen tracts formed by contractile premalignant acinar cells and fibroblasts. Using fluorescence microscopy and second harmonic generation, we quantified the collagen densification, fiber alignment, and strains that remain within the tracts after cellular forces are abolished. We explained these observations using a theoretical fiber network model that accounts for the stretch-dependent formation of weak cross-links between nearby fibers. We tested the predictions of our model using shear rheology experiments. Both our model and rheological experiments demonstrated that increasing collagen concentration leads to substantial increases in plasticity. We also considered the effect of permanent elongation of fibers on network plasticity and derived a phase diagram that classifies the dominant mechanisms of plasticity based on the rate and magnitude of deformation and the mechanical properties of individual fibers. Plasticity is caused by the formation of new cross-links if moderate strains are applied at small rates or due to permanent fiber elongation if large strains are applied over short periods. Finally, we developed a coarse-grained model for plastic deformation of collagen networks that can be employed to simulate multicellular interactions in processes such as morphogenesis, cancer invasion, and fibrosis.
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Affiliation(s)
- Ehsan Ban
- Center for Engineering Mechanobiology, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Materials Science and Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - J Matthew Franklin
- Departments of Bioengineering and Chemical Engineering, Stanford University, Stanford, California
| | - Sungmin Nam
- Department of Mechanical Engineering, Stanford University, Stanford, California
| | - Lucas R Smith
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hailong Wang
- Center for Engineering Mechanobiology, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Materials Science and Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rebecca G Wells
- Center for Engineering Mechanobiology, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, Stanford, California
| | - Jan T Liphardt
- Departments of Bioengineering and Chemical Engineering, Stanford University, Stanford, California
| | - Vivek B Shenoy
- Center for Engineering Mechanobiology, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Materials Science and Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania.
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11
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Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nat Methods 2016; 13:1013-1020. [PMID: 27749837 DOI: 10.1038/nmeth.4031] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/19/2016] [Indexed: 01/10/2023]
Abstract
Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis. Integration of ATAC-see with flow cytometry enables automated quantitation and prospective cell isolation as a function of chromatin accessibility, and it reveals a cell-cycle dependence of chromatin accessibility that is especially dynamic in G1 phase. The integration of imaging and epigenomics provides a general and scalable approach for deciphering the spatiotemporal architecture of gene control.
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Affiliation(s)
- Xingqi Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Ying Shen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Will Draper
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Jason D Buenrostro
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA
| | - Ulrike Litzenburger
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
| | - Rajarshi P Ghosh
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Alexandra East-Seletsky
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, California, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Jan T Liphardt
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA
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12
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Lowe AR, Tang JH, Yassif J, Graf M, Huang WYC, Groves JT, Weis K, Liphardt JT. Importin-β modulates the permeability of the nuclear pore complex in a Ran-dependent manner. eLife 2015; 4. [PMID: 25748139 PMCID: PMC4375889 DOI: 10.7554/elife.04052] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 02/27/2015] [Indexed: 11/13/2022] Open
Abstract
Soluble karyopherins of the importin-β (impβ) family use RanGTP to transport cargos directionally through the nuclear pore complex (NPC). Whether impβ or RanGTP regulate the permeability of the NPC itself has been unknown. In this study, we identify a stable pool of impβ at the NPC. A subpopulation of this pool is rapidly turned-over by RanGTP, likely at Nup153. Impβ, but not transportin-1 (TRN1), alters the pore's permeability in a Ran-dependent manner, suggesting that impβ is a functional component of the NPC. Upon reduction of Nup153 levels, inert cargos more readily equilibrate across the NPC yet active transport is impaired. When purified impβ or TRN1 are mixed with Nup153 in vitro, higher-order, multivalent complexes form. RanGTP dissolves the impβ•Nup153 complexes but not those of TRN1•Nup153. We propose that impβ and Nup153 interact at the NPC's nuclear face to form a Ran-regulated mesh that modulates NPC permeability. DOI:http://dx.doi.org/10.7554/eLife.04052.001 In our cells, genetic material is contained within the nucleus, which is separated from the rest of the cell by a double-layered membrane called the nuclear envelope. Within this membrane there are pores that allow proteins and other molecules to enter and exit the nucleus. Small molecules can pass through these pores unaided, which is known as ‘passive’ transport. However, larger cargos need help from transport receptor proteins in a process called ‘active’ transport. Large cargos bind to transport receptors, such as importin-β, in the cytoplasm and are then guided through the pore. Once the cargo and importin-β are inside the nucleus, a protein called RanGTP binds to importin-β to release the cargo. It is thought that importin-β and RanGTP are only important for the active transport of cargo. Here, Lowe et al. studied how importin-β interacts with the pore. The experiments show that in the absence of RanGTP, importin-β accumulates inside the pore and binds to a protein called Nup153, which is part of the complex of proteins that makes up the pore. However, when RanGTP is present, some of the importin-β is displaced from Nup153 and leaves the pore, which makes it easier for cargo to pass through. Further experiments show that when Nup153 and importin-β are mixed, they associate into a gel-like material that can be ‘melted’ by RanGTP. Lowe et al. propose a model for how RanGTP may control the flow of cargo through the nuclear pore by affecting the binding of importin-β to Nup153. Lowe et al.'s findings suggest that passive and active transport of cargo across the nuclear pore are fundamentally connected and suggest that RanGTP provides the cell with an additional layer of control over nucleocytoplasmic transport. DOI:http://dx.doi.org/10.7554/eLife.04052.002
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Affiliation(s)
- Alan R Lowe
- Institute for Structural and Molecular Biology, University College London and Birkbeck College, London, United Kingdom
| | - Jeffrey H Tang
- Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Jaime Yassif
- Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Michael Graf
- Section of Life Sciences and Technologies, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - William Y C Huang
- Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jay T Groves
- QB3, University of California, Berkeley, Berkeley, United States
| | - Karsten Weis
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jan T Liphardt
- Department of Physics, University of California, Berkeley, Berkeley, United States
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Tang JH, Lowe AR, Yassif J, Graf M, Huang WY, Groves JT, Weis K, Liphardt JT. A Ran-Dependent Importin-Beta/Nup153 Barrier in the Nuclear Pore Complex. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Andersen KR, Onischenko E, Tang JH, Kumar P, Chen JZ, Ulrich A, Liphardt JT, Weis K, Schwartz TU. Scaffold nucleoporins Nup188 and Nup192 share structural and functional properties with nuclear transport receptors. eLife 2013; 2:e00745. [PMID: 23795296 PMCID: PMC3679522 DOI: 10.7554/elife.00745] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/08/2013] [Indexed: 02/07/2023] Open
Abstract
Nucleocytoplasmic transport is mediated by nuclear pore complexes (NPCs) embedded in the nuclear envelope. About 30 different proteins (nucleoporins, nups) arrange around a central eightfold rotational axis to build the modular NPC. Nup188 and Nup192 are related and evolutionary conserved, large nucleoporins that are part of the NPC scaffold. Here we determine the structure of Nup188. The protein folds into an extended stack of helices where an N-terminal 130 kDa segment forms an intricate closed ring, while the C-terminal region is a more regular, superhelical structure. Overall, the structure has distant similarity with flexible S-shaped nuclear transport receptors (NTRs). Intriguingly, like NTRs, both Nup188 and Nup192 specifically bind FG-repeats and are able to translocate through NPCs by facilitated diffusion. This blurs the existing dogma of a clear distinction between stationary nups and soluble NTRs and suggests an evolutionary relationship between the NPC and the soluble nuclear transport machinery. DOI:http://dx.doi.org/10.7554/eLife.00745.001 The nucleus of a cell is surrounded by a two-layered membrane that controls the flow of molecules from the cytoplasm into the nucleus and vice versa. The molecular traffic between the cytoplasm and nucleus is essentially controlled by nuclear pore complexes—large, multi-protein structures that are embedded in the membrane. Each nuclear pore complex contains about 30 different proteins called nucleoporins or nups, which combine to form a structure with a central pore that allows the molecules to enter and leave the nucleus. The centre of the nuclear pore complex is thought to be filled with protein filaments that contain a large number of so-called FG repeats (where F and G are the amino acids phenylalanine and glycine). Specialized molecules called soluble nuclear transport receptors, which carry various cargoes between the cytoplasm and nucleus, can bind to these FG repeats, and the interaction between the receptors and the FG repeats is crucial for the selective transport of molecules between the cytoplasm and the nucleus. The large size of the nuclear pore complex has hindered efforts to work out its structure, but in recent years researchers have been able to obtain structures for many individual nups and their subcomplexes. Now, Andersen et al. have determined the structure of one of the largest nups, Nup188. This has led to the discovery that it and a related nup, Nup192, share unexpected features with soluble nuclear transport receptors. In general the first step when attempting to determine the structure of a biomolecule is to form a crystal. Since full-length Nup188 did not crystallize, Andersen et al. instead crystallized two large fragments of Nup188, determined the structures of these fragments, and then combined these to produce the likely structure of the full-length protein. They found that Nup188 has a structure that consists of stacked helices and is more flexible than other nups. Moreover, its structure was very similar to those of soluble nuclear transport receptors, and this led Andersen et al. to investigate whether Nup188 also had similar functional features. Surprisingly, they discovered that both Nup188 and Nup192 could bind FG repeats, just like nuclear transport receptors. What is more, this binding allowed both nups to travel through nuclear pore complexes in in vitro transport reactions. These findings have implications for the understanding of the organization and function of FG-repeats and suggest that the stationary elements of the nuclear pore complex and soluble nuclear transport receptors are evolutionarily related. DOI:http://dx.doi.org/10.7554/eLife.00745.002
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Affiliation(s)
- Kasper R Andersen
- Department of Biology , Massachusetts Institute of Technology , Cambridge , United States
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15
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Tang JH, Lowe AR, Yassif JM, Weis K, Liphardt JT. Importin-Beta and Ran Regulate the Passive Permeability Barrier in the Nuclear Pore Complex. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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16
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Paszek MJ, DuFort CC, Rubashkin MG, Davidson MW, Thorn KS, Liphardt JT, Weaver VM. Scanning angle interference microscopy reveals cell dynamics at the nanoscale. Nat Methods 2012; 9:825-7. [PMID: 22751201 PMCID: PMC3454456 DOI: 10.1038/nmeth.2077] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/25/2012] [Indexed: 11/09/2022]
Abstract
Emerging questions in cell biology necessitate nanoscale imaging in live cells. Here we present scanning angle interference microscopy, which is capable of localizing fluorescent objects with nanoscale precision along the optical axis in motile cellular structures. We use this approach to resolve nanotopographical features of the cell membrane and cytoskeleton as well as the temporal evolution, three-dimensional architecture and nanoscale dynamics of focal adhesion complexes.
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Affiliation(s)
- Matthew J. Paszek
- Deparment of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143
- Bay Area Physical Sciences-Oncology Center, University of California, Berkeley, Berkeley CA 94720
| | - Christopher C. DuFort
- Deparment of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143
- Bay Area Physical Sciences-Oncology Center, University of California, Berkeley, Berkeley CA 94720
| | - Matthew G. Rubashkin
- Deparment of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143
- Bay Area Physical Sciences-Oncology Center, University of California, Berkeley, Berkeley CA 94720
| | - Mike W. Davidson
- National High Magnetic Field Laboratory and Department of Biological Science, The Florida State University, Tallahassee, FL 32310
| | - Kurt S. Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
| | - Jan T. Liphardt
- Bay Area Physical Sciences-Oncology Center, University of California, Berkeley, Berkeley CA 94720
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
| | - Valerie M. Weaver
- Deparment of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, CA 94143
- Bay Area Physical Sciences-Oncology Center, University of California, Berkeley, Berkeley CA 94720
- Department of Physics and QB3, University of California, Berkeley, Berkeley, CA 94720; Departments of Anatomy and Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143
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Lowe AR, Siegel J, Kalab P, Siu M, Weis K, Liphardt JT. A Functional Map of the Nuclear Pore Complex Via High Precision Tracking of Single Molecules. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.1672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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