1
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Lou J, Deng Q, Zhang X, Bell CC, Das AB, Bediaga NG, Zlatic CO, Johanson TM, Allan RS, Griffin MDW, Paradkar P, Harvey KF, Dawson MA, Hinde E. Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture. Nucleic Acids Res 2024:gkae720. [PMID: 39193905 DOI: 10.1093/nar/gkae720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 07/29/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Our understanding of heterochromatin nanostructure and its capacity to mediate gene silencing in a living cell has been prevented by the diffraction limit of optical microscopy. Thus, here to overcome this technical hurdle, and directly measure the nucleosome arrangement that underpins this dense chromatin state, we coupled fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) between histones core to the nucleosome, with molecular editing of heterochromatin protein 1 alpha (HP1α). Intriguingly, this super-resolved readout of nanoscale chromatin structure, alongside fluorescence fluctuation spectroscopy (FFS) and FLIM-FRET analysis of HP1α protein-protein interaction, revealed nucleosome arrangement to be differentially regulated by HP1α oligomeric state. Specifically, we found HP1α monomers to impart a previously undescribed global nucleosome spacing throughout genome architecture that is mediated by trimethylation on lysine 9 of histone H3 (H3K9me3) and locally reduced upon HP1α dimerisation. Collectively, these results demonstrate HP1α to impart a dual action on chromatin that increases the dynamic range of nucleosome proximity. We anticipate that this finding will have important implications for our understanding of how live cell heterochromatin structure regulates genome function.
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Affiliation(s)
- Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Qiji Deng
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Xiaomeng Zhang
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Andrew B Das
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Naiara G Bediaga
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
| | - Courtney O Zlatic
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - PrasadN Paradkar
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong3220, Australia
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Anatomy and Developmental Biology and Biomedicine Discovery Institute, Monash University, Clayton, VIC 3168, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC 3010, Australia
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2
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Gillis A, Berry S. Global control of RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195024. [PMID: 38552781 DOI: 10.1016/j.bbagrm.2024.195024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
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Affiliation(s)
- Alexander Gillis
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
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3
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Mørch AM, Schneider F. Investigating Diffusion Dynamics and Interactions with Scanning Fluorescence Correlation Spectroscopy (sFCS). Methods Mol Biol 2023; 2654:61-89. [PMID: 37106176 DOI: 10.1007/978-1-0716-3135-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Activation of immune cells and formation of immunological synapses (IS) rely critically on the reorganization of the plasma membrane. These highly orchestrated processes are driven by diffusion and oligomerization dynamics, as well as by single molecule interactions. While slow macro- and meso-scale changes in organization can be observed with conventional imaging, fast nano-scale dynamics are often missed with traditional approaches, but resolving them is, nonetheless, essential to understand the underlying biological mechanisms at play. Here, we describe the use of scanning fluorescence correlation spectroscopy (sFCS) and scanning fluorescence cross-correlation spectroscopy (sFCCS) to study reorganization and changes in molecular diffusion dynamics and interactions during IS formation and in other biological settings. We focus on the practical aspects of the measurements including calibration and alignment of the optical setup, present a comprehensive protocol to perform the measurements, and provide data analysis pipelines and strategies. Finally, we show an exemplary application of the technology to studying Lck diffusion during T-cell signaling.
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Affiliation(s)
| | - Falk Schneider
- Translational Imaging Center, University of Southern California, Los Angeles, California, USA.
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4
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Solano A, Lou J, Scipioni L, Gratton E, Hinde E. Radial pair correlation of molecular brightness fluctuations maps protein diffusion as a function of oligomeric state within live-cell nuclear architecture. Biophys J 2022; 121:2152-2167. [PMID: 35490296 PMCID: PMC9247470 DOI: 10.1016/j.bpj.2022.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/16/2021] [Accepted: 04/26/2022] [Indexed: 11/22/2022] Open
Abstract
Nuclear proteins can modulate their DNA binding activity and the exploration volume available during DNA target search by self-associating into higher-order oligomers. Directly tracking this process in the nucleoplasm of a living cell is, however, a complex task. Thus, here we present a microscopy method based on radial pair correlation of molecular brightness fluctuations (radial pCOMB) that can extract the mobility of a fluorescently tagged nuclear protein as a function of its oligomeric state and spatiotemporally map the anisotropy of this parameter with respect to nuclear architecture. By simply performing a rapid frame scan acquisition, radial pCOMB has the capacity to detect, within each pixel, protein oligomer formation and the size-dependent obstruction nuclear architecture imparts on this complex's transport across sub-micrometer distances. From application of radial pCOMB to an oligomeric transcription factor and DNA repair protein, we demonstrate that homo-oligomer formation differentially regulates chromatin accessibility and interaction with the DNA template.
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Affiliation(s)
- Ashleigh Solano
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne
| | - Jieqiong Lou
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California, Irvine
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine.
| | - Elizabeth Hinde
- School of Physics, University of Melbourne; Department of Biochemistry and Pharmacology, University of Melbourne.
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5
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Lau D, Magnan C, Hill K, Cooper A, Gambin Y, Sierecki E. Single Molecule Fingerprinting Reveals Different Amplification Properties of α-Synuclein Oligomers and Preformed Fibrils in Seeding Assay. ACS Chem Neurosci 2022; 13:883-896. [PMID: 35286811 PMCID: PMC8990999 DOI: 10.1021/acschemneuro.1c00553] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The quantification of α-synuclein aggregates has emerged as a promising biomarker for synucleinopathies. Assays that amplify and detect such aggregates have revealed the presence of seeding-competent species in biosamples of patients diagnosed with Parkinson's disease. However, multiple species, such as oligomers and amyloid fibrils, are formed during the aggregation of α-synuclein; these species are likely to coexist in biological samples, and thus it remains unclear which species(s) are contributing to the signal detected in seeding assays. To identify individual contributions to the amplification process, recombinant oligomers and preformed fibrils were produced and purified to characterize their individual biochemical and seeding potential. Here, we used single molecule spectroscopy to track the formation and purification of oligomers and fibrils at the single particle level and compare their respective seeding potential in an amplification assay. Single molecule detection validates that size-exclusion chromatography efficiently separates oligomers from fibrils. Oligomers were found to be seeding-competent, but our results reveal that their seeding behavior is very different compared to that of preformed fibrils, in our amplification assay. Overall, our data suggest that even a low number of preformed fibrils present in biosamples is likely to dominate the response in seeding assays.
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Affiliation(s)
- Derrick Lau
- EMBL Australia Node for Single Molecule Sciences and School of Medical Sciences, Faculty of Medicine, the University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Chloé Magnan
- EMBL Australia Node for Single Molecule Sciences and School of Medical Sciences, Faculty of Medicine, the University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Kathryn Hill
- The Australian Parkinson’s Mission, The Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Antony Cooper
- The Australian Parkinson’s Mission, The Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
- St Vincent’s Clinical School, UNSW Sydney, Darlinghurst, New South Wales 2010, Australia
| | - Yann Gambin
- EMBL Australia Node for Single Molecule Sciences and School of Medical Sciences, Faculty of Medicine, the University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Emma Sierecki
- EMBL Australia Node for Single Molecule Sciences and School of Medical Sciences, Faculty of Medicine, the University of New South Wales, Sydney, New South Wales 2052, Australia
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6
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Owyong TC, Hong Y. Emerging fluorescence tools for the study of proteostasis in cells. Curr Opin Chem Biol 2022; 67:102116. [PMID: 35176555 DOI: 10.1016/j.cbpa.2022.102116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/22/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
Understanding how cells maintain the functional proteome and respond to stress conditions is critical for deciphering molecular pathogenesis and developing treatments for conditions such as neurodegenerative diseases. Efforts towards finer quantification of cellular proteostasis machinery efficiency, phase transitions and local environment changes remain a priority. Herein, we describe recent developments in fluorescence-based strategy and methodology, building on the experimental toolkit, for the study of proteostasis (protein homeostasis) in cells. We hope this review can assist in bridging gaps between a multitude of research disciplines and promote interdisciplinary collaboration to address the crucial topic of proteostasis.
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Affiliation(s)
- Tze Cin Owyong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia; ARC Centre of Excellence in Exciton Science, School of Chemistry, Bio21 Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Yuning Hong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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7
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Shembrey C, Smith J, Grandin M, Williams N, Cho HJ, Mølck C, Behrenbruch C, Thomson BNJ, Heriot AG, Merino D, Hollande F. Longitudinal Monitoring of Intra-Tumoural Heterogeneity Using Optical Barcoding of Patient-Derived Colorectal Tumour Models. Cancers (Basel) 2022; 14:581. [PMID: 35158849 PMCID: PMC8833441 DOI: 10.3390/cancers14030581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 02/01/2023] Open
Abstract
Geno- and phenotypic heterogeneity amongst cancer cell subpopulations are established drivers of treatment resistance and tumour recurrence. However, due to the technical difficulty associated with studying such intra-tumoural heterogeneity, this phenomenon is seldom interrogated in conventional cell culture models. Here, we employ a fluorescent lineage technique termed "optical barcoding" (OBC) to perform simultaneous longitudinal tracking of spatio-temporal fate in 64 patient-derived colorectal cancer subclones. To do so, patient-derived cancer cell lines and organoids were labelled with discrete combinations of reporter constructs, stably integrated into the genome and thus passed on from the founder cell to all its clonal descendants. This strategy enables the longitudinal monitoring of individual cell lineages based upon their unique optical barcodes. By designing a novel panel of six fluorescent proteins, the maximum theoretical subpopulation resolution of 64 discriminable subpopulations was achieved, greatly improving throughput compared with previous studies. We demonstrate that all subpopulations can be purified from complex clonal mixtures via flow cytometry, permitting the downstream isolation and analysis of any lineages of interest. Moreover, we outline an optimized imaging protocol that can be used to image optical barcodes in real-time, allowing for clonal dynamics to be resolved in live cells. In contrast with the limited intra-tumour heterogeneity observed in conventional 2D cell lines, the OBC technique was successfully used to quantify dynamic clonal expansions and contractions in 3D patient-derived organoids, which were previously demonstrated to better recapitulate the heterogeneity of their parental tumour material. In summary, we present OBC as a user-friendly, inexpensive, and high-throughput technique for monitoring intra-tumoural heterogeneity in in vitro cell culture models.
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Affiliation(s)
- Carolyn Shembrey
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia; (C.S.); (J.S.); (M.G.); (N.W.); (C.M.); (C.B.)
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, VIC 3000, Australia
| | - Jai Smith
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia; (C.S.); (J.S.); (M.G.); (N.W.); (C.M.); (C.B.)
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, VIC 3000, Australia
| | - Mélodie Grandin
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia; (C.S.); (J.S.); (M.G.); (N.W.); (C.M.); (C.B.)
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, VIC 3000, Australia
| | - Nathalia Williams
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia; (C.S.); (J.S.); (M.G.); (N.W.); (C.M.); (C.B.)
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, VIC 3000, Australia
| | - Hyun-Jung Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, VIC 3010, Australia;
| | - Christina Mølck
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia; (C.S.); (J.S.); (M.G.); (N.W.); (C.M.); (C.B.)
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, VIC 3000, Australia
| | - Corina Behrenbruch
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia; (C.S.); (J.S.); (M.G.); (N.W.); (C.M.); (C.B.)
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, VIC 3000, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia;
- Department of General Surgical Specialties, The Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC 3050, Australia;
| | - Benjamin NJ. Thomson
- Department of General Surgical Specialties, The Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC 3050, Australia;
- Department of Surgery, the Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC 3050, Australia
| | - Alexander G. Heriot
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia;
- Department of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Department of Surgery, St Vincent’s Hospital, Melbourne, VIC 3065, Australia
| | - Delphine Merino
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Melbourne, VIC 3086, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia
- Department of Medical Biology, The Faculty of Medicine, Dentistry and Health Science, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Frédéric Hollande
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia; (C.S.); (J.S.); (M.G.); (N.W.); (C.M.); (C.B.)
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Melbourne, VIC 3000, Australia
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8
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Pannek A, Houghton FJ, Verhagen AM, Dower SK, Hinde E, Gleeson PA. Dynamics of intracellular neonatal Fc receptor-ligand interactions in primary macrophages using biophysical fluorescence techniques. Mol Biol Cell 2021; 33:ar6. [PMID: 34731029 PMCID: PMC8886815 DOI: 10.1091/mbc.e21-02-0061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The neonatal Fc receptor (FcRn) is responsible for the recycling of endocytosed albumin and IgG, and contributes to their long plasma half-life. We recently identified an FcRn-dependent recycling pathway from macropinosomes in macrophages; however, little is known about the dynamics of intracellular FcRn–ligand interactions to promote recycling. Here we demonstrate a multiplexed biophysical fluorescent microscopy approach to resolve the spatiotemporal dynamics of albumin–FcRn interactions in living bone marrow–derived macrophages (BMDMs). We used the phasor approach to fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) to detect the interaction of a FcRn–mCherry fusion protein with endocytosed Alexa Fluor 488–labeled human serum albumin (HSA–AF488) in BMDMs, and raster image correlation spectroscopy (RICS) analysis of single fluorescent-labeled albumin molecules to monitor the diffusion kinetics of internalized albumin. Our data identified a major fraction of immobile HSA–AF488 molecules in endosomal structures of human FcRn-positive mouse macrophages and an increase in FLIM-FRET following endocytosis, including detection of FRET in tubular-like structures. A nonbinding mutant of albumin showed minimum FLIM-FRET and high mobility. These data reveal the kinetics of FcRn–ligand binding within endosomal structures for recruitment into transport carriers for recycling. These approaches have wide applicability for analyses of intracellular ligand–receptor interactions.
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Affiliation(s)
- Andreas Pannek
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010.,Institute of Experimental Immunology, University of Bonn, Venusberg Campus, D-53127, Germany
| | - Fiona J Houghton
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010
| | - Anne M Verhagen
- CSL Limited, Research, Bio21 Molecular Science and Biotechnology Institute, Victoria 3010, Australia
| | - Steven K Dower
- CSL Limited, Research, Bio21 Molecular Science and Biotechnology Institute, Victoria 3010, Australia
| | - Elizabeth Hinde
- School of Physics and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Pharmacology, The University of Melbourne, Victoria 3010, Australia
| | - Paul A Gleeson
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010
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9
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Priest DG, Bernardini A, Lou J, Mantovani R, Hinde E. Live cell dynamics of the NF-Y transcription factor. Sci Rep 2021; 11:10992. [PMID: 34040015 PMCID: PMC8155045 DOI: 10.1038/s41598-021-90081-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/29/2021] [Indexed: 11/24/2022] Open
Abstract
Transcription factors (TFs) are core players in the control of gene expression, evolutionarily selected to recognise a subset of specific DNA sequences and nucleate the recruitment of the transcriptional machinery. How TFs assemble and move in the nucleus to locate and bind their DNA targets and cause a transcriptional response, remains mostly unclear. NF-Y is a highly conserved, heterotrimeric TF with important roles in both housekeeping and lineage-specific gene expression, functioning as a promoter organiser. Despite a large number of biochemical, structural and genomic studies of NF-Y, there is a lack of experiments in single living cells; therefore, basic assumptions of NF-Y biology remain unproven in vivo. Here we employ a series of dynamic fluorescence microscopy methods (FLIM-FRET, NB, RICS and FRAP) to study NF-Y dynamics and complex formation in live cells. Specifically, we provide quantitative measurement of NF-Y subunit association and diffusion kinetics in the nucleus that collectively suggest NF-Y to move and bind chromatin as a trimeric complex in vivo.
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Affiliation(s)
- David G Priest
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Melbourne, VIC, Australia.
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia.
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10
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Lou J, Priest DG, Solano A, Kerjouan A, Hinde E. Spatiotemporal dynamics of 53BP1 dimer recruitment to a DNA double strand break. Nat Commun 2020; 11:5776. [PMID: 33188174 PMCID: PMC7666136 DOI: 10.1038/s41467-020-19504-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 10/15/2020] [Indexed: 01/08/2023] Open
Abstract
Tumor suppressor p53-binding protein 1 (53BP1) is a DNA repair protein essential for the detection, assessment, and resolution of DNA double strand breaks (DSBs). The presence of a DSB is signaled to 53BP1 via a local histone modification cascade that triggers the binding of 53BP1 dimers to chromatin flanking this type of lesion. While biochemical studies have established that 53BP1 exists as a dimer, it has never been shown in a living cell when or where 53BP1 dimerizes upon recruitment to a DSB site, or upon arrival at this nuclear location, how the DSB histone code to which 53BP1 dimers bind regulates retention and self-association into higher-order oligomers. Thus, here in live-cell nuclear architecture we quantify the spatiotemporal dynamics of 53BP1 oligomerization during a DSB DNA damage response by coupling fluorescence fluctuation spectroscopy (FFS) with the DSB inducible via AsiSI cell system (DIvA). From adopting this multiplexed approach, we find that preformed 53BP1 dimers relocate from the nucleoplasm to DSB sites, where consecutive recognition of ubiquitinated lysine 15 of histone 2A (H2AK15ub) and di-methylated lysine 20 of histone 4 (H4K20me2), leads to the assembly of 53BP1 oligomers and a mature 53BP1 foci structure.
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Affiliation(s)
- Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - David G Priest
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Ashleigh Solano
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Adèle Kerjouan
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Melbourne, Victoria, Australia. .,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
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11
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Jiang Y, Xu B, Melnykov A, Genin GM, Elson EL. Fluorescence Correlation Spectroscopy and Photon Counting Histograms in Finite, Bounded Domains. Biophys J 2020; 119:265-273. [PMID: 32621863 PMCID: PMC7376089 DOI: 10.1016/j.bpj.2020.05.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/29/2020] [Accepted: 05/18/2020] [Indexed: 01/20/2023] Open
Abstract
Analysis of fluctuations arising as fluorescent particles pass through a focused laser beam has enabled quantitative characterization of a broad range of molecular kinetic processes. Two key mathematical frameworks that have enabled these quantifications are fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis. Although these frameworks are effective and accurate when the focused laser beam is well approximated by an infinite Gaussian beam with a waist that is small compared to the size of the region over which the fluorescent particles can diffuse, they cannot be applied to situations in which this region is bounded at the nanoscale. We therefore derived general forms of the FCS and PCH frameworks for bounded systems. The finite-domain form of FCS differs from the classical form in its boundary and initial conditions and requires development of a new Fourier space solution for fitting data. Our finite-domain FCS predicts simulated data accurately and reduces to a previous model for the special case when the system is much larger than the Gaussian beam and can be considered to be infinite. We also derived the PCH form for the bounded systems. Our approach enables estimation of the concentration of diffusing fluorophores within a finite domain for the first time, to our knowledge. The method opens the possibility of quantification of kinetics in several systems for which this has never been possible.
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Affiliation(s)
- Yanfei Jiang
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri; Division of Biological Sciences, University of California San Diego, La Jolla, California.
| | - Bingxian Xu
- Division of Biological Sciences, University of California San Diego, La Jolla, California
| | - Artem Melnykov
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Guy M Genin
- NSF Science and Technology Center for Engineering Mechanobiology, Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, Missouri
| | - Elliot L Elson
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.
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Frank L, Rippe K. Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation. J Mol Biol 2020; 432:4270-4286. [DOI: 10.1016/j.jmb.2020.04.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022]
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