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Patange S, Ball DA, Karpova TS, Larson DR. Towards a 'Spot On' Understanding of Transcription in the Nucleus. J Mol Biol 2021; 433:167016. [PMID: 33951451 PMCID: PMC8184600 DOI: 10.1016/j.jmb.2021.167016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022]
Abstract
Regulation of transcription by RNA Polymerase II (RNAPII) is a rapidly evolving area of research. Technological developments in microscopy have revealed insight into the dynamics, structure, and localization of transcription components within single cells. A frequent observation in many studies is the appearance of 'spots' in cell nuclei associated with the transcription process. In this review we highlight studies that characterize the temporal and spatial characteristics of these spots, examine possible pitfalls in interpreting these kind of imaging data, and outline directions where single-cell imaging may advance in ways to further our understanding of transcription regulation.
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Affiliation(s)
- Simona Patange
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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Tau forms oligomeric complexes on microtubules that are distinct from tau aggregates. Proc Natl Acad Sci U S A 2021; 118:2021461118. [PMID: 33952699 DOI: 10.1073/pnas.2021461118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tau is a microtubule-associated protein, which promotes neuronal microtubule assembly and stability. Accumulation of tau into insoluble aggregates known as neurofibrillary tangles (NFTs) is a pathological hallmark of several neurodegenerative diseases. The current hypothesis is that small, soluble oligomeric tau species preceding NFT formation cause toxicity. However, thus far, visualizing the spatial distribution of tau monomers and oligomers inside cells under physiological or pathological conditions has not been possible. Here, using single-molecule localization microscopy, we show that tau forms small oligomers on microtubules ex vivo. These oligomers are distinct from those found in cells exhibiting tau aggregation and could be precursors of aggregated tau in pathology. Furthermore, using an unsupervised shape classification algorithm that we developed, we show that different tau phosphorylation states are associated with distinct tau aggregate species. Our work elucidates tau's nanoscale composition under nonaggregated and aggregated conditions ex vivo.
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 253] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
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| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
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| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
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| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
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| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
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Tenner B, Getz M, Ross B, Ohadi D, Bohrer CH, Greenwald E, Mehta S, Xiao J, Rangamani P, Zhang J. Spatially compartmentalized phase regulation of a Ca 2+-cAMP-PKA oscillatory circuit. eLife 2020; 9:e55013. [PMID: 33201801 PMCID: PMC7671691 DOI: 10.7554/elife.55013] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/07/2020] [Indexed: 01/31/2023] Open
Abstract
Signaling networks are spatiotemporally organized to sense diverse inputs, process information, and carry out specific cellular tasks. In β cells, Ca2+, cyclic adenosine monophosphate (cAMP), and Protein Kinase A (PKA) exist in an oscillatory circuit characterized by a high degree of feedback. Here, we describe a mode of regulation within this circuit involving a spatial dependence of the relative phase between cAMP, PKA, and Ca2+. We show that in mouse MIN6 β cells, nanodomain clustering of Ca2+-sensitive adenylyl cyclases (ACs) drives oscillations of local cAMP levels to be precisely in-phase with Ca2+ oscillations, whereas Ca2+-sensitive phosphodiesterases maintain out-of-phase oscillations outside of the nanodomain. Disruption of this precise phase relationship perturbs Ca2+ oscillations, suggesting the relative phase within an oscillatory circuit can encode specific functional information. This work unveils a novel mechanism of cAMP compartmentation utilized for localized tuning of an oscillatory circuit and has broad implications for the spatiotemporal regulation of signaling networks.
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Affiliation(s)
- Brian Tenner
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of MedicineBaltimoreUnited States
- Department of Pharmacology, University of California, San DiegoLa JollaUnited States
| | - Michael Getz
- Chemical Engineering Graduate Program, University of California, San DiegoLa JollaUnited States
| | - Brian Ross
- Department of Pharmacology, University of California, San DiegoLa JollaUnited States
| | - Donya Ohadi
- Department of Mechanical and Aerospace Engineering, University of California, San DiegoLa JollaUnited States
| | - Christopher H Bohrer
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Eric Greenwald
- Department of Pharmacology, University of California, San DiegoLa JollaUnited States
| | - Sohum Mehta
- Department of Pharmacology, University of California, San DiegoLa JollaUnited States
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Padmini Rangamani
- Chemical Engineering Graduate Program, University of California, San DiegoLa JollaUnited States
- Department of Mechanical and Aerospace Engineering, University of California, San DiegoLa JollaUnited States
| | - Jin Zhang
- Department of Pharmacology, University of California, San DiegoLa JollaUnited States
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
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