1
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Cisneros-Soberanis F, Simpson EL, Beckett AJ, Pucekova N, Corless S, Kochanova NY, Prior IA, Booth DG, Earnshaw WC. Near millimolar concentration of nucleosomes in mitotic chromosomes from late prometaphase into anaphase. J Cell Biol 2024; 223:e202403165. [PMID: 39186086 PMCID: PMC11346515 DOI: 10.1083/jcb.202403165] [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: 03/27/2024] [Revised: 07/05/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024] Open
Abstract
Chromosome compaction is a key feature of mitosis and critical for accurate chromosome segregation. However, a precise quantitative analysis of chromosome geometry during mitotic progression is lacking. Here, we use volume electron microscopy to map, with nanometer precision, chromosomes from prometaphase through telophase in human RPE1 cells. During prometaphase, chromosomes acquire a smoother surface, their arms shorten, and the primary centromeric constriction is formed. The chromatin is progressively compacted, ultimately reaching a remarkable nucleosome concentration of over 750 µM in late prometaphase that remains relatively constant during metaphase and early anaphase. Surprisingly, chromosomes then increase their volume in late anaphase prior to deposition of the nuclear envelope. The plateau of total chromosome volume from late prometaphase through early anaphase described here is consistent with proposals that the final stages of chromatin condensation in mitosis involve a limit density, such as might be expected for a process involving phase separation.
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Affiliation(s)
| | - Eva L Simpson
- Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Alison J Beckett
- Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Nina Pucekova
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Samuel Corless
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | | | - Ian A Prior
- Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel G Booth
- Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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2
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Carignano MA, Kroeger M, Almassalha LM, Agrawal V, Li WS, Pujadas-Liwag EM, Nap RJ, Backman V, Szleifer I. Local volume concentration, packing domains, and scaling properties of chromatin. eLife 2024; 13:RP97604. [PMID: 39331520 PMCID: PMC11434620 DOI: 10.7554/elife.97604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2024] Open
Abstract
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally defined domains observed by single-cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as RAD21 degradation.
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Affiliation(s)
- Marcelo A Carignano
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
| | - Martin Kroeger
- Magnetism and Interface Physics & Computational Polymer Physics, Department of Materials, ETH ZurichZurichSwitzerland
| | - Luay M Almassalha
- Department of Gastroenterology and Hepatology, Northwestern Memorial HospitalEvanstonUnited States
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
| | - Wing Shun Li
- Applied Physics Program, Northwestern UniversityChicagoUnited States
| | | | - Rikkert J Nap
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern UniversityEvanstonUnited States
- Department of Chemistry, Northwestern UniversityEvanstonUnited States
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3
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Goel VY, Aboreden NG, Jusuf JM, Zhang H, Mori LP, Mirny LA, Blobel GA, Banigan EJ, Hansen AS. Dynamics of microcompartment formation at the mitosis-to-G1 transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.611917. [PMID: 39345388 PMCID: PMC11430094 DOI: 10.1101/2024.09.16.611917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
As cells exit mitosis and enter G1, mitotic chromosomes decompact and transcription is reestablished. Previously, Hi-C studies showed that essentially all interphase 3D genome features including A/B-compartments, TADs, and CTCF loops, are lost during mitosis. However, Hi-C remains insensitive to features such as microcompartments, nested focal interactions between cis -regulatory elements (CREs). We therefore applied Region Capture Micro-C to cells from mitosis to G1. Unexpectedly, we observe microcompartments in prometaphase, which further strengthen in ana/telophase before gradually weakening in G1. Loss of loop extrusion through condensin depletion differentially impacts microcompartments and large A/B-compartments, suggesting that they are partially distinct. Using polymer modeling, we show that microcompartment formation is favored by chromatin compaction and disfavored by loop extrusion activity, explaining why ana/telophase likely provides a particularly favorable environment. Our results suggest that CREs exhibit intrinsic homotypic affinity leading to microcompartment formation, which may explain transient transcriptional spiking observed upon mitotic exit.
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4
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Liu M, Jin S, Agabiti SS, Jensen TB, Yang T, Radda JSD, Ruiz CF, Baldissera G, Rajaei M, Townsend JP, Muzumdar MD, Wang S. Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.23.550157. [PMID: 37546882 PMCID: PMC10401964 DOI: 10.1101/2023.07.23.550157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Although three-dimensional (3D) genome structures are altered in cancer cells, little is known about how these changes evolve and diversify during cancer progression. Leveraging genome-wide chromatin tracing to visualize 3D genome folding directly in tissues, we generated 3D genome cancer atlases of murine lung and pancreatic adenocarcinoma. Our data reveal stereotypical, non-monotonic, and stage-specific alterations in 3D genome folding heterogeneity, compaction, and compartmentalization as cancers progress from normal to preinvasive and ultimately to invasive tumors, discovering a potential structural bottleneck in early tumor progression. Remarkably, 3D genome architectures distinguish histologic cancer states in single cells, despite considerable cell-to-cell heterogeneity. Gene-level analyses of evolutionary changes in 3D genome compartmentalization not only showed compartment-associated genes are more homogeneously regulated, but also elucidated prognostic and dependency genes in lung adenocarcinoma and a previously unappreciated role for polycomb-group protein Rnf2 in 3D genome regulation. Our results demonstrate the utility of mapping the single-cell cancer 3D genome in tissues and illuminate its potential to identify new diagnostic, prognostic, and therapeutic biomarkers in cancer.
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Affiliation(s)
- Miao Liu
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Shengyan Jin
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Sherry S. Agabiti
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Biology Institute, Yale University; West Haven, CT 06516, USA
| | - Tyler B. Jensen
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- M.D.-Ph.D. Program, Yale University; New Haven, CT 06510, USA
| | - Tianqi Yang
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Jonathan S. D. Radda
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Christian F. Ruiz
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Biology Institute, Yale University; West Haven, CT 06516, USA
| | - Gabriel Baldissera
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Moein Rajaei
- Department of Biostatistics, Yale School of Public Health, Yale University; New Haven, CT 06510, USA
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, Yale University; New Haven, CT 06510, USA
- Program in Computational Biology and Bioinformatics, Yale University; New Haven, CT 06510, USA
- Program in Genetics, Genomics, and Epigenetics, Yale Cancer Center, Yale University; New Haven, CT 06510, USA
| | - Mandar Deepak Muzumdar
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Biology Institute, Yale University; West Haven, CT 06516, USA
- M.D.-Ph.D. Program, Yale University; New Haven, CT 06510, USA
- Program in Genetics, Genomics, and Epigenetics, Yale Cancer Center, Yale University; New Haven, CT 06510, USA
- Department of Internal Medicine, Section of Medical Oncology, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University; New Haven, CT 06510, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University; New Haven, CT 06510, USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- M.D.-Ph.D. Program, Yale University; New Haven, CT 06510, USA
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University; New Haven, CT 06510, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University; New Haven, CT 06510, USA
- Department of Cell Biology, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Biochemistry, Quantitative Biology, Biophysics, and Structural Biology Program, Yale University; New Haven, CT 06510, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Liver Center, Yale University School of Medicine; New Haven, CT 06510, USA
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5
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Vizjak P, Kamp D, Hepp N, Scacchetti A, Gonzalez Pisfil M, Bartho J, Halic M, Becker PB, Smolle M, Stigler J, Mueller-Planitz F. ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. Nat Struct Mol Biol 2024; 31:1331-1340. [PMID: 38664566 DOI: 10.1038/s41594-024-01290-x] [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: 11/03/2022] [Accepted: 03/25/2024] [Indexed: 05/07/2024]
Abstract
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. Here we investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner, qualitatively agree with our data. We speculate that monkey-bar mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.
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Affiliation(s)
- Petra Vizjak
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Dieter Kamp
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Hepp
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alessandro Scacchetti
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Joseph Bartho
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michaela Smolle
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- BioPhysics Core Facility, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- ViraTherapeutics GmbH, Rum, Austria
| | - Johannes Stigler
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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6
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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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7
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Alom S, Daneshkhah A, Acosta N, Anthony N, Liwag EP, Backman V, Gaire SK. Deep Learning-driven Automatic Nuclei Segmentation of Label-free Live Cell Chromatin-sensitive Partial Wave Spectroscopic Microscopy Imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.20.608885. [PMID: 39229026 PMCID: PMC11370422 DOI: 10.1101/2024.08.20.608885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Chromatin-sensitive Partial Wave Spectroscopic (csPWS) microscopy offers a non-invasive glimpse into the mass density distribution of cellular structures at the nanoscale, leveraging the spectroscopic information. Such capability allows us to analyze the chromatin structure and organization and the global transcriptional state of the cell nuclei for the study of its role in carcinogenesis. Accurate segmentation of the nuclei in csPWS microscopy images is an essential step in isolating them for further analysis. However, manual segmentation is error-prone, biased, time-consuming, and laborious, resulting in disrupted nuclear boundaries with partial or over-segmentation. Here, we present an innovative deep-learning-driven approach to automate the accurate nuclei segmentation of label-free live cell csPWS microscopy imaging data. Our approach, csPWS-seg, harnesses the Convolutional Neural Networks-based U-Net model with an attention mechanism to automate the accurate cell nuclei segmentation of csPWS microscopy images. We leveraged the structural, physical, and biological differences between the cytoplasm, nucleus, and nuclear periphery to construct three distinct csPWS feature images for nucleus segmentation. Using these images of HCT116 cells, csPWS-seg achieved superior performance with a median Intersection over Union (IoU) of 0.80 and a Dice Similarity Coefficient (DSC) score of 0.88. The csPWS-seg overcame the segmentation performance over the baseline U-Net model and another attention-based model, SE-U-Net, marking a significant improvement in segmentation accuracy. Further, we analyzed the performance of our proposed model with four loss functions: binary cross-entropy loss, focal loss, dice loss, and Jaccard loss. The csPWS-seg with focal loss provided the best results compared to other loss functions. The automatic and accurate nuclei segmentation offered by the csPWS-seg not only automates, accelerates, and streamlines csPWS data analysis but also enhances the reliability of subsequent chromatin analysis research, paving the way for more accurate diagnostics, treatment, and understanding of cellular mechanisms for carcinogenesis.
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Affiliation(s)
- Shahin Alom
- Department of Electrical and Computer Engineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
| | - Ali Daneshkhah
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Nicolas Acosta
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Nick Anthony
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Emily Pujadas Liwag
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Sunil Kumar Gaire
- Department of Electrical and Computer Engineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
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8
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Starkov D, Belan S. Effect of active loop extrusion on the two-contact correlations in the interphase chromosome. J Chem Phys 2024; 161:074903. [PMID: 39149990 DOI: 10.1063/5.0221933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024] Open
Abstract
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance between them. However, these datasets do not tell us anything about the joint statistics of simultaneous contacts between genomic loci in individual cells. This kind of statistical information can be extracted using the single-cell Hi-C method, which is capable of detecting a large fraction of simultaneous contacts within a single cell, as well as through modern methods of fluorescent labeling and super-resolution imaging. Motivated by the prospect of the imminent availability of relevant experimental data, in this work, we theoretically model the joint statistics of pairs of contacts located along a line perpendicular to the main diagonal of the single-cell contact map. The analysis is performed within the framework of an ideal polymer model with quenched disorder of random loops, which, as previous studies have shown, allows us to take into account the influence of the loop extrusion process on the conformational properties of interphase chromatin.
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Affiliation(s)
- Dmitry Starkov
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova Ave., 142432 Chernogolovka, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Sergey Belan
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova Ave., 142432 Chernogolovka, Russia
- Faculty of Physics, National Research University Higher School of Economics, Myasnitskaya 20, 101000 Moscow, Russia
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9
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Hibino K, Sakai Y, Tamura S, Takagi M, Minami K, Natsume T, Shimazoe MA, Kanemaki MT, Imamoto N, Maeshima K. Single-nucleosome imaging unveils that condensins and nucleosome-nucleosome interactions differentially constrain chromatin to organize mitotic chromosomes. Nat Commun 2024; 15:7152. [PMID: 39169041 PMCID: PMC11339268 DOI: 10.1038/s41467-024-51454-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
For accurate mitotic cell division, replicated chromatin must be assembled into chromosomes and faithfully segregated into daughter cells. While protein factors like condensin play key roles in this process, it is unclear how chromosome assembly proceeds as molecular events of nucleosomes in living cells and how condensins act on nucleosomes to organize chromosomes. To approach these questions, we investigate nucleosome behavior during mitosis of living human cells using single-nucleosome tracking, combined with rapid-protein depletion technology and computational modeling. Our results show that local nucleosome motion becomes increasingly constrained during mitotic chromosome assembly, which is functionally distinct from condensed apoptotic chromatin. Condensins act as molecular crosslinkers, locally constraining nucleosomes to organize chromosomes. Additionally, nucleosome-nucleosome interactions via histone tails constrain and compact whole chromosomes. Our findings elucidate the physical nature of the chromosome assembly process during mitosis.
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Affiliation(s)
- Kayo Hibino
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Yuji Sakai
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Biosystems Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masatoshi Takagi
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Toyoaki Natsume
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masa A Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Masato T Kanemaki
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Molecular Cell Engineering Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan.
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10
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Nahali N, Oshaghi M, Paulsen J. Modeling properties of chromosome territories using polymer filaments in diverse confinement geometries. Chromosome Res 2024; 32:11. [PMID: 39126507 PMCID: PMC11316705 DOI: 10.1007/s10577-024-09753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/06/2024] [Accepted: 06/20/2024] [Indexed: 08/12/2024]
Abstract
Interphase chromosomes reside within distinct nuclear regions known as chromosome territories (CTs). Recent observations from Hi-C analyses, a method mapping chromosomal interactions, have revealed varied decay in contact probabilities among different chromosomes. Our study explores the relationship between this contact decay and the particular shapes of the chromosome territories they occupy. For this, we employed molecular dynamics (MD) simulations to examine how confined polymers, resembling chromosomes, behave within different confinement geometries similar to chromosome territory boundaries. Our simulations unveil so far unreported relationships between contact probabilities and end-to-end distances varying based on different confinement geometries. These findings highlight the crucial impact of chromosome territories on shaping the larger-scale properties of 3D genome organization. They emphasize the intrinsic connection between the shapes of these territories and the contact behaviors exhibited by chromosomes. Understanding these correlations is key to accurately interpret Hi-C and microscopy data, and offers vital insights into the foundational principles governing genomic organization.
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Affiliation(s)
- Negar Nahali
- Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
| | - Mohammadsaleh Oshaghi
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Jonas Paulsen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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11
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Aljahani A, Mauksch C, Oudelaar AM. The relationship between nucleosome positioning and higher-order genome folding. Curr Opin Cell Biol 2024; 89:102398. [PMID: 38991477 DOI: 10.1016/j.ceb.2024.102398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Eukaryotic genomes are organized into 3D structures, which range from small-scale nucleosome arrays to large-scale chromatin domains. These structures have an important role in the regulation of transcription and other nuclear processes. Despite advances in our understanding of the properties, functions, and underlying mechanisms of genome structures, there are many open questions about the interplay between these structures across scales. In particular, it is not well understood if and how 1D features of nucleosome arrays influence large-scale 3D genome folding patterns. In this review, we discuss recent studies that address these questions and summarize our current understanding of the relationship between nucleosome positioning and higher-order genome folding.
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Affiliation(s)
- Abrar Aljahani
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany; University of Göttingen, Göttingen, Germany
| | - Clemens Mauksch
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany; University of Göttingen, Göttingen, Germany
| | - A Marieke Oudelaar
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany.
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12
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Rahman F, Augoustides V, Tyler E, Daugird TA, Arthur C, Legant WR. Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.27.605159. [PMID: 39211261 PMCID: PMC11360932 DOI: 10.1101/2024.07.27.605159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The nucleus coordinates many different processes. Visualizing how these are spatially organized requires imaging protein complexes, epigenetic marks, and DNA across scales from single molecules to the whole nucleus. To accomplish this, we developed a multiplexed imaging protocol to localize 13 different nuclear targets with nanometer precision in single cells. We show that nuclear specification into active and repressive states exists along a spectrum of length scales, emerging below one micron and becoming strengthened at the nanoscale with unique organizational principles in both heterochromatin and euchromatin. HP1-α was positively correlated with DNA at the microscale but uncorrelated at the nanoscale. RNA Polymerase II, p300, and CDK9 were positively correlated at the microscale but became partitioned below 300 nm. Perturbing histone acetylation or transcription disrupted nanoscale organization but had less effect at the microscale. We envision that our imaging and analysis pipeline will be useful to reveal the organizational principles not only of the cell nucleus but also other cellular compartments.
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13
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Clerkin AB, Pagane N, West DW, Spakowitz AJ, Risca VI. Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.28.605011. [PMID: 39131347 PMCID: PMC11312488 DOI: 10.1101/2024.07.28.605011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The three-dimensional structure of chromatin has emerged as an important feature of eukaryotic gene regulation. Recent technological advances in DNA sequencing-based assays have revealed locus- and chromatin state-specific structural patterns at the length scale of a few nucleosomes (~1 kb). However, interpreting these data sets remains challenging. Radiation-induced correlated cleavage of chromatin (RICC-seq) is one such chromatin structure assay that maps DNA-DNA-contacts at base pair resolution by sequencing single-stranded DNA fragments released from irradiated cells. Here, we develop a flexible modeling and simulation framework to enable the interpretation of RICC-seq data in terms of oligonucleosome structure ensembles. Nucleosomes are modeled as rigid bodies with excluded volume and adjustable DNA wrapping, connected by linker DNA modeled as a worm-like chain. We validate the model's parameters against cryo-electron microscopy and sedimentation data. Our results show that RICC-seq is sensitive to nucleosome spacing, nucleosomal DNA wrapping, and the strength of inter-nucleosome interactions. We show that nucleosome repeat lengths consistent with orthogonal assays can be extracted from experimental RICC-seq data using a 1D convolutional neural net trained on RICC-seq signal predicted from simulated ensembles. We thus provide a suite of analysis tools that add quantitative structural interpretability to RICC-seq experiments.
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Affiliation(s)
- Ariana Brenner Clerkin
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
- Tri-Institutional PhD Program in Computational Biology and Medicine, Cornell University, New York, NY
| | - Nicole Pagane
- Present affiliation: Computational and Systems Biology PhD Program, Massachusetts Institute of Technology, Cambridge, MA
| | - Devany W. West
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | | | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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14
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Lequieu J. A physical model of euchromatin organization. Proc Natl Acad Sci U S A 2024; 121:e2410751121. [PMID: 39008683 PMCID: PMC11287279 DOI: 10.1073/pnas.2410751121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024] Open
Affiliation(s)
- Joshua Lequieu
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA19104
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15
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Lakadamyali M. From feulgen to modern methods: marking a century of DNA imaging advances. Histochem Cell Biol 2024; 162:13-22. [PMID: 38753186 PMCID: PMC11227465 DOI: 10.1007/s00418-024-02291-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2024] [Indexed: 07/07/2024]
Abstract
The mystery of how human DNA is compactly packaged into a nucleus-a space a hundred thousand times smaller-while still allowing for the regulation of gene function, has long been one of the greatest enigmas in cell biology. This puzzle is gradually being solved, thanks in part to the advent of new technologies. Among these, innovative genome-labeling techniques combined with high-resolution imaging methods have been pivotal. These methods facilitate the visualization of DNA within intact nuclei and have significantly contributed to our current understanding of genome organization. This review will explore various labeling and imaging approaches that are revolutionizing our understanding of the three-dimensional organization of the genome, shedding light on the relationship between its structure and function.
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Affiliation(s)
- Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, USA.
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16
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Presman DM, Benítez B, Lafuente AL, Vázquez Lareu A. Chromatin structure and dynamics: one nucleosome at a time. Histochem Cell Biol 2024; 162:79-90. [PMID: 38607419 DOI: 10.1007/s00418-024-02281-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2024] [Indexed: 04/13/2024]
Abstract
Eukaryotic genomes store information on many levels, including their linear DNA sequence, the posttranslational modifications of its constituents (epigenetic modifications), and its three-dimensional folding. Understanding how this information is stored and read requires multidisciplinary collaborations from many branches of science beyond biology, including physics, chemistry, and computer science. Concurrent recent developments in all these areas have enabled researchers to image the genome with unprecedented spatial and temporal resolution. In this review, we focus on what single-molecule imaging and tracking of individual proteins in live cells have taught us about chromatin structure and dynamics. Starting with the basics of single-molecule tracking (SMT), we describe some advantages over in situ imaging techniques and its current limitations. Next, we focus on single-nucleosome studies and what they have added to our current understanding of the relationship between chromatin dynamics and transcription. In celebration of Robert Feulgen's ground-breaking discovery that allowed us to start seeing the genome, we discuss current models of chromatin structure and future challenges ahead.
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Affiliation(s)
- Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
| | - Belén Benítez
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Agustina L Lafuente
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Alejo Vázquez Lareu
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
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17
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Girard M, de la Cruz MO, Marko JF, Erbaş A. Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus. Phys Rev E 2024; 110:014403. [PMID: 39160964 PMCID: PMC11371272 DOI: 10.1103/physreve.110.014403] [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: 10/18/2023] [Accepted: 05/29/2024] [Indexed: 08/21/2024]
Abstract
The highly and slightly condensed forms of chromatin, heterochromatin and euchromatin, respectively, segregate in the cell nucleus. Heterochromatin is more abundant in the nucleus periphery. Here we study the mechanism of heterochromatin segregation by modeling interphase chromosomes as diblock ring copolymers confined in a rigid spherical shell using molecular dynamics simulations. In our model, heterochromatin and euchromatin are distinguished by their bending stiffnesses only, while an interaction potential between the spherical shell and chromatin is used to model lamin-associated proteins. Our simulations indicate that in the absence of attractive interactions between the nuclear shell and the chromatin, most heterochromatin segregates towards the nuclear interior due to the depletion of less flexible heterochromatin segments from the nuclear periphery. This inverted chromatin distribution,which is opposite to the conventional case with heterochromatin dominating at the periphery, is in accord with experimental observations in rod cells. This "inversion" is also found to be independent of the heterochromatin concentration and chromosome number. The chromatin distribution at the periphery found in vivo can be recovered by further increasing the bending stiffness of heterochromatin segments or by turning on attractive interactions between the nuclear shell and heterochromatin. Our results indicate that the bending stiffness of chromatin could be a contributor to chromosome organization along with differential effects of HP1α-driven phase segregation and of loop extruders and interactions with the nuclear envelope and topological constraints.
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Affiliation(s)
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Department of Chemistry, Department of Chemical and Biological Engineering, and Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
| | | | - Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara 06800, Turkey
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18
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Liu S, Athreya A, Lao Z, Zhang B. From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization. Annu Rev Biophys 2024; 53:221-245. [PMID: 38346246 PMCID: PMC11369498 DOI: 10.1146/annurev-biophys-030822-032650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Chromatin organization plays a critical role in cellular function by regulating access to genetic information. However, understanding chromatin folding is challenging due to its complex, multiscale nature. Significant progress has been made in studying in vitro systems, uncovering the structure of individual nucleosomes and their arrays, and elucidating the role of physicochemical forces in stabilizing these structures. Additionally, remarkable advancements have been achieved in characterizing chromatin organization in vivo, particularly at the whole-chromosome level, revealing important features such as chromatin loops, topologically associating domains, and nuclear compartments. However, bridging the gap between in vitro and in vivo studies remains challenging. The resemblance between in vitro and in vivo chromatin conformations and the relevance of internucleosomal interactions for chromatin folding in vivo are subjects of debate. This article reviews experimental and computational studies conducted at various length scales, highlighting the significance of intrinsic interactions between nucleosomes and their roles in chromatin folding in vivo.
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Affiliation(s)
- Shuming Liu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Advait Athreya
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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19
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Wakim JG, Spakowitz AJ. Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins. Proc Natl Acad Sci U S A 2024; 121:e2317911121. [PMID: 38900792 PMCID: PMC11214050 DOI: 10.1073/pnas.2317911121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 04/15/2024] [Indexed: 06/22/2024] Open
Abstract
Euchromatin is an accessible phase of genetic material containing genes that encode proteins with increased expression levels. The structure of euchromatin in vitro has been described as a 30-nm fiber formed from ordered nucleosome arrays. However, recent advances in microscopy have revealed an in vivo euchromatin architecture that is much more disordered, characterized by variable-length linker DNA and sporadic nucleosome clusters. In this work, we develop a theoretical model to elucidate factors contributing to the disordered in vivo architecture of euchromatin. We begin by developing a 1D model of nucleosome positioning that captures the interactions between bound epigenetic reader proteins to predict the distribution of DNA linker lengths between adjacent nucleosomes. We then use the predicted linker lengths to construct 3D chromatin configurations consistent with the physical properties of DNA within the nucleosome array, and we evaluate the distribution of nucleosome cluster sizes in those configurations. Our model reproduces experimental cluster-size distributions, which are dramatically influenced by the local pattern of epigenetic marks and the concentration of reader proteins. Based on our model, we attribute the disordered arrangement of euchromatin to the heterogeneous binding of reader proteins and subsequent short-range interactions between bound reader proteins on adjacent nucleosomes. By replicating experimental results with our physics-based model, we propose a mechanism for euchromatin organization in the nucleus that impacts gene regulation and the maintenance of epigenetic marks.
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Affiliation(s)
- Joseph G. Wakim
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
| | - Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Materials Science and Engineering, Stanford University, Stanford, CA94305
- Biophysics Program, Stanford University, Stanford, CA94305
- Department of Applied Physics, Stanford University, Stanford, CA94305
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20
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Hsiao YT, Liao IH, Wu BK, Chu HPC, Hsieh CL. Probing chromatin condensation dynamics in live cells using interferometric scattering correlation spectroscopy. Commun Biol 2024; 7:763. [PMID: 38914653 PMCID: PMC11196589 DOI: 10.1038/s42003-024-06457-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
Chromatin organization and dynamics play important roles in governing the regulation of nuclear processes of biological cells. However, due to the constant diffusive motion of chromatin, examining chromatin nanostructures in living cells has been challenging. In this study, we introduce interferometric scattering correlation spectroscopy (iSCORS) to spatially map nanoscopic chromatin configurations within unlabeled live cell nuclei. This label-free technique captures time-varying linear scattering signals generated by the motion of native chromatin on a millisecond timescale, allowing us to deduce chromatin condensation states. Using iSCORS imaging, we quantitatively examine chromatin dynamics over extended periods, revealing spontaneous fluctuations in chromatin condensation and heterogeneous compaction levels in interphase cells, independent of cell phases. Moreover, we observe changes in iSCORS signals of chromatin upon transcription inhibition, indicating that iSCORS can probe nanoscopic chromatin structures and dynamics associated with transcriptional activities. Our scattering-based optical microscopy, which does not require labeling, serves as a powerful tool for visualizing dynamic chromatin nano-arrangements in live cells. This advancement holds promise for studying chromatin remodeling in various crucial cellular processes, such as stem cell differentiation, mechanotransduction, and DNA repair.
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Affiliation(s)
- Yi-Teng Hsiao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - I-Hsin Liao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Bo-Kuan Wu
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | | | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan.
- Department of Physics, National Taiwan University, Taipei, Taiwan.
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21
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Carignano M, Kröger M, Almassalha LM, Agrawal V, Li WS, Pujadas-Liwag EM, Nap RJ, Backman V, Szleifer I. Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin. ARXIV 2024:arXiv:2310.02257v3. [PMID: 38495560 PMCID: PMC10942481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally-defined domains observed by single cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as Rad21 degradation.
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Affiliation(s)
- Marcelo Carignano
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Martin Kröger
- Magnetism and Interface Physics & Computational Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Luay Matthew Almassalha
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago IL 60611, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Wing Shun Li
- Applied Physics Program, Northwestern, University, Evanston, IL 60208, USA
| | | | - Rikkert J. Nap
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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22
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Neděla V, Tihlaříková E, Cápal P, Doležel J. Advanced environmental scanning electron microscopy reveals natural surface nano-morphology of condensed mitotic chromosomes in their native state. Sci Rep 2024; 14:12998. [PMID: 38844535 PMCID: PMC11156959 DOI: 10.1038/s41598-024-63515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
The challenge of in-situ handling and high-resolution low-dose imaging of intact, sensitive and wet samples in their native state at nanometer scale, including live samples is met by Advanced Environmental Scanning Electron Microscopy (A-ESEM). This new generation of ESEM utilises machine learning-based optimization of thermodynamic conditions with respect to sample specifics to employ a low temperature method and an ionization secondary electron detector with an electrostatic separator. A modified electron microscope was used, equipped with temperature, humidity and gas pressure sensors for in-situ and real-time monitoring of the sample. A transparent ultra-thin film of ionic liquid is used to increase thermal and electrical conductivity of the samples and to minimize sample damage by free radicals. To validate the power of the new method, we analyze condensed mitotic metaphase chromosomes to reveal new structural features of their perichromosomal layer, and the organization of chromatin fibers, not observed before by any microscopic technique. The ability to resolve nano-structural details of chromosomes using A-ESEM is validated by measuring gold nanoparticles with achievable resolution in the lower nanometre units.
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Affiliation(s)
- Vilém Neděla
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, 612 00, Czech Republic.
| | - Eva Tihlaříková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, 612 00, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, Olomouc, 772 00, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, Olomouc, 772 00, Czech Republic
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23
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Orsetti A, van Oosten D, Vasarhelyi RG, Dănescu TM, Huertas J, van Ingen H, Cojocaru V. Structural dynamics in chromatin unraveling by pioneer transcription factors. Biophys Rev 2024; 16:365-382. [PMID: 39099839 PMCID: PMC11297019 DOI: 10.1007/s12551-024-01205-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/18/2024] [Indexed: 08/06/2024] Open
Abstract
Pioneer transcription factors are proteins with a dual function. First, they regulate transcription by binding to nucleosome-free DNA regulatory elements. Second, they bind to DNA while wrapped around histone proteins in the chromatin and mediate chromatin opening. The molecular mechanisms that connect the two functions are yet to be discovered. In recent years, pioneer factors received increased attention mainly because of their crucial role in promoting cell fate transitions that could be used for regenerative therapies. For example, the three factors required to induce pluripotency in somatic cells, Oct4, Sox2, and Klf4 were classified as pioneer factors and studied extensively. With this increased attention, several structures of complexes between pioneer factors and chromatin structural units (nucleosomes) have been resolved experimentally. Furthermore, experimental and computational approaches have been designed to study two unresolved, key scientific questions: First, do pioneer factors induce directly local opening of nucleosomes and chromatin fibers upon binding? And second, how do the unstructured tails of the histones impact the structural dynamics involved in such conformational transitions? Here we review the current knowledge about transcription factor-induced nucleosome dynamics and the role of the histone tails in this process. We discuss what is needed to bridge the gap between the static views obtained from the experimental structures and the key structural dynamic events in chromatin opening. Finally, we propose that integrating nuclear magnetic resonance spectroscopy with molecular dynamics simulations is a powerful approach to studying pioneer factor-mediated dynamics of nucleosomes and perhaps small chromatin fibers using native DNA sequences.
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Affiliation(s)
- Andrea Orsetti
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Daphne van Oosten
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | | | - Theodor-Marian Dănescu
- Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Jan Huertas
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, England
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Vlad Cojocaru
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
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24
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Rudnizky S, Murray PJ, Wolfe CH, Ha T. Single-Macromolecule Studies of Eukaryotic Genomic Maintenance. Annu Rev Phys Chem 2024; 75:209-230. [PMID: 38382570 DOI: 10.1146/annurev-physchem-090722-010601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.
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Affiliation(s)
- Sergei Rudnizky
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter J Murray
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
| | - Clara H Wolfe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
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25
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Shim AR, Frederick J, Pujadas EM, Kuo T, Ye IC, Pritchard JA, Dunton CL, Gonzalez PC, Acosta N, Jain S, Anthony NM, Almassalha LM, Szleifer I, Backman V. Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure. PLoS One 2024; 19:e0301000. [PMID: 38805476 PMCID: PMC11132451 DOI: 10.1371/journal.pone.0301000] [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: 08/01/2023] [Accepted: 03/10/2024] [Indexed: 05/30/2024] Open
Abstract
As imaging techniques rapidly evolve to probe nanoscale genome organization at higher resolution, it is critical to consider how the reagents and procedures involved in sample preparation affect chromatin at the relevant length scales. Here, we investigate the effects of fluorescent labeling of DNA sequences within chromatin using the gold standard technique of three-dimensional fluorescence in situ hybridization (3D FISH). The chemical reagents involved in the 3D FISH protocol, specifically formamide, cause significant alterations to the sub-200 nm (sub-Mbp) chromatin structure. Alternatively, two labeling methods that do not rely on formamide denaturation, resolution after single-strand exonuclease resection (RASER)-FISH and clustered regularly interspaced short palindromic repeats (CRISPR)-Sirius, had minimal impact on the three-dimensional organization of chromatin. We present a polymer physics-based analysis of these protocols with guidelines for their interpretation when assessing chromatin structure using currently available techniques.
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Affiliation(s)
- Anne R. Shim
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Emily M. Pujadas
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Tiffany Kuo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - I. Chae Ye
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Joshua A. Pritchard
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Cody L. Dunton
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Paola Carrillo Gonzalez
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Nicolas Acosta
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Surbhi Jain
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Nicholas M. Anthony
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
| | - Luay M. Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, Illinois, United States of America
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Department of Chemistry, Northwestern University, Evanston, Illinois, United States of America
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, United States of America
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, Illinois, United States of America
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America
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26
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Zhang M, Díaz-Celis C, Liu J, Tao J, Ashby PD, Bustamante C, Ren G. Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography. Nat Commun 2024; 15:4395. [PMID: 38782894 PMCID: PMC11116431 DOI: 10.1038/s41467-024-48305-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.
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Affiliation(s)
- Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Applied Science and Technology Graduate Group, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - César Díaz-Celis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jinhui Tao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Ashby
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carlos Bustamante
- Applied Science and Technology Graduate Group, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Department of Physics, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Kavli Energy Nanoscience Institute, University of California, Berkeley, CA, USA.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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27
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Kant A, Guo Z, Vinayak V, Neguembor MV, Li WS, Agrawal V, Pujadas E, Almassalha L, Backman V, Lakadamyali M, Cosma MP, Shenoy VB. Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization. Nat Commun 2024; 15:4338. [PMID: 38773126 PMCID: PMC11109243 DOI: 10.1038/s41467-024-48698-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this relationship, considering chromatin-chromatin interactions, histone modifications, and chromatin extrusion. We predict that the size of heterochromatic domains is governed by a balance among the diffusive flux of methylated histones sustaining them and the acetylation reactions in the domains and the process of loop extrusion via supercoiling by RNAPII at their periphery, which contributes to size reduction. Super-resolution and nano-imaging of five distinct cell lines confirm the predictions indicating that the absence of transcription leads to larger heterochromatin domains. Furthermore, the model accurately reproduces the findings regarding how transcription-mediated supercoiling loss can mitigate the impacts of excessive cohesin loading. Our findings shed light on the role of transcription in genome organization, offering insights into chromatin dynamics and potential therapeutic targets.
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Affiliation(s)
- Aayush Kant
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zixian Guo
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vinayak Vinayak
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Wing Shun Li
- Department of Applied Physics, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Vasundhara Agrawal
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Emily Pujadas
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
| | - Luay Almassalha
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL, 60611, USA
| | - Vadim Backman
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60202, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Melike Lakadamyali
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- ICREA, Barcelona, 08010, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain
| | - Vivek B Shenoy
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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28
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Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR. Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. Nat Commun 2024; 15:4178. [PMID: 38755200 PMCID: PMC11099156 DOI: 10.1038/s41467-024-48562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we present an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrate that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacts nucleosome diffusive properties in a manner that is dependent both on local chromatin density and on relative location within the nucleus. Our results support a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Additionally, they reveal that nuclear heterogeneity arises from both active and passive processes and highlight the need to account for different organizational principles when modeling different chromatin environments.
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Affiliation(s)
- Timothy A Daugird
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yu Shi
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA
| | - Katie L Holland
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Hosein Rostamian
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Joseph Rodriguez
- National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wesley R Legant
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA.
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29
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Choudhury R, Venkateswaran Venkatasubramani A, Hua J, Borsò M, Franconi C, Kinkley S, Forné I, Imhof A. The role of RNA in the maintenance of chromatin domains as revealed by antibody-mediated proximity labelling coupled to mass spectrometry. eLife 2024; 13:e95718. [PMID: 38717135 PMCID: PMC11147508 DOI: 10.7554/elife.95718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Eukaryotic chromatin is organized into functional domains, that are characterized by distinct proteomic compositions and specific nuclear positions. In contrast to cellular organelles surrounded by lipid membranes, the composition of distinct chromatin domains is rather ill described and highly dynamic. To gain molecular insight into these domains and explore their composition, we developed an antibody-based proximity biotinylation method targeting the RNA and proteins constituents. The method that we termed antibody-mediated proximity labelling coupled to mass spectrometry (AMPL-MS) does not require the expression of fusion proteins and therefore constitutes a versatile and very sensitive method to characterize the composition of chromatin domains based on specific signature proteins or histone modifications. To demonstrate the utility of our approach we used AMPL-MS to characterize the molecular features of the chromocenter as well as the chromosome territory containing the hyperactive X chromosome in Drosophila. This analysis identified a number of known RNA-binding proteins in proximity of the hyperactive X and the centromere, supporting the accuracy of our method. In addition, it enabled us to characterize the role of RNA in the formation of these nuclear bodies. Furthermore, our method identified a new set of RNA molecules associated with the Drosophila centromere. Characterization of these novel molecules suggested the formation of R-loops in centromeres, which we validated using a novel probe for R-loops in Drosophila. Taken together, AMPL-MS improves the selectivity and specificity of proximity ligation allowing for novel discoveries of weak protein-RNA interactions in biologically diverse domains.
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Affiliation(s)
- Rupam Choudhury
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Anuroop Venkateswaran Venkatasubramani
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Jie Hua
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Marco Borsò
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Celeste Franconi
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Sarah Kinkley
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Axel Imhof
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
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30
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Oberbeckmann E, Oudelaar AM. Genome organization across scales: mechanistic insights from in vitro reconstitution studies. Biochem Soc Trans 2024; 52:793-802. [PMID: 38451192 PMCID: PMC11088924 DOI: 10.1042/bst20230883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Eukaryotic genomes are compacted and organized into distinct three-dimensional (3D) structures, which range from small-scale nucleosome arrays to large-scale chromatin domains. These chromatin structures play an important role in the regulation of transcription and other nuclear processes. The molecular mechanisms that drive the formation of chromatin structures across scales and the relationship between chromatin structure and function remain incompletely understood. Because the processes involved are complex and interconnected, it is often challenging to dissect the underlying principles in the nuclear environment. Therefore, in vitro reconstitution systems provide a valuable approach to gain insight into the molecular mechanisms by which chromatin structures are formed and to determine the cause-consequence relationships between the processes involved. In this review, we give an overview of in vitro approaches that have been used to study chromatin structures across scales and how they have increased our understanding of the formation and function of these structures. We start by discussing in vitro studies that have given insight into the mechanisms of nucleosome positioning. Next, we discuss recent efforts to reconstitute larger-scale chromatin domains and loops and the resulting insights into the principles of genome organization. We conclude with an outlook on potential future applications of chromatin reconstitution systems and how they may contribute to answering open questions concerning chromatin architecture.
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Affiliation(s)
- Elisa Oberbeckmann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - A. Marieke Oudelaar
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
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31
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Hildebrand EM, Polovnikov K, Dekker B, Liu Y, Lafontaine DL, Fox AN, Li Y, Venev SV, Mirny LA, Dekker J. Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. Mol Cell 2024; 84:1422-1441.e14. [PMID: 38521067 DOI: 10.1016/j.molcel.2024.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/23/2023] [Accepted: 02/24/2024] [Indexed: 03/25/2024]
Abstract
The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations, and multi-contact 3C and find that, by contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a topoisomerase-II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias topoisomerase II activity toward decatenation. At the second stage, the loops are released, and the formation of new entanglements is prevented by lower topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed in experiments and models, a normal interphase state cannot be acquired.
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Affiliation(s)
- Erica M Hildebrand
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - Bastiaan Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Yu Liu
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Temple Health, Philadelphia, PA 19111, USA
| | - Denis L Lafontaine
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - A Nicole Fox
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ying Li
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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32
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Movilla Miangolarra A, Saxton DS, Yan Z, Rine J, Howard M. Two-way feedback between chromatin compaction and histone modification state explains Saccharomyces cerevisiae heterochromatin bistability. Proc Natl Acad Sci U S A 2024; 121:e2403316121. [PMID: 38593082 PMCID: PMC11032488 DOI: 10.1073/pnas.2403316121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/02/2024] [Indexed: 04/11/2024] Open
Abstract
Compact chromatin is closely linked with gene silencing in part by sterically masking access to promoters, inhibiting transcription factor binding and preventing polymerase from efficiently transcribing a gene. However, a broader hypothesis suggests that chromatin compaction can be both a cause and a consequence of the locus histone modification state, with a tight bidirectional interaction underpinning bistable transcriptional states. To rigorously test this hypothesis, we developed a mathematical model for the dynamics of the HMR locus in Saccharomyces cerevisiae, that incorporates activating histone modifications, silencing proteins, and a dynamic, acetylation-dependent, three-dimensional locus size. Chromatin compaction enhances silencer protein binding, which in turn feeds back to remove activating histone modifications, leading to further compaction. The bistable output of the model was in good agreement with prior quantitative data, including switching rates from expressed to silent states (and vice versa), and protein binding/histone modification levels within the locus. We then tested the model by predicting changes in switching rates as the genetic length of the locus was increased, which were then experimentally verified. Such bidirectional feedback between chromatin compaction and the histone modification state may be a widespread and important regulatory mechanism given the hallmarks of many heterochromatic regions: physical chromatin compaction and dimerizing (or multivalent) silencing proteins.
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Affiliation(s)
| | - Daniel S. Saxton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Zhi Yan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
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33
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Lizana L, Schwartz YB. The scales, mechanisms, and dynamics of the genome architecture. SCIENCE ADVANCES 2024; 10:eadm8167. [PMID: 38598632 PMCID: PMC11006219 DOI: 10.1126/sciadv.adm8167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Even when split into several chromosomes, DNA molecules that make up our genome are too long to fit into the cell nuclei unless massively folded. Such folding must accommodate the need for timely access to selected parts of the genome by transcription factors, RNA polymerases, and DNA replication machinery. Here, we review our current understanding of the genome folding inside the interphase nuclei. We consider the resulting genome architecture at three scales with a particular focus on the intermediate (meso) scale and summarize the insights gained from recent experimental observations and diverse computational models.
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Affiliation(s)
- Ludvig Lizana
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
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34
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Zülske T, Attou A, Groß L, Hörl D, Harz H, Wedemann G. Nucleosome spacing controls chromatin spatial structure and accessibility. Biophys J 2024; 123:847-857. [PMID: 38419332 PMCID: PMC10995425 DOI: 10.1016/j.bpj.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
Recent research highlights the significance of the three-dimensional structure of chromatin in regulating various cellular processes, particularly transcription. This is achieved through dynamic chromatin structures that facilitate long-range contacts and control spatial accessibility. Chromatin consists of DNA and a variety of proteins, of which histones play an essential structural role by forming nucleosomes. Extensive experimental and theoretical research in recent decades has yielded conflicting results about key factors that regulate the spatial structure of chromatin, which remains enigmatic. By using a computer model that allows us to simulate chromatin volumes containing physiological nucleosome concentrations, we investigated whether nucleosome spacing or nucleosome density is fundamental for three-dimensional chromatin accessibility. Unexpectedly, the regularity of the nucleosome spacing is crucial for determining the accessibility of the chromatin network to diffusive processes, whereas variation in nucleosome concentrations has only minor effects. Using only the basic physical properties of DNA and nucleosomes was sufficient to generate chromatin structures consistent with published electron microscopy data. Contrary to other work, we found that nucleosome density did not substantially alter the properties of chromatin fibers or contact probabilities of genomic loci. No breakup of fiber-like structures was observed at high molar density. These findings challenge previous assumptions and highlight the importance of nucleosome spacing as a key driver of chromatin organization. These results identified changes in nucleosome spacing as a tentative mechanism for altering the spatial chromatin structure and thus genomic functions.
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Affiliation(s)
- Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Aymen Attou
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany; Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Laurens Groß
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - David Hörl
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hartmann Harz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
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35
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Chang A, Prabhala S, Daneshkhah A, Lin J, Subramanian H, Roy HK, Backman V. Early screening of colorectal cancer using feature engineering with artificial intelligence-enhanced analysis of nanoscale chromatin modifications. Sci Rep 2024; 14:7808. [PMID: 38565871 PMCID: PMC10987630 DOI: 10.1038/s41598-024-58016-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Colonoscopy is accurate but inefficient for colorectal cancer (CRC) prevention due to the low (~ 7 to 8%) prevalence of target lesions, advanced adenomas. We leveraged rectal mucosa to identify patients who harbor CRC field carcinogenesis by evaluating chromatin 3D architecture. Supranucleosomal disordered chromatin chains (~ 5 to 20 nm, ~1 kbp) fold into chromatin packing domains (~ 100 to 200 nm, ~ 100 to 1000 kbp). In turn, the fractal-like conformation of DNA within chromatin domains and the folding of the genome into packing domains has been shown to influence multiple facets of gene transcription, including the transcriptional plasticity of cancer cells. We deployed an optical spectroscopic nanosensing technique, chromatin-sensitive partial wave spectroscopic microscopy (csPWS), to evaluate the packing density scaling D of the chromatin chain conformation within packing domains from rectal mucosa in 256 patients with varying degrees of progression to colorectal cancer. We found average packing scaling D of chromatin domains was elevated in tumor cells, histologically normal-appearing cells 4 cm proximal to the tumor, and histologically normal-appearing rectal mucosa compared to cells from control patients (p < 0.001). Nuclear D had a robust correlation with the model of 5-year risk of CRC with r2 = 0.94. Furthermore, rectal D was evaluated as a screening biomarker for patients with advanced adenomas presenting an AUC of 0.85 and 85% sensitivity and specificity. artificial intelligence-enhanced csPWS improved diagnostic performance with AUC = 0.90. Considering the low sensitivity of existing CRC tests, including liquid biopsies, to early-stage cancers our work highlights the potential of chromatin biomarkers of field carcinogenesis in detecting early, significant precancerous colon lesions.
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Affiliation(s)
- Andrew Chang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Sravya Prabhala
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Ali Daneshkhah
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | | | - Hariharan Subramanian
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- NanoCytomics, Evanston, IL, USA
| | | | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
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36
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Li NN, Lun DX, Gong N, Meng G, Du XY, Wang H, Bao X, Li XY, Song JW, Hu K, Li L, Li SY, Liu W, Zhu W, Zhang Y, Li J, Yao T, Mou L, Han X, Hao F, Hu Y, Liu L, Zhu H, Wu Y, Liu B. Targeting the chromatin structural changes of antitumor immunity. J Pharm Anal 2024; 14:100905. [PMID: 38665224 PMCID: PMC11043877 DOI: 10.1016/j.jpha.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 04/28/2024] Open
Abstract
Epigenomic imbalance drives abnormal transcriptional processes, promoting the onset and progression of cancer. Although defective gene regulation generally affects carcinogenesis and tumor suppression networks, tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes, which may have significant implications for the development and application of epigenetic therapy, cancer immunotherapy, and their combinations. Herein, we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes, DNA methylation, histone post-translational modification, and chromatin structure in tumor immunogenicity, and introduce these epigenetic research methods. We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immunotherapy through the complex interaction between cancer epigenetics and cancer immunology.
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Affiliation(s)
- Nian-nian Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Deng-xing Lun
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Ningning Gong
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, Shaanxi, 725000, China
| | - Xin-ying Du
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - He Wang
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiangxiang Bao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xin-yang Li
- Guizhou Education University, Guiyang, 550018, China
| | - Ji-wu Song
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Kewei Hu
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Lala Li
- Guizhou Normal University, Guiyang, 550025, China
| | - Si-ying Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wenbo Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wanping Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yunlong Zhang
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jikai Li
- Department of Bone and Soft Tissue Oncology, Tianjin Hospital, Tianjin, 300299, China
| | - Ting Yao
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
| | - Leming Mou
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaoqing Han
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Furong Hao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yongcheng Hu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Lin Liu
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongguang Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yuyun Wu
- Xinqiao Hospital of Army Military Medical University, Chongqing, 400038, China
| | - Bin Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
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37
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Belan S, Parfenyev V. Footprints of loop extrusion in statistics of intra-chromosomal distances: An analytically solvable model. J Chem Phys 2024; 160:124901. [PMID: 38516975 DOI: 10.1063/5.0199573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Active loop extrusion-the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes-is a firmly established mechanism responsible for chromatin spatial organization at different stages of a cell cycle in eukaryotes and bacteria. The theoretical insight into the effect of loop extrusion on the experimentally measured statistics of chromatin conformation can be gained with an appropriately chosen polymer model. Here, we consider the simplest analytically solvable model of an interphase chromosome, which is treated as an ideal chain with disorder of sufficiently sparse random loops whose conformations are sampled from the equilibrium ensemble. This framework allows us to arrive at the closed-form analytical expression for the mean-squared distance between pairs of genomic loci, which is valid beyond the one-loop approximation in diagrammatic representation. In addition, we analyze the loop-induced deviation of chain conformations from the Gaussian statistics by calculating kurtosis of probability density of the pairwise separation vector. The presented results suggest the possible ways of estimating the characteristics of the loop extrusion process based on the experimental data on the scale-dependent statistics of intra-chromosomal pair-wise distances.
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Affiliation(s)
- Sergey Belan
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova Av., 142432 Chernogolovka, Russia
- National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
| | - Vladimir Parfenyev
- Landau Institute for Theoretical Physics, Russian Academy of Sciences, 1-A Akademika Semenova Av., 142432 Chernogolovka, Russia
- National Research University Higher School of Economics, Faculty of Physics, Myasnitskaya 20, 101000 Moscow, Russia
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38
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Pujadas Liwag EM, Wei X, Acosta N, Carter LM, Yang J, Almassalha LM, Jain S, Daneshkhah A, Rao SSP, Seker-Polat F, MacQuarrie KL, Ibarra J, Agrawal V, Aiden EL, Kanemaki MT, Backman V, Adli M. Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism. Genome Biol 2024; 25:77. [PMID: 38519987 PMCID: PMC10958841 DOI: 10.1186/s13059-024-03212-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/07/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND B-type lamins are critical nuclear envelope proteins that interact with the three-dimensional genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been challenging as their joint depletion severely impacts cell viability. To overcome this, we engineered mammalian cells to rapidly and completely degrade endogenous B-type lamins using Auxin-inducible degron technology. RESULTS Using live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, Stochastic Optical Reconstruction Microscopy (STORM), in situ Hi-C, CRISPR-Sirius, and fluorescence in situ hybridization (FISH), we demonstrate that lamin B1 and lamin B2 are critical structural components of the nuclear periphery that create a repressive compartment for peripheral-associated genes. Lamin B1 and lamin B2 depletion minimally alters higher-order chromatin folding but disrupts cell morphology, significantly increases chromatin mobility, redistributes both constitutive and facultative heterochromatin, and induces differential gene expression both within and near lamin-associated domain (LAD) boundaries. Critically, we demonstrate that chromatin territories expand as upregulated genes within LADs radially shift inwards. Our results indicate that the mechanism of action of B-type lamins comes from their role in constraining chromatin motion and spatial positioning of gene-specific loci, heterochromatin, and chromatin domains. CONCLUSIONS Our findings suggest that, while B-type lamin degradation does not significantly change genome topology, it has major implications for three-dimensional chromatin conformation at the single-cell level both at the lamina-associated periphery and the non-LAD-associated nuclear interior with concomitant genome-wide transcriptional changes. This raises intriguing questions about the individual and overlapping roles of lamin B1 and lamin B2 in cellular function and disease.
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Affiliation(s)
- Emily M Pujadas Liwag
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Xiaolong Wei
- Department of Surgery, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Nicolas Acosta
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Lucas M Carter
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- IBIS Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Jiekun Yang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Luay M Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, IL, 60611, USA
| | - Surbhi Jain
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Ali Daneshkhah
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, 77030, USA
- School of Medicine, Stanford University, Stanford, CA, 94305, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fidan Seker-Polat
- Feinberg School of Medicine, Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL, 60611, USA
| | - Kyle L MacQuarrie
- Feinberg School of Medicine, Robert Lurie Comprehensive Cancer Center, Department of Pediatrics, Northwestern University, Chicago, IL, 60611, USA
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Joe Ibarra
- Feinberg School of Medicine, Robert Lurie Comprehensive Cancer Center, Department of Pediatrics, Northwestern University, Chicago, IL, 60611, USA
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Vasundhara Agrawal
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Erez Lieberman Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77030, USA
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX, 77030, USA
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Center for Physical Genomics and Engineering, Northwestern University, Evanston, IL, 60208, USA.
| | - Mazhar Adli
- Feinberg School of Medicine, Robert Lurie Comprehensive Cancer Center, Department of Obstetrics and Gynecology, Northwestern University, Chicago, IL, 60611, USA.
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39
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Santarelli P, Rosti V, Vivo M, Lanzuolo C. Chromatin organization of muscle stem cell. Curr Top Dev Biol 2024; 158:375-406. [PMID: 38670713 DOI: 10.1016/bs.ctdb.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The proper functioning of skeletal muscles is essential throughout life. A crucial crosstalk between the environment and several cellular mechanisms allows striated muscles to perform successfully. Notably, the skeletal muscle tissue reacts to an injury producing a completely functioning tissue. The muscle's robust regenerative capacity relies on the fine coordination between muscle stem cells (MuSCs or "satellite cells") and their specific microenvironment that dictates stem cells' activation, differentiation, and self-renewal. Critical for the muscle stem cell pool is a fine regulation of chromatin organization and gene expression. Acquiring a lineage-specific 3D genome architecture constitutes a crucial modulator of muscle stem cell function during development, in the adult stage, in physiological and pathological conditions. The context-dependent relationship between genome structure, such as accessibility and chromatin compartmentalization, and their functional effects will be analysed considering the improved 3D epigenome knowledge, underlining the intimate liaison between environmental encounters and epigenetics.
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Affiliation(s)
- Philina Santarelli
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Valentina Rosti
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy
| | - Maria Vivo
- Università degli studi di Salerno, Fisciano, Italy.
| | - Chiara Lanzuolo
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy.
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40
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Wang Z, Zhang Z, Luo S, Zhou T, Zhang J. Power-law behavior of transcriptional bursting regulated by enhancer-promoter communication. Genome Res 2024; 34:106-118. [PMID: 38171575 PMCID: PMC10903953 DOI: 10.1101/gr.278631.123] [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: 04/12/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Revealing how transcriptional bursting kinetics are genomically encoded is challenging because genome structures are stochastic at the organization level and are suggestively linked to gene transcription. To address this challenge, we develop a generic theoretical framework that integrates chromatin dynamics, enhancer-promoter (E-P) communication, and gene-state switching to study transcriptional bursting. The theory predicts that power law can be a general rule to quantitatively describe bursting modulations by E-P spatial communication. Specifically, burst frequency and burst size are up-regulated by E-P communication strength, following power laws with positive exponents. Analysis of the scaling exponents further reveals that burst frequency is preferentially regulated. Bursting kinetics are down-regulated by E-P genomic distance with negative power-law exponents, and this negative modulation desensitizes at large distances. The mutual information between burst frequency (or burst size) and E-P spatial distance further reveals essential characteristics of the information transfer from E-P communication to transcriptional bursting kinetics. These findings, which are in agreement with experimental observations, not only reveal fundamental principles of E-P communication in transcriptional bursting but also are essential for understanding cellular decision-making.
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Affiliation(s)
- Zihao Wang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Zhenquan Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Songhao Luo
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China;
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jiajun Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China;
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
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41
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Lin X, Zhang B. Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 2024; 12:RP90073. [PMID: 38289342 PMCID: PMC10945522 DOI: 10.7554/elife.90073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 kBT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono- and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9 kBT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
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42
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Li Z, Schlick T. Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics. Nucleic Acids Res 2024; 52:583-599. [PMID: 38015443 PMCID: PMC10810283 DOI: 10.1093/nar/gkad1121] [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: 07/06/2023] [Revised: 10/12/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXA and Fbn2 mouse genes ranging in size from 50 to 100 kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.
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Affiliation(s)
- Zilong Li
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA
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43
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Liang J, Han J, Gao X, Jia H, Li R, Tse ECM, Li Y. Clickable APEX2 Probes for Enhanced RNA Proximity Labeling in Live Cells. Anal Chem 2024; 96:685-693. [PMID: 38099807 DOI: 10.1021/acs.analchem.3c03614] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Although APEX2-mediated proximity labeling has been extensively implemented for studying RNA subcellular localization in live cells, the biotin-phenoxyl radical used for labeling RNAs has a relatively low efficiency, which can limit its compatibility with other profiling methods. Herein, a set of phenol derivatives were designed as APEX2 probes through balancing reactivity, hydrophilicity, and lipophilicity. Among these derivatives, Ph_N3 exhibited reliable labeling ability and enabled two biotinylation routes for downstream analysis. As a proof of concept, we used APEX2/Ph_N3 labeling with high-throughput sequencing analysis to examine the transcriptomes in the mitochondrial matrix, demonstrating high sensitivity and specificity. To further expand the utility of Ph_N3, we employed mechanistically orthogonal APEX2 and singlet oxygen (1O2)-mediated strategies for dual location labeling in live cells. Specifically, DRAQ5, a DNA-intercalating photosensitizer, was applied for nucleus-restricted 1O2 labeling. We validated the orthogonality of APEX2/Ph_N3 and DRAQ5-1O2 at the imaging level, providing an attractive and feasible approach for future studies of RNA translocation in live cells.
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Affiliation(s)
- Jiying Liang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jinghua Han
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xutao Gao
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Han Jia
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ran Li
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing 100871, China
| | - Edmund C M Tse
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong, China
| | - Ying Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong, China
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44
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Luo B, Zhang Z, Li B, Zhang H, Ma J, Li J, Han Z, Zhang C, Zhang S, Yu T, Zhang G, Ma P, Lan Y, Zhang X, Liu D, Wu L, Gao D, Gao S, Su S, Zhang X, Gao S. Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:33-52. [PMID: 37731059 DOI: 10.1111/tpj.16468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/28/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023]
Abstract
Chromatin in eukaryotes folds into a complex three-dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low-Pi treatment led to greater chromatin volume. Furthermore, low-Pi stress increased the insulation score and the number of TAD-like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD-like boundaries, whereas RdDM peak levels at conserved TAD-like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome-wide RdDM sites near TAD-like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low-Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low-Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP-seq results revealed that ZmDDM1A could bind to Pi- and root development-related genes. Strong associations were found between interacting genes in significantly different chromatin-interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low-Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.
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Affiliation(s)
- Bowen Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Ziqi Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Binyang Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Haiying Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Junchi Ma
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Zheng Han
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Chong Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shuhao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Ting Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Guidi Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Peng Ma
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
- Mianyang Academy of Agricultural Sciences, Mianyang, 621023, Sichuan, China
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang, China
| | - Yuzhou Lan
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422, Lomma, Sweden
| | - Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Dan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Ling Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Duojiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shiqiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shunzong Su
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Shibin Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
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45
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Liang Z, Solano A, Lou J, Hinde E. Histone FRET reports the spatial heterogeneity in nanoscale chromatin architecture that is imparted by the epigenetic landscape at the level of single foci in an intact cell nucleus. Chromosoma 2024; 133:5-14. [PMID: 38265456 PMCID: PMC10904561 DOI: 10.1007/s00412-024-00815-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Genome sequencing has identified hundreds of histone post-translational modifications (PTMs) that define an open or compact chromatin nanostructure at the level of nucleosome proximity, and therefore serve as activators or repressors of gene expression. Direct observation of this epigenetic mode of transcriptional regulation in an intact single nucleus, is however, a complex task. This is because despite the development of fluorescent probes that enable observation of specific histone PTMs and chromatin density, the changes in nucleosome proximity regulating gene expression occur on a spatial scale well below the diffraction limit of optical microscopy. In recent work, to address this research gap, we demonstrated that the phasor approach to fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) between fluorescently labelled histones core to the nucleosome, is a readout of chromatin nanostructure that can be multiplexed with immunofluorescence (IF) against specific histone PTMs. Here from application of this methodology to gold standard gene activators (H3K4Me3 and H3K9Ac) versus repressors (e.g., H3K9Me3 and H3K27Me), we find that while on average these histone marks do impart an open versus compact chromatin nanostructure, at the level of single chromatin foci, there is significant spatial heterogeneity. Collectively this study illustrates the importance of studying the epigenetic landscape as a function of space within intact nuclear architecture and opens the door for the study of chromatin foci sub-populations defined by combinations of histone marks, as is seen in the context of bivalent chromatin.
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Affiliation(s)
- Zhen Liang
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia
- Cancer and RNA Laboratory, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medicine, Melbourne Medical School, St Vincent's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Ashleigh Solano
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
| | - Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
| | - Elizabeth Hinde
- Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia.
- School of Physics, University of Melbourne, Melbourne, VIC, Australia.
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46
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Castillon GA, Phan S, Hu J, Boassa D, Adams SR, Ellisman MH. Proximal Molecular Probe Transfer (PROMPT), a new approach for identifying sites of protein/nucleic acid interaction in cells by correlated light and electron microscopy. Sci Rep 2023; 13:21462. [PMID: 38052818 PMCID: PMC10697944 DOI: 10.1038/s41598-023-45413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/19/2023] [Indexed: 12/07/2023] Open
Abstract
The binding and interaction of proteins with nucleic acids such as DNA and RNA constitutes a fundamental biochemical and biophysical process in all living organisms. Identifying and visualizing such temporal interactions in cells is key to understanding their function. To image sites of these events in cells across scales, we developed a method, named PROMPT for PROximal Molecular Probe Transfer, which is applicable to both light and correlative electron microscopy. This method relies on the transfer of a bound photosensitizer from a protein known to associate with specific nucleic acid sequence, allowing the marking of the binding site on DNA or RNA in fixed cells. The method produces a fluorescent mark at the site of their interaction, that can be made electron dense and reimaged at high resolution in the electron microscope. As proof of principle, we labeled in situ the interaction sites between the histone H2B and nuclear DNA. As an example of application for specific RNA localizations we labeled different nuclear and nucleolar fractions of the protein Fibrillarin to mark and locate where it associates with RNAs, also using electron tomography. While the current PROMPT method is designed for microscopy, with minimal variations, it can be potentially expanded to analytical techniques.
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Affiliation(s)
- Guillaume A Castillon
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sebastien Phan
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Junru Hu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniela Boassa
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Stephen R Adams
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, 92093, USA.
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Vizjak P, Kamp D, Hepp N, Scacchetti A, Pisfil MG, Bartho J, Halic M, Becker PB, Smolle M, Stigler J, Mueller-Planitz F. ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569516. [PMID: 38106060 PMCID: PMC10723341 DOI: 10.1101/2023.12.04.569516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. We investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner qualitatively agree with our data. We speculate that 'monkey-bar' mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.
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Affiliation(s)
- Petra Vizjak
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Dieter Kamp
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Nicola Hepp
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- Current address: Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Alessandro Scacchetti
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- Current address: Epigenetics Institute & Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia (PA), USA
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Joseph Bartho
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Michaela Smolle
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- BioPhysics Core Facility, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Johannes Stigler
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
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Sokolova V, Miratsky J, Svetlov V, Brenowitz M, Vant J, Lewis T, Dryden K, Lee G, Sarkar S, Nudler E, Singharoy A, Tan D. Structural mechanism of HP1α-dependent transcriptional repression and chromatin compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569387. [PMID: 38076844 PMCID: PMC10705452 DOI: 10.1101/2023.11.30.569387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. In this study, we employed a multidisciplinary approach to unravel the interactions between human HP1α and nucleosomes. We have elucidated the cryo-EM structure of an HP1α dimer bound to an H2A.Z nucleosome, revealing that the HP1α dimer interfaces with nucleosomes at two distinct sites. The primary binding site is located at the N-terminus of histone H3, specifically at the trimethylated K9 (K9me3) region, while a novel secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. This study offers a model that explains how HP1α functions in heterochromatin maintenance and gene silencing, particularly in the context of H3K9me-dependent mechanisms. Additionally, it sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.
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Affiliation(s)
- Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Jacob Miratsky
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John Vant
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Tyler Lewis
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Kelly Dryden
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903 USA
| | - Gahyun Lee
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Shayan Sarkar
- Department of Pathology, Stony Brook University; Stony Brook, New York, 11794 USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
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49
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Owen JA, Osmanović D, Mirny L. Design principles of 3D epigenetic memory systems. Science 2023; 382:eadg3053. [PMID: 37972190 PMCID: PMC11075759 DOI: 10.1126/science.adg3053] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Abstract
Cells remember their identities, in part, by using epigenetic marks-chemical modifications placed along the genome. How can mark patterns remain stable over cell generations despite their constant erosion by replication and other processes? We developed a theoretical model that reveals that three-dimensional (3D) genome organization can stabilize epigenetic memory as long as (i) there is a large density difference between chromatin compartments, (ii) modifying "reader-writer" enzymes spread marks in three dimensions, and (iii) the enzymes are limited in abundance relative to their histone substrates. Analogous to an associative memory that encodes memory in neuronal connectivity, mark patterns are encoded in a 3D network of chromosomal contacts. Our model provides a unified account of diverse observations and reveals a key role of 3D genome organization in epigenetic memory.
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Affiliation(s)
- Jeremy A. Owen
- Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
| | - Dino Osmanović
- Department of Mechanical and Aeronautical Engineering, UCLA; Los Angeles, USA
| | - Leonid Mirny
- Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
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50
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Lin X, Zhang B. Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541030. [PMID: 37293007 PMCID: PMC10245791 DOI: 10.1101/2023.05.16.541030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 kBT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9 kBT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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