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Ames A, Seman M, Larkin A, Raiymbek G, Chen Z, Levashkevich A, Kim B, Biteen JS, Ragunathan K. Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein 1. bioRxiv 2024:2023.11.28.569027. [PMID: 38077059 PMCID: PMC10705379 DOI: 10.1101/2023.11.28.569027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
HP1 proteins are essential for establishing and maintaining transcriptionally silent heterochromatin. They dimerize, forming a binding interface to recruit diverse chromatin-associated factors. HP1 proteins are specialized and rapidly evolve, but the extent of variation required to achieve functional specialization is unknown. To investigate how changes in amino acid sequence impacts epigenetic inheritance, we performed a targeted mutagenesis screen of the S. pombe HP1 homolog, Swi6. Substitutions within an auxiliary surface adjacent to the HP1 dimerization interface produced Swi6 variants with divergent maintenance properties. Remarkably, substitutions at a single amino acid position led to the persistent gain or loss of epigenetic inheritance. These substitutions increased Swi6 chromatin occupancy in vivo and altered Swi6-protein interactions that reprogram H3K9me maintenance. We show that relatively minor changes in Swi6 amino acid composition can lead to profound changes in epigenetic inheritance which provides a redundant mechanism to evolve novel effector specificity. .
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2
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Schlissel G, Meziane M, Narducci D, Hansen AS, Li P. Diffusion barriers imposed by tissue topology shape morphogen gradients. bioRxiv 2024:2024.05.01.592050. [PMID: 38746265 PMCID: PMC11092646 DOI: 10.1101/2024.05.01.592050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Animals use a small number of morphogens to pattern tissues, but it is unclear how evolution modulates morphogen signaling range to match tissues of varying sizes. Here, we used single molecule imaging in reconstituted morphogen gradients and in tissue explants to determine that Hedgehog diffused extra-cellularly as a monomer, and rapidly transitioned between membrane-confined and -unconfined states. Unexpectedly, the vertebrate-specific protein SCUBE1 expanded Hedgehog gradients by accelerating the transition rates between states without affecting the relative abundance of molecules in each state. This observation could not be explained under existing models of morphogen diffusion. Instead, we developed a topology-limited diffusion model in which cell-cell gaps create diffusion barriers, and morphogens can only overcome the barrier by passing through a membrane-unconfined state. Under this model, SCUBE1 promotes Hedgehog secretion and diffusion by allowing it to transiently overcome diffusion barriers. This multiscale understanding of morphogen gradient formation unified prior models and discovered novel knobs that nature can use to tune morphogen gradient sizes across tissues and organisms.
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3
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Mukherjee A, Fallacaro S, Ratchasanmuang P, Zinski J, Boka A, Shankta K, Mir M. A fine kinetic balance of interactions directs transcription factor hubs to genes. bioRxiv 2024:2024.04.16.589811. [PMID: 38659757 PMCID: PMC11042322 DOI: 10.1101/2024.04.16.589811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Eukaryotic gene regulation relies on the binding of sequence-specific transcription factors (TFs). TFs bind chromatin transiently yet occupy their target sites by forming high-local concentration microenvironments (hubs and condensates) that increase the frequency of binding events. Despite their ubiquity, such microenvironments have been difficult to study in endogenous contexts due to technical limitations. Here, we overcome these limitations and investigate how hubs drive TF occupancy at their targets. Using a DNA binding perturbation to a hub-forming TF, Zelda, in Drosophila embryos, we find that hub properties, including the stability and frequencies of associations to targets, are key determinants of TF occupancy. Our data suggest that the targeting of these hubs is driven not just by specific DNA motif recognition, but also by a fine-tuned kinetic balance of interactions between TFs and their co-binding partners.
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Affiliation(s)
- Apratim Mukherjee
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Samantha Fallacaro
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Developmental, Stem Cell, and Regenerative Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Puttachai Ratchasanmuang
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Howard Hughes Medical Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Joseph Zinski
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Alan Boka
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kareena Shankta
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Roy and Diana Vagelos Program in Life Sciences and Management, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Howard Hughes Medical Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
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4
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Ling YH, Ye Z, Liang C, Yu C, Park G, Corden JL, Wu C. Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets. Nat Cell Biol 2024; 26:581-592. [PMID: 38548891 DOI: 10.1038/s41556-024-01382-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/01/2023] [Accepted: 02/21/2024] [Indexed: 04/09/2024]
Abstract
Efficient gene expression requires RNA polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in three-dimensional nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. In the present study, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is required for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation and reduces transcription bursting. The present study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression.
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Affiliation(s)
- Yick Hin Ling
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Ziyang Ye
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Chloe Liang
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Chuofan Yu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Giho Park
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffry L Corden
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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5
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Hayward-Lara G, Fischer MD, Mir M. Dynamic microenvironments shape nuclear organization and gene expression. Curr Opin Genet Dev 2024; 86:102177. [PMID: 38461773 DOI: 10.1016/j.gde.2024.102177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Live imaging has revealed that the regulation of gene expression is largely driven by transient interactions. For example, many regulatory proteins bind chromatin for just seconds, and loop-like genomic contacts are rare and last only minutes. These discoveries have been difficult to reconcile with our canonical models that are predicated on stable and hierarchical interactions. Proteomic microenvironments that concentrate nuclear factors may explain how brief interactions can still mediate gene regulation by creating conditions where reactions occur more frequently. Here, we summarize new imaging technologies and recent discoveries implicating microenvironments as a potential driver of nuclear function. Finally, we propose that key properties of proteomic microenvironments, such as their size, enrichment, and lifetimes, are directly linked to regulatory function.
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Affiliation(s)
- Gabriela Hayward-Lara
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Developmental, Stem Cell, and Regenerative Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. https://twitter.com/@GHaywardLara
| | - Matthew D Fischer
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Howard Hughes Medical Institute, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. https://twitter.com/@MustafaMir16
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6
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Ferrie JJ, Karr JP, Graham TGW, Dailey GM, Zhang G, Tjian R, Darzacq X. p300 is an obligate integrator of combinatorial transcription factor inputs. Mol Cell 2024; 84:234-243.e4. [PMID: 38159566 DOI: 10.1016/j.molcel.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/15/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Transcription coactivators are proteins or protein complexes that mediate transcription factor (TF) function. However, they lack DNA-binding capacity, prompting the question of how they engage target loci. Three non-exclusive hypotheses have been posited: coactivators are recruited by complexing with TFs, by binding histones through epigenetic reader domains, or by partitioning into condensates through their extensive intrinsically disordered regions. Using p300 as a prototypical coactivator, we systematically mutated its annotated domains and show by single-molecule tracking in live U2OS cells that coactivator-chromatin binding depends entirely on combinatorial binding of multiple TF-interaction domains. Furthermore, we demonstrate that acetyltransferase activity opposes p300-chromatin association and that the N-terminal TF-interaction domains regulate that activity. Single TF-interaction domains are insufficient for chromatin binding and regulation of catalytic activity, implying a principle that we speculate could broadly apply to eukaryotic gene regulation: a TF must act in coordination with other TFs to recruit coactivator activity.
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Affiliation(s)
- John J Ferrie
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan P Karr
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas G W Graham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gloria Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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7
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Zhang Y, Ge F, Lin X, Xue J, Song Y, Xie H, He Y. Extract latent features of single-particle trajectories with historical experience learning. Biophys J 2023; 122:4451-4466. [PMID: 37885178 PMCID: PMC10698327 DOI: 10.1016/j.bpj.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/30/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Single-particle tracking has enabled real-time, in situ quantitative studies of complex systems. However, inferring dynamic state changes from noisy and undersampling trajectories encounters challenges. Here, we introduce a data-driven method for extracting features of subtrajectories with historical experience learning (Deep-SEES), where a single-particle tracking analysis pipeline based on a self-supervised architecture automatically searches for the latent space, allowing effective segmentation of the underlying states from noisy trajectories without prior knowledge on the particle dynamics. We validated our method on a variety of noisy simulated and experimental data. Our results showed that the method can faithfully capture both stable states and their dynamic switch. In highly random systems, our method outperformed commonly used unsupervised methods in inferring motion states, which is important for understanding nanoparticles interacting with living cell membranes, active enzymes, and liquid-liquid phase separation. Self-generating latent features of trajectories could potentially improve the understanding, estimation, and prediction of many complex systems.
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Affiliation(s)
- Yongyu Zhang
- Department of Chemistry, Tsinghua University, Beijing, P.R. China
| | - Feng Ge
- Department of Chemistry, Tsinghua University, Beijing, P.R. China
| | - Xijian Lin
- Department of Chemistry, Tsinghua University, Beijing, P.R. China
| | - Jianfeng Xue
- Department of Chemistry, Tsinghua University, Beijing, P.R. China
| | - Yuxin Song
- Department of Chemistry, Tsinghua University, Beijing, P.R. China
| | - Hao Xie
- Department of Automation, Tsinghua University, Beijing, P.R. China.
| | - Yan He
- Department of Chemistry, Tsinghua University, Beijing, P.R. China.
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8
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Svensson CM, Reglinski K, Schliebs W, Erdmann R, Eggeling C, Figge MT. Quantitative analysis of peroxisome tracks using a Hidden Markov Model. Sci Rep 2023; 13:19694. [PMID: 37951993 PMCID: PMC10640649 DOI: 10.1038/s41598-023-46812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 09/07/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
Diffusion and mobility are essential for cellular functions, as molecules are usually distributed throughout the cell and have to meet to interact and perform their function. This also involves the cytosolic migration of cellular organelles. However, observing such diffusion and interaction dynamics is challenging due to the high spatial and temporal resolution required and the accurate analysis of the diffusional tracks. The latter is especially important when identifying anomalous diffusion events, such as directed motions, which are often rare. Here, we investigate the migration modes of peroxisome organelles in the cytosol of living cells. Peroxisomes predominantly migrate randomly, but occasionally they bind to the cell's microtubular network and perform directed migration, which is difficult to quantify, and so far, accurate analysis of switching between these migration modes is missing. We set out to solve this limitation by experiments and analysis with high statistical accuracy. Specifically, we collect temporal diffusion tracks of thousands of individual peroxisomes in the HEK 293 cell line using two-dimensional spinning disc fluorescence microscopy at a high acquisition rate of 10 frames/s. We use a Hidden Markov Model with two hidden states to (1) automatically identify directed migration segments of the tracks and (2) quantify the migration properties for comparison between states and between different experimental conditions. Comparing different cellular conditions, we show that the knockout of the peroxisomal membrane protein PEX14 leads to a decrease in the directed movement due to a lowered binding probability to the microtubule. However, it does not eradicate binding, highlighting further microtubule-binding mechanisms of peroxisomes than via PEX14. In contrast, structural changes of the microtubular network explain perceived eradication of directed movement by disassembly of microtubules by Nocodazole-treatment.
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Affiliation(s)
- Carl-Magnus Svensson
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Katharina Reglinski
- Leibniz-Institute of Photonic Technologies, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- University Hospital Jena, Jena, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Christian Eggeling
- Leibniz-Institute of Photonic Technologies, Jena, Germany.
- Institute of Applied Optics and Biophysics, Friedrich-Schiller University Jena, Jena, Germany.
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Jena Center for Soft Matter (JCSM), Jena, Germany.
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich-Schiller University Jena, Jena, Germany.
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9
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Chen Z, Seman M, Farhat A, Fyodorova Y, Biswas S, Levashkevich A, Freddolino PL, Biteen JS, Ragunathan K. Tracking live-cell single-molecule dynamics enables measurements of heterochromatinassociated protein-protein interactions. bioRxiv 2023:2023.03.08.531771. [PMID: 36945633 PMCID: PMC10028927 DOI: 10.1101/2023.03.08.531771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression. Here, we extended live-cell single-molecule tracking studies in fission yeast to determine how HP1 proteins interact with their binding partners in the nucleus. We measured how genetic perturbations that affect H3K9me alter the diffusive properties of HP1 proteins and each of their binding partners based on which we inferred their most likely interaction sites. Our results indicate that H3K9me promotes specific complex formation between HP1 proteins and their interactors in a spatially restricted manner, while attenuating their ability to form off-chromatin complexes. As opposed to being an inert platform or scaffold to direct HP1 binding, our studies propose a novel function for H3K9me as an active participant in enhancing HP1-associated complex formation in living cells.
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Affiliation(s)
- Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104 USA
| | - Melissa Seman
- Department of Biology, Brandeis University, Waltham, MA 02451 USA
| | - Ali Farhat
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Saikat Biswas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48104 USA
- Current address: Pacific Biosciences, Menlo Park, CA 94025, USA
| | | | - P. Lydia Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48104 USA
| | - Julie S. Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104 USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48104 USA
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10
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Dahal L, Graham TGW, Dailey GM, Heckert A, Tjian R, Darzacq X. Surprising Features of Nuclear Receptor Interaction Networks Revealed by Live Cell Single Molecule Imaging. bioRxiv 2023:2023.09.16.558083. [PMID: 37745337 PMCID: PMC10516011 DOI: 10.1101/2023.09.16.558083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Type 2 Nuclear Receptors (T2NRs) require heterodimerization with a common partner, the Retinoid X Receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and over-expression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged retinoid X receptor (RXR) and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
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Affiliation(s)
- Liza Dahal
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Thomas GW Graham
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Alec Heckert
- Eikon Therapeutics Inc., Hayward, California, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
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11
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Zhou J, Cattoglio C, Shao Y, Tirumala HP, Vetralla C, Bajikar SS, Li Y, Chen H, Wang Q, Wu Z, Tang B, Zahabiyon M, Bajic A, Meng X, Ferrie JJ, LaGrone A, Zhang P, Kim JJ, Tang J, Liu Z, Darzacq X, Heintz N, Tjian R, Zoghbi HY. A novel pathogenic mutation of MeCP2 impairs chromatin association independent of protein levels. Genes Dev 2023; 37:883-900. [PMID: 37890975 PMCID: PMC10691473 DOI: 10.1101/gad.350733.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 04/20/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023]
Abstract
Loss-of-function mutations in MECP2 cause Rett syndrome (RTT), a severe neurological disorder that mainly affects girls. Mutations in MECP2 do occur in males occasionally and typically cause severe encephalopathy and premature lethality. Recently, we identified a missense mutation (c.353G>A, p.Gly118Glu [G118E]), which has never been seen before in MECP2, in a young boy who suffered from progressive motor dysfunction and developmental delay. To determine whether this variant caused the clinical symptoms and study its functional consequences, we established two disease models, including human neurons from patient-derived iPSCs and a knock-in mouse line. G118E mutation partially reduces MeCP2 abundance and its DNA binding, and G118E mice manifest RTT-like symptoms seen in the patient, affirming the pathogenicity of this mutation. Using live-cell and single-molecule imaging, we found that G118E mutation alters MeCP2's chromatin interaction properties in live neurons independently of its effect on protein levels. Here we report the generation and characterization of RTT models of a male hypomorphic variant and reveal new insight into the mechanism by which this pathological mutation affects MeCP2's chromatin dynamics. Our ability to quantify protein dynamics in disease models lays the foundation for harnessing high-resolution single-molecule imaging as the next frontier for developing innovative therapies for RTT and other diseases.
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Affiliation(s)
- Jian Zhou
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Yingyao Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Harini P Tirumala
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Carlo Vetralla
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
- School of Medicine and Surgery, University of Milan-Bicocca, Milano 20126, Italy
| | - Sameer S Bajikar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Yan Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Hu Chen
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Qi Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhenyu Wu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bing Tang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mahla Zahabiyon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Aleksandar Bajic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
| | - Xiangling Meng
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jack J Ferrie
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Anel LaGrone
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ping Zhang
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jean J Kim
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jianrong Tang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
| | - Nathaniel Heintz
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine (CIRM) Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA;
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
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12
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Royer CA, Tyers M, Tollis S. Absolute quantification of protein number and dynamics in single cells. Curr Opin Struct Biol 2023; 82:102673. [PMID: 37595512 DOI: 10.1016/j.sbi.2023.102673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/07/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023]
Abstract
Quantitative characterization of protein abundance and interactions in live cells is necessary to understand and predict cellular behavior. The accurate determination of copy number for individual proteins and heterologous complexes in individual cells is critical because small changes in protein dosage, often less than two-fold, can have strong phenotypic consequences. Here, we review the merits and pitfalls of different quantitative fluorescence imaging methods for single-cell determination of protein abundance, localization, interactions, and dynamics. In particular, we discuss how scanning number and brightness (sN&B) and its variation, Raster scanning image correlation spectroscopy (RICS), exploit stochastic noise in small measurement volumes to quantify protein abundance, stoichiometry, and dynamics with high accuracy.
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Affiliation(s)
- Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy NY 12180, USA.
| | - Mike Tyers
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210 Finland
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13
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Prindle JR, de Cuba OIC, Gahlmann A. Single-molecule tracking to determine the abundances and stoichiometries of freely-diffusing protein complexes in living cells: Past applications and future prospects. J Chem Phys 2023; 159:071002. [PMID: 37589409 PMCID: PMC10908566 DOI: 10.1063/5.0155638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/21/2023] [Accepted: 07/06/2023] [Indexed: 08/18/2023] Open
Abstract
Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein participates in homo- and hetero-oligomeric complexes of different size and subunit composition are therefore critical to advance our understanding of how cellular physiology is governed by these molecular interactions. Biomolecular complex formation changes the diffusion coefficient of constituent proteins, and these changes can be measured using fluorescence microscopy-based approaches, such as single-molecule tracking, fluorescence correlation spectroscopy, and fluorescence recovery after photobleaching. In this review, we focus on the use of single-molecule tracking to identify, resolve, and quantify the presence of freely-diffusing proteins and protein complexes in living cells. We compare and contrast different data analysis methods that are currently employed in the field and discuss experimental designs that can aid the interpretation of the obtained results. Comparisons of diffusion rates for different proteins and protein complexes in intracellular aqueous environments reported in the recent literature reveal a clear and systematic deviation from the Stokes-Einstein diffusion theory. While a complete and quantitative theoretical explanation of why such deviations manifest is missing, the available data suggest the possibility of weighing freely-diffusing proteins and protein complexes in living cells by measuring their diffusion coefficients. Mapping individual diffusive states to protein complexes of defined molecular weight, subunit stoichiometry, and structure promises to provide key new insights into how protein-protein interactions regulate protein conformational, translational, and rotational dynamics, and ultimately protein function.
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Affiliation(s)
- Joshua Robert Prindle
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Olivia Isabella Christiane de Cuba
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, USA
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14
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Collombet S, Rall I, Dugast-Darzacq C, Heckert A, Halavatyi A, Le Saux A, Dailey G, Darzacq X, Heard E. RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization. Nat Struct Mol Biol 2023; 30:1216-1223. [PMID: 37291424 PMCID: PMC10442225 DOI: 10.1038/s41594-023-01008-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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] [Received: 04/15/2021] [Accepted: 04/28/2023] [Indexed: 06/10/2023]
Abstract
Subnuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome in distinct physical and biochemical environments. During X chromosome inactivation (XCI), the noncoding Xist RNA coats the X chromosome, triggers gene silencing and forms a dense body of heterochromatin from which the transcription machinery appears to be excluded. Phase separation has been proposed to be involved in XCI, and might explain the exclusion of the transcription machinery by preventing its diffusion into the Xist-coated territory. Here, using quantitative fluorescence microscopy and single-particle tracking, we show that RNA polymerase II (RNAPII) freely accesses the Xist territory during the initiation of XCI. Instead, the apparent depletion of RNAPII is due to the loss of its chromatin stably bound fraction. These findings indicate that initial exclusion of RNAPII from the inactive X reflects the absence of actively transcribing RNAPII, rather than a consequence of putative physical compartmentalization of the inactive X heterochromatin domain.
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Affiliation(s)
| | - Isabell Rall
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Alec Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Agnes Le Saux
- Curie Institute, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France
| | - Gina Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA.
| | - Edith Heard
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Curie Institute, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France.
- College de France, Paris, France.
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15
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Wagh K, Stavreva DA, Jensen RAM, Paakinaho V, Fettweis G, Schiltz RL, Wüstner D, Mandrup S, Presman DM, Upadhyaya A, Hager GL. Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states. Sci Adv 2023; 9:eade1122. [PMID: 37315128 PMCID: PMC10954219 DOI: 10.1126/sciadv.ade1122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
How chromatin dynamics relate to transcriptional activity remains poorly understood. Using single-molecule tracking, coupled with machine learning, we show that histone H2B and multiple chromatin-bound transcriptional regulators display two distinct low-mobility states. Ligand activation results in a marked increase in the propensity of steroid receptors to bind in the lowest-mobility state. Mutational analysis revealed that interactions with chromatin in the lowest-mobility state require an intact DNA binding domain and oligomerization domains. These states are not spatially separated as previously believed, but individual H2B and bound-TF molecules can dynamically switch between them on time scales of seconds. Single bound-TF molecules with different mobilities exhibit different dwell time distributions, suggesting that the mobility of TFs is intimately coupled with their binding dynamics. Together, our results identify two unique and distinct low-mobility states that appear to represent common pathways for transcription activation in mammalian cells.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Diana A. Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rikke A. M. Jensen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Institute of Biomedicine, University of Eastern Finland, Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - R. Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Diego M. Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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16
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Ferrie JJ, Karr JP, Graham TG, Dailey GM, Zhang G, Tjian R, Darzacq X. p300 Is an Obligate Integrator of Combinatorial Transcription Factor Inputs. bioRxiv 2023:2023.05.18.541220. [PMID: 37292840 PMCID: PMC10245728 DOI: 10.1101/2023.05.18.541220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transcription coactivators are proteins or protein complexes that mediate transcription factor (TF) function. However, they lack DNA binding capacity, prompting the question of how they engage target loci. Three non-exclusive hypotheses have been posited: coactivators are recruited by complexing with TFs, by binding histones through epigenetic reader domains, or by partitioning into phase-separated compartments through their extensive intrinsically disordered regions (IDRs). Using p300 as a prototypical coactivator, we systematically mutated its annotated domains and show by single-molecule tracking in live cells that coactivator-chromatin binding depends entirely on combinatorial binding of multiple TF-interaction domains. Furthermore, we demonstrate that acetyltransferase activity negatively impacts p300-chromatin association and that the N-terminal TF-interaction domains regulate that activity. Single TF-interaction domains are insufficient for both chromatin binding and regulation of catalytic activity, implying a principle that could broadly inform eukaryotic gene regulation: a TF must act in coordination with other TFs to recruit coactivator activity.
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Affiliation(s)
- John J. Ferrie
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jonathan P. Karr
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Thomas G.W. Graham
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Gina M. Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Gloria Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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17
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Dahal L, Walther N, Tjian R, Darzacq X, Graham TGW. Single-molecule tracking (SMT): a window into live-cell transcription biochemistry. Biochem Soc Trans 2023:BST20221242. [PMID: 36876879 DOI: 10.1042/BST20221242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023]
Abstract
How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as a case study, we describe how SMT works, what it can tell us about molecular biology, and how it has changed our perspective on the inner workings of the nucleus. We also describe what SMT cannot yet tell us and how new technical advances seek to overcome its limitations. This ongoing progress will be imperative to address outstanding questions about how dynamic molecular machines function in live cells.
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18
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Ball DA, Jalloh B, Karpova TS. Impact of Saccharomyces cerevisiae on the Field of Single-Molecule Biophysics. Int J Mol Sci 2022; 23:ijms232415895. [PMID: 36555532 PMCID: PMC9781480 DOI: 10.3390/ijms232415895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Cellular functions depend on the dynamic assembly of protein regulator complexes at specific cellular locations. Single Molecule Tracking (SMT) is a method of choice for the biochemical characterization of protein dynamics in vitro and in vivo. SMT follows individual molecules in live cells and provides direct information about their behavior. SMT was successfully applied to mammalian models. However, mammalian cells provide a complex environment where protein mobility depends on numerous factors that are difficult to control experimentally. Therefore, yeast cells, which are unicellular and well-studied with a small and completely sequenced genome, provide an attractive alternative for SMT. The simplicity of organization, ease of genetic manipulation, and tolerance to gene fusions all make yeast a great model for quantifying the kinetics of major enzymes, membrane proteins, and nuclear and cellular bodies. However, very few researchers apply SMT techniques to yeast. Our goal is to promote SMT in yeast to a wider research community. Our review serves a dual purpose. We explain how SMT is conducted in yeast cells, and we discuss the latest insights from yeast SMT while putting them in perspective with SMT of higher eukaryotes.
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19
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Chen Y, Cattoglio C, Dailey GM, Zhu Q, Tjian R, Darzacq X. Mechanisms governing target search and binding dynamics of hypoxia-inducible factors. eLife 2022; 11:e75064. [PMID: 36322456 PMCID: PMC9681212 DOI: 10.7554/elife.75064] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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] [Received: 10/30/2021] [Accepted: 11/01/2022] [Indexed: 11/07/2022] Open
Abstract
Transcription factors (TFs) are classically attributed a modular construction, containing well-structured sequence-specific DNA-binding domains (DBDs) paired with disordered activation domains (ADs) responsible for protein-protein interactions targeting co-factors or the core transcription initiation machinery. However, this simple division of labor model struggles to explain why TFs with identical DNA-binding sequence specificity determined in vitro exhibit distinct binding profiles in vivo. The family of hypoxia-inducible factors (HIFs) offer a stark example: aberrantly expressed in several cancer types, HIF-1α and HIF-2α subunit isoforms recognize the same DNA motif in vitro - the hypoxia response element (HRE) - but only share a subset of their target genes in vivo, while eliciting contrasting effects on cancer development and progression under certain circumstances. To probe the mechanisms mediating isoform-specific gene regulation, we used live-cell single particle tracking (SPT) to investigate HIF nuclear dynamics and how they change upon genetic perturbation or drug treatment. We found that HIF-α subunits and their dimerization partner HIF-1β exhibit distinct diffusion and binding characteristics that are exquisitely sensitive to concentration and subunit stoichiometry. Using domain-swap variants, mutations, and a HIF-2α specific inhibitor, we found that although the DBD and dimerization domains are important, another main determinant of chromatin binding and diffusion behavior is the AD-containing intrinsically disordered region (IDR). Using Cut&Run and RNA-seq as orthogonal genomic approaches, we also confirmed IDR-dependent binding and activation of a specific subset of HIF target genes. These findings reveal a previously unappreciated role of IDRs in regulating the TF search and binding process that contribute to functional target site selectivity on chromatin.
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Affiliation(s)
- Yu Chen
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, BerkeleyBerkeleyUnited States
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, BerkeleyBerkeleyUnited States
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, BerkeleyBerkeleyUnited States
| | - Qiulin Zhu
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, BerkeleyBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Li Ka Shing Center for Biomedical & Health Sciences, University of California, BerkeleyBerkeleyUnited States
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20
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Heckert A, Dahal L, Tjian R, Darzacq X. Recovering mixtures of fast-diffusing states from short single-particle trajectories. eLife 2022; 11:e70169. [PMID: 36066004 PMCID: PMC9451534 DOI: 10.7554/elife.70169] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 05/07/2021] [Accepted: 08/04/2022] [Indexed: 12/15/2022] Open
Abstract
Single-particle tracking (SPT) directly measures the dynamics of proteins in living cells and is a powerful tool to dissect molecular mechanisms of cellular regulation. Interpretation of SPT with fast-diffusing proteins in mammalian cells, however, is complicated by technical limitations imposed by fast image acquisition. These limitations include short trajectory length due to photobleaching and shallow depth of field, high localization error due to the low photon budget imposed by short integration times, and cell-to-cell variability. To address these issues, we investigated methods inspired by Bayesian nonparametrics to infer distributions of state parameters from SPT data with short trajectories, variable localization precision, and absence of prior knowledge about the number of underlying states. We discuss the advantages and disadvantages of these approaches relative to other frameworks for SPT analysis.
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Affiliation(s)
- Alec Heckert
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, University of California, BerkeleyBerkeleyUnited States
| | - Liza Dahal
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, University of California, BerkeleyBerkeleyUnited States
- CIRM Center of Excellence, University of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- CIRM Center of Excellence, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical InstituteBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, University of California, BerkeleyBerkeleyUnited States
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21
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Graham TGW, Ferrie JJ, Dailey GM, Tjian R, Darzacq X. Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA). eLife 2022; 11:e76870. [PMID: 35976226 PMCID: PMC9531946 DOI: 10.7554/elife.76870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 01/07/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging to track single molecules while simultaneously detecting their interactions. Here, we describe a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), in which one fluorophore (the 'sender') can reactivate a second fluorophore (the 'receiver') from a dark state. PAPA requires proximity between the two fluorophores, yet it operates at a longer average intermolecular distance than Förster resonance energy transfer (FRET). We show that PAPA can be used in live cells both to detect protein-protein interactions and to highlight a subpopulation of labeled protein complexes in which two different labels are in proximity. In proof-of-concept experiments, PAPA detected the expected correlation between androgen receptor self-association and chromatin binding at the single-cell level. These results establish a new way in which a photophysical property of fluorophores can be harnessed to study molecular interactions in single-molecule imaging of live cells.
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Affiliation(s)
- Thomas GW Graham
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - John Joseph Ferrie
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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22
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Hsieh TS, Cattoglio C, Slobodyanyuk E, Hansen AS, Darzacq X, Tjian R. Enhancer-promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1. Nat Genet 2022; 54:1919-32. [PMID: 36471071 DOI: 10.1038/s41588-022-01223-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/11/2022] [Indexed: 12/12/2022]
Abstract
It remains unclear why acute depletion of CTCF (CCCTC-binding factor) and cohesin only marginally affects expression of most genes despite substantially perturbing three-dimensional (3D) genome folding at the level of domains and structural loops. To address this conundrum, we used high-resolution Micro-C and nascent transcript profiling in mouse embryonic stem cells. We find that enhancer-promoter (E-P) interactions are largely insensitive to acute (3-h) depletion of CTCF, cohesin or WAPL. YY1 has been proposed as a structural regulator of E-P loops, but acute YY1 depletion also had minimal effects on E-P loops, transcription and 3D genome folding. Strikingly, live-cell, single-molecule imaging revealed that cohesin depletion reduced transcription factor (TF) binding to chromatin. Thus, although CTCF, cohesin, WAPL or YY1 is not required for the short-term maintenance of most E-P interactions and gene expression, our results suggest that cohesin may facilitate TFs to search for and bind their targets more efficiently.
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23
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Irgen-Gioro S, Yoshida S, Walling V, Chong S. Fixation can change the appearance of phase separation in living cells. eLife 2022; 11:79903. [PMID: 36444977 PMCID: PMC9817179 DOI: 10.7554/elife.79903] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022] Open
Abstract
Fixing cells with paraformaldehyde (PFA) is an essential step in numerous biological techniques as it is thought to preserve a snapshot of biomolecular transactions in living cells. Fixed-cell imaging techniques such as immunofluorescence have been widely used to detect liquid-liquid phase separation (LLPS) in vivo. Here, we compared images, before and after fixation, of cells expressing intrinsically disordered proteins that are able to undergo LLPS. Surprisingly, we found that PFA fixation can both enhance and diminish putative LLPS behaviors. For specific proteins, fixation can even cause their droplet-like puncta to artificially appear in cells that do not have any detectable puncta in the live condition. Fixing cells in the presence of glycine, a molecule that modulates fixation rates, can reverse the fixation effect from enhancing to diminishing LLPS appearance. We further established a kinetic model of fixation in the context of dynamic protein-protein interactions. Simulations based on the model suggest that protein localization in fixed cells depends on an intricate balance of protein-protein interaction dynamics, the overall rate of fixation, and notably, the difference between fixation rates of different proteins. Consistent with simulations, live-cell single-molecule imaging experiments showed that a fast overall rate of fixation relative to protein-protein interaction dynamics can minimize fixation artifacts. Our work reveals that PFA fixation changes the appearance of LLPS from living cells, presents a caveat in studying LLPS using fixation-based methods, and suggests a mechanism underlying the fixation artifact.
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Affiliation(s)
- Shawn Irgen-Gioro
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shawn Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States,Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Victoria Walling
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
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