1
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Valades-Cruz CA, Barth R, Abdellah M, Shaban HA. Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D. Nat Protoc 2024:10.1038/s41596-024-01038-3. [PMID: 39198619 DOI: 10.1038/s41596-024-01038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/22/2024] [Indexed: 09/01/2024]
Abstract
To understand the dynamic nature of the genome, the localization and rearrangement of DNA and DNA-binding proteins must be analyzed across the entire nucleus of single living cells. Recently, we developed a computational light microscopy technique, called high-resolution diffusion (Hi-D) mapping, which can accurately detect, classify and map diffusion dynamics and biophysical parameters such as the diffusion constant, the anomalous exponent, drift velocity and model physical diffusion from the data at a high spatial resolution across the genome in living cells. Hi-D combines dense optical flow to detect and track local chromatin and nuclear protein motion genome-wide and Bayesian inference to characterize this local movement at nanoscale resolution. Here we present the Python implementation of Hi-D, with an option for parallelizing the calculations to run on multicore central processing units (CPUs). The functionality of Hi-D is presented to the users via user-friendly documented Python notebooks. Hi-D reduces the analysis time to less than 1 h using a multicore CPU with a single compute node. We also present different applications of Hi-D for live-imaging of DNA, histone H2B and RNA polymerase II sequences acquired with spinning disk confocal and super-resolution structured illumination microscopy.
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Affiliation(s)
- Cesar Augusto Valades-Cruz
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Roman Barth
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands
| | - Marwan Abdellah
- Ecole polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Haitham A Shaban
- Spectroscopy Department, Institute of Physics Research National Research Centre, Cairo, Egypt.
- Agora Cancer Research Center, Lausanne, Switzerland.
- Precision Oncology Center, Department of Oncology Lausanne University Hospital, Lausanne, Switzerland.
- Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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2
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Agbleke M, Shaban H, Broker TR, Agbleke AA. First FASEB conference in Africa-The 2023 FASEB conference on Imaging Cellular and Chromosome Dynamics held on August 27-30, 2023 in Accra, Ghana. FASEB J 2024; 38:e23741. [PMID: 38896550 DOI: 10.1096/fj.202400058] [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: 01/09/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
Access to scientific meetings and conferences is limited in low- and middle-income countries (LMIC). Efforts are being implemented to rectify this issue through short workshops, seminars, and conferences. Sena Institute of Technology (SIT), a nonprofit research institute based in Ghana, is one such organization championing this initiative. Through a partnership with the Federation of American Societies for Experimental Biology (FASEB), SIT hosted the first FASEB conference in Africa from August 27-30, 2023 in Ghana. The 3-day conference brought together scientists specialized in imaging, genetics, and cell biology from across the globe to discuss the theme "Imaging Cellular and Chromosome Dynamics." The Ghanaian Ministry of Environment, Science, Technology and Innovation (MESTI) and the Ghana Tourism Authority (GTA) provided local support to the meeting. At the end of the conference, participants recommended continuing engagement and the organization of more such meetings on the African continent.
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Affiliation(s)
| | - Haitham Shaban
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Physics Research Institute National Research Centre, Cairo, Egypt
| | - Thomas R Broker
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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3
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Chiu K, Berrada Y, Eskndir N, Song D, Fong C, Naughton S, Chen T, Moy S, Gyurmey S, James L, Ezeiruaku C, Capistran C, Lowey D, Diwanji V, Peterson S, Parakh H, Burgess AR, Probert C, Zhu A, Anderson B, Levi N, Gerlitz G, Packard MC, Dorfman KA, Bahiru MS, Stephens AD. CTCF is essential for proper mitotic spindle structure and anaphase segregation. Chromosoma 2024; 133:183-194. [PMID: 37728741 DOI: 10.1007/s00412-023-00810-w] [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] [Received: 01/11/2023] [Revised: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
Mitosis is an essential process in which the duplicated genome is segregated equally into two daughter cells. CTCF has been reported to be present in mitosis and has a role in localizing CENP-E, but its importance for mitotic fidelity remains to be determined. To evaluate the importance of CTCF in mitosis, we tracked mitotic behaviors in wild-type and two different CTCF CRISPR-based genetic knockdowns. We find that knockdown of CTCF results in prolonged mitoses and failed anaphase segregation via time-lapse imaging of SiR-DNA. CTCF knockdown did not alter cell cycling or the mitotic checkpoint, which was activated upon nocodazole treatment. Immunofluorescence imaging of the mitotic spindle in CTCF knockdowns revealed disorganization via tri/tetrapolar spindles and chromosomes behind the spindle pole. Imaging of interphase nuclei showed that nuclear size increased drastically, consistent with failure to divide the duplicated genome in anaphase. Long-term inhibition of CNEP-E via GSK923295 recapitulates CTCF knockdown abnormal mitotic spindles with polar chromosomes and increased nuclear sizes. Population measurements of nuclear shape in CTCF knockdowns do not display decreased circularity or increased nuclear blebbing relative to wild-type. However, failed mitoses do display abnormal nuclear morphologies relative to successful mitoses, suggesting that population images do not capture individual behaviors. Thus, CTCF is important for both proper metaphase organization and anaphase segregation which impacts the size and shape of the interphase nucleus likely through its known role in recruiting CENP-E.
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Affiliation(s)
- Katherine Chiu
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Yasmin Berrada
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Nebiyat Eskndir
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Dasol Song
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Claire Fong
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Sarah Naughton
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Tina Chen
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Savanna Moy
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Sarah Gyurmey
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Liam James
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Chimere Ezeiruaku
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Caroline Capistran
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Daniel Lowey
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Vedang Diwanji
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Samantha Peterson
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Harshini Parakh
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Ayanna R Burgess
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Cassandra Probert
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Annie Zhu
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Bryn Anderson
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Nehora Levi
- Biology Department of Molecular Biology, Faculty of Life Sciences, Ariel University, 40700, Ariel, Israel
| | - Gabi Gerlitz
- Biology Department of Molecular Biology, Faculty of Life Sciences, Ariel University, 40700, Ariel, Israel
| | - Mary C Packard
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Katherine A Dorfman
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Michael Seifu Bahiru
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Andrew D Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
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4
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Mehra D, Puchner EM. Correlative Conventional and Super-resolution Photoactivated Localization Microscopy (PALM) Imaging to Characterize Chromatin Structure and Dynamics in Live Mammalian Cells. Bio Protoc 2023; 13:e4850. [PMID: 37900107 PMCID: PMC10603262 DOI: 10.21769/bioprotoc.4850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 10/31/2023] Open
Abstract
A fundamental understanding of gene regulation requires a quantitative characterization of the spatial organization and dynamics of chromatin. The advent of fluorescence super-resolution microscopy techniques such as photoactivated localization microscopy (PALM) presented a breakthrough to visualize structural features with a resolution of ~20 nm in fixed cells. However, until recently the long acquisition time of super-resolution images prevented high-resolution measurements in living cells due to spreading of localizations caused by chromatin motion. Here, we present a step-by step protocol for our recently developed approach for correlatively imaging telomeres with conventional fluorescence and PALM, in order to obtain time-averaged super-resolution images and dynamic parameters in living cells. First, individual single molecule localizations are assigned to a locus as it moves, allowing to discriminate between bound and unbound dCas9 molecules, whose mobilities overlap. By subtracting the telomere trajectory from the localization of bound molecules, the motion blurring is then corrected, and high-resolution structural characterizations can be made. These structural parameters can also be related to local chromatin motion or larger scale domain movement. This protocol therefore improves the ability to analyze the mobility and time-averaged nanoscopic structure of locus-specific chromatin with single-molecule sensitivity.
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Affiliation(s)
- Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Twin Cities, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Twin Cities, MN, USA
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5
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Shaban HA, Gasser SM. Dynamic 3D genome reorganization during senescence: defining cell states through chromatin. Cell Death Differ 2023:10.1038/s41418-023-01197-y. [PMID: 37596440 DOI: 10.1038/s41418-023-01197-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023] Open
Abstract
Cellular senescence, a cell state characterized by growth arrest and insensitivity to growth stimulatory hormones, is accompanied by a massive change in chromatin organization. Senescence can be induced by a range of physiological signals and pathological stresses and was originally thought to be an irreversible state, implicated in normal development, wound healing, tumor suppression and aging. Recently cellular senescence was shown to be reversible in some cases, with exit being triggered by the modulation of the cell's transcriptional program by the four Yamanaka factors, the suppression of p53 or H3K9me3, PDK1, and/or depletion of AP-1. Coincident with senescence reversal are changes in chromatin organization, most notably the loss of senescence-associated heterochromatin foci (SAHF) found in oncogene-induced senescence. In addition to fixed-cell imaging, chromatin conformation capture and multi-omics have been used to examine chromatin reorganization at different spatial resolutions during senescence. They identify determinants of SAHF formation and other key features that differentiate distinct types of senescence. Not surprisingly, multiple factors, including the time of induction, the type of stress experienced, and the type of cell involved, influence the global reorganization of chromatin in senescence. Here we discuss how changes in the three-dimensional organization of the genome contribute to the regulation of transcription at different stages of senescence. In particular, the distinct contributions of heterochromatin- and lamina-mediated interactions, changes in gene expression, and other cellular control mechanisms are discussed. We propose that high-resolution temporal and spatial analyses of the chromatin landscape during senescence will identify early markers of the different senescence states to help guide clinical diagnosis.
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Affiliation(s)
- Haitham A Shaban
- Precision Oncology Center, Department of Oncology, Lausanne University Hospital, 1005, Lausanne, Switzerland.
- Agora Cancer Research Center Lausanne, Rue du Bugnon 25A, 1005, Lausanne, Switzerland.
- Spectroscopy Department, Institute of Physics Research National Research Centre, Cairo, 33 El-Behouth St., Dokki, Giza, 12311, Egypt.
| | - Susan M Gasser
- Fondation ISREC, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
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6
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Kramer HM, Cook DE, Seidl MF, Thomma BP. Epigenetic regulation of nuclear processes in fungal plant pathogens. PLoS Pathog 2023; 19:e1011525. [PMID: 37535497 PMCID: PMC10399791 DOI: 10.1371/journal.ppat.1011525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.
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Affiliation(s)
- H. Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - David E. Cook
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Bart P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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7
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Pagella P, Söderholm S, Nordin A, Zambanini G, Ghezzi V, Jauregi-Miguel A, Cantù C. The time-resolved genomic impact of Wnt/β-catenin signaling. Cell Syst 2023; 14:563-581.e7. [PMID: 37473729 DOI: 10.1016/j.cels.2023.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 03/24/2023] [Accepted: 06/12/2023] [Indexed: 07/22/2023]
Abstract
Wnt signaling orchestrates gene expression via its effector, β-catenin. However, it is unknown whether β-catenin binds its target genomic regions simultaneously and how this impacts chromatin dynamics to modulate cell behavior. Using a combination of time-resolved CUT&RUN against β-catenin, ATAC-seq, and perturbation assays in different cell types, we show that Wnt/β-catenin physical targets are tissue-specific, β-catenin "moves" on different loci over time, and its association to DNA accompanies changing chromatin accessibility landscapes that determine cell behavior. In particular, Wnt/β-catenin progressively shapes the chromatin of human embryonic stem cells (hESCs) as they undergo mesodermal differentiation, a behavior that we define as "plastic." In HEK293T cells, on the other hand, Wnt/β-catenin drives a transient chromatin opening, followed by re-establishment of the pre-stimulation state, a response that we define as "elastic." Future experiments shall assess whether other cell communication mechanisms, in addition to Wnt signaling, are ruled by time, cellular idiosyncrasies, and chromatin constraints. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Simon Söderholm
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Valeria Ghezzi
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Amaia Jauregi-Miguel
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, 58185 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, 58185 Linköping, Sweden.
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8
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Zhang Y, He XJ, Barron AB, Li Z, Jin MJ, Wang ZL, Huang Q, Zhang LZ, Wu XB, Yan WY, Zeng ZJ. The diverging epigenomic landscapes of honeybee queens and workers revealed by multiomic sequencing. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 155:103929. [PMID: 36906046 DOI: 10.1016/j.ibmb.2023.103929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 05/10/2023]
Abstract
The role of the epigenome in phenotypic plasticity is unclear presently. Here we used a multiomics approach to explore the nature of the epigenome in developing honey bee (Apis mellifera) workers and queens. Our data clearly showed distinct queen and worker epigenomic landscapes during the developmental process. Differences in gene expression between workers and queens become more extensive and more layered during the process of development. Genes known to be important for caste differentiation were more likely to be regulated by multiple epigenomic systems than other differentially expressed genes. We confirmed the importance of two candidate genes for caste differentiation by using RNAi to manipulate the expression of two genes that differed in expression between workers and queens were regulated by multiple epigenomic systems. For both genes the RNAi manipulation resulted in a decrease in weight and fewer ovarioles of newly emerged queens compared to controls. Our data show that the distinct epigenomic landscapes of worker and queen bees differentiate during the course of larval development.
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Affiliation(s)
- Yong Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Xu Jiang He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Andrew B Barron
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Zhen Li
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Meng Jie Jin
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Zi Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Li Zhen Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Xiao Bo Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Wei Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Zhi Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China.
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9
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Chen LF, Lee J, Boettiger A. Recent progress and challenges in single-cell imaging of enhancer-promoter interaction. Curr Opin Genet Dev 2023; 79:102023. [PMID: 36854248 DOI: 10.1016/j.gde.2023.102023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/13/2023] [Accepted: 01/25/2023] [Indexed: 02/27/2023]
Abstract
In the past two years, approaches relying on high-resolution microscopy and live-cell imaging have increasingly contributed to our understanding of the 3D genome organization and its importance for transcriptional control. Here, we describe recent progress that has highlighted how flexible and heterogeneous 3D chromatin structure is, on the length scales relevant to transcriptional control. We describe work that has investigated how robust transcriptional outcomes may be derived from such flexible organization without the need for clearly distinct structures in active and silent cells. We survey the latest state of the art in directly observing the dynamics of chromatin interactions, and suggest how some recent, apparently contradictory conclusions may be reconciled.
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Affiliation(s)
- Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University, USA
| | - Joo Lee
- Department of Developmental Biology, Stanford University, USA
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10
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Shi D, Huang Y, Bai C. Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases. Polymers (Basel) 2023; 15:polym15071763. [PMID: 37050377 PMCID: PMC10096840 DOI: 10.3390/polym15071763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome’s dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Yuxin Huang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
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11
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Liu S, Tang Q, Zhao K. Analysis of Chromatin Interaction and Accessibility by Trac-Looping. Methods Mol Biol 2023; 2611:85-97. [PMID: 36807066 DOI: 10.1007/978-1-0716-2899-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Spatial organization of the genome modulates pivotal biological processes. The emerging new technologies have provided novel insights into genome structure and its role in regulating cell activities. To examine the genome-wide chromatin interactions at accessible chromatin regions, we developed a DNA transposase-mediated analysis of chromatin looping (Trac-looping) method for simultaneously detecting chromatin interactions and chromatin accessibility. Here, we describe a detailed protocol of generating Trac-looping libraries.
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Affiliation(s)
- Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Qingsong Tang
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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12
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Chiu K, Berrada Y, Eskndir N, Song D, Fong C, Naughton S, Chen T, Moy S, Gyurmey S, James L, Ezeiruaku C, Capistran C, Lowey D, Diwanji V, Peterson S, Parakh H, Burgess AR, Probert C, Zhu A, Anderson B, Levi N, Gerlitz G, Packard MC, Dorfman KA, Bahiru MS, Stephens AD. CTCF is essential for proper mitotic spindle structure and anaphase segregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523293. [PMID: 36712070 PMCID: PMC9881978 DOI: 10.1101/2023.01.09.523293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mitosis is an essential process in which the duplicated genome is segregated equally into two daughter cells. CTCF has been reported to be present in mitosis but its importance for mitotic fidelity remains to be determined. To evaluate the importance of CTCF in mitosis, we tracked mitotic behaviors in wild type and two different CTCF CRISPR-based genetic knockdowns. We find that knockdown of CTCF results in prolonged mitoses and failed anaphase segregation via time lapse imaging of SiR-DNA. CTCF knockdown did not alter cell cycling or the mitotic checkpoint, which was activated upon nocodazole treatment. Immunofluorescence imaging of the mitotic spindle in CTCF knockdowns revealed disorganization via tri/tetrapolar spindles and chromosomes behind the spindle pole. Imaging of interphase nuclei showed that nuclear size increased drastically, consistent with failure to divide the duplicated genome in anaphase. Population measurements of nuclear shape in CTCF knockdowns do not display decreased circularity or increased nuclear blebbing relative to wild type. However, failed mitoses do display abnormal nuclear morphologies relative to successful mitoses, suggesting population images do not capture individual behaviors. Thus, CTCF is important for both proper metaphase organization and anaphase segregation which impacts the size and shape of the interphase nucleus.
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Affiliation(s)
- Katherine Chiu
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Yasmin Berrada
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Nebiyat Eskndir
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Dasol Song
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Claire Fong
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sarah Naughton
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Tina Chen
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Savanna Moy
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sarah Gyurmey
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Liam James
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Chimere Ezeiruaku
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Caroline Capistran
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Daniel Lowey
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Vedang Diwanji
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Samantha Peterson
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Harshini Parakh
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ayanna R. Burgess
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Cassandra Probert
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Annie Zhu
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Bryn Anderson
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Nehora Levi
- Biology Department of Molecular Biology, Faculty of Life Sciences, Ariel University, Ariel 40700, Israel
| | - Gabi Gerlitz
- Biology Department of Molecular Biology, Faculty of Life Sciences, Ariel University, Ariel 40700, Israel
| | - Mary C. Packard
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | | | | | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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13
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Ingersoll S, Brown K, Ma B, Ren X. Quantifying the Binding and Target-Search Kinetics of Transcriptional Regulatory Factors by Live-Cell Single-Molecule Tracking. Methods Mol Biol 2023; 2599:141-162. [PMID: 36427148 DOI: 10.1007/978-1-0716-2847-8_11] [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] [Indexed: 06/16/2023]
Abstract
Eukaryotic transcriptional regulatory factors, such as transcription factors and epigenetic regulatory factors, must locate, bind, and assemble at specific genomic regions to execute functions within the complex and crowded environment of the nucleus. These dynamic processes are typically at nonequilibrium, so quantifying their binding and target-search processes within the native environment is essential for understanding transcriptional mechanisms. Live-cell single-molecule tracking (SMT) is an emerging technique that can be utilized to observe molecular trajectories of individual transcriptional regulatory complexes within the nucleus. Here, we describe the use of live-cell SMT to observe trajectories of individual transcriptional regulatory complexes. We delineate the imaging analysis to obtain chromatin-bound fraction and residence time. Finally, we elaborate on the kinetic modeling to estimate target-search parameters. These binding and target-search parameters facilitate the understanding of how transcription is spatially and temporally regulated under physiological and pathological conditions.
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Affiliation(s)
- Steven Ingersoll
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA
| | - Kyle Brown
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA
| | - Brian Ma
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA.
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14
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Abstract
In animals, the sequences for controlling gene expression do not concentrate just at the transcription start site of genes, but are frequently thousands to millions of base pairs distal to it. The interaction of these sequences with one another and their transcription start sites is regulated by factors that shape the three-dimensional (3D) organization of the genome within the nucleus. Over the past decade, indirect tools exploiting high-throughput DNA sequencing have helped to map this 3D organization, have identified multiple key regulators of its structure and, in the process, have substantially reshaped our view of how 3D genome architecture regulates transcription. Now, new tools for high-throughput super-resolution imaging of chromatin have directly visualized the 3D chromatin organization, settling some debates left unresolved by earlier indirect methods, challenging some earlier models of regulatory specificity and creating hypotheses about the role of chromatin structure in transcriptional regulation.
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15
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Rampias T, Klinakis A. Using Sister Chromatid Exchange Assay to Detect Homologous Recombination Deficiency in Epigenetically Deregulated Urothelial Carcinoma Cells. Methods Mol Biol 2023; 2684:133-144. [PMID: 37410231 DOI: 10.1007/978-1-0716-3291-8_7] [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: 07/07/2023]
Abstract
Sister chromatid exchange (SCE) is the process of exchanging regions between two sister chromatids during DNA replication. Exchanges between replicated chromatids and their sisters can be visualized in cells when DNA synthesis in one chromatid is labelled by 5-bromo-2'-deoxyuridine (BrdU). Homologous recombination (HR) is considered as the principal mechanism responsible for the sister chromatid exchange (SCE) upon replication fork collapse, and therefore SCE frequency upon genotoxic conditions reflects the capacity of HR repair to respond to replication stress. During tumorigenesis, inactivating mutations or altered transcriptome can affect a plethora of epigenetic factors that participate in DNA repair processes, and there are an increasing number of reports which demonstrate a link between epigenetic deregulation in cancer and homologous recombination deficiency (HRD). Therefore, the SCE assay can provide valuable information regarding the HR functionality in tumors with epigenetic deficiencies. In this chapter, we provide a method to visualize SCEs. The technique outlined below is characterized by high sensitivity and specificity and has been successfully applied to human bladder cancer cell lines. In this context, this technique could be used to characterize the dynamics of HR repair in tumors with deregulated epigenome.
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Affiliation(s)
- Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
| | - Apostolos Klinakis
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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16
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Shaban HA. Nucleus-wide analysis of coherent RNA pol II movement in the context of chromatin dynamics in living cancer cells. Nucleus 2022; 13:313-318. [PMID: 36512483 PMCID: PMC9754109 DOI: 10.1080/19491034.2022.2157133] [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] [Indexed: 12/15/2022] Open
Abstract
Activation of transcription results in coordinated movement of chromatin over a range of micrometers. To investigate how transcriptional regulation affects the mobility of RNA Pol II molecules and whether this movement response depends on the coordinated movement of chromatin, we used our Dense Flow reConstruction and Correlation (DFCC) method. Using DFCC, we studies the nucleus-wide coherent movements of RNA Pol II in the context of DNA in humancancer cells. This study showed the dependance of coherent movements of RNA Pol II molecules (above 1 µm) on transcriptional activity. Here, we share the dataset of this study, includes nucleus-wide live imaging and analysis of DNA and RNA polymerase II in different transcription states, and the code for teh analysis. Our dataset may provide researchers interested in the long-range organization of chromatin in living cell images with the ability to link the structural genomic compartment to dynamic information. .
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Affiliation(s)
- Haitham A. Shaban
- Agora Cancer Research Center, Lausanne, Switzerland,Precision Oncology Center, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland,Spectroscopy Department, Physics Division, National Research Centre, Cairo, Egypt,CONTACT Haitham A. Shaban Precision Oncology Center, Department of Oncology, Lausanne University Hospital, Lausanne1005, Switzerland
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17
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Barth R, Shaban HA. Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion. Nucleus 2022; 13:194-202. [PMID: 35723020 PMCID: PMC9225503 DOI: 10.1080/19491034.2022.2088988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/04/2022] Open
Abstract
Gene transcription by RNA polymerase II (RNAPol II) is a tightly regulated process in the genomic, temporal, and spatial context. Recently, we have shown that chromatin exhibits spatially coherently moving regions over the entire nucleus, which is enhanced by transcription. Yet, it remains unclear how the mobility of RNA Pol II molecules is affected by transcription regulation and whether this response depends on the coordinated chromatin movement. We applied our Dense Flow reConstruction and Correlation method to analyze nucleus-wide coherent movements of RNA Pol II in living human cancer cells. We observe a spatially coherent movement of RNA Pol II molecules over ≈ 1 μm, which depends on transcriptional activity. Inducing transcription in quiescent cells decreased the coherent motion of RNA Pol II. We then quantify the spatial correlation length of RNA Pol II in the context of DNA motion. RNA Pol II and chromatin spatially coherent motions respond oppositely to transcriptional activities. Our study holds the potential of studying the chromatin environment in different nuclear processes.
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Affiliation(s)
- Roman Barth
- Department of Bionanoscience, Delft University of Technology, CJ Delft, The Netherlands
| | - Haitham A. Shaban
- Spectroscopy Department, Physics Division, National Research Centre, Dokki, Egypt
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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18
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Chromatin accessibility dynamics dictate renal tubular epithelial cell response to injury. Nat Commun 2022; 13:7322. [PMID: 36443310 PMCID: PMC9705299 DOI: 10.1038/s41467-022-34854-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Renal tubular epithelial cells (TECs) can initiate an adaptive response to completely recover from mild acute kidney injury (AKI), whereas severe injury often leads to persistence of maladaptive repair and progression to kidney fibrosis. Through profiling of active DNA regulatory elements by ATAC-seq, we reveal widespread, dynamic changes in the chromatin accessibility of TECs after ischemia-reperfusion injury. We show that injury-specific domains of regulatory chromatin become accessible prior to gene activation, creating poised chromatin states to activate the consequent gene expression program and injury response. We further identify RXRα as a key transcription factor in promoting adaptive repair. Activation of RXRα by bexarotene, an FDA-approved RXRα agonist, restores the chromatin state and gene expression program to protect TECs against severe kidney injury. Together, our findings elucidate a chromatin-mediated mechanism underlying differential responses of TECs to varying injuries and identify RXRα as a therapeutic target of acute kidney injury.
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19
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Fleming M, Nelson F, Wallace I, Eskiw CH. Genome Tectonics: Linking Dynamic Genome Organization with Cellular Nutrients. Lifestyle Genom 2022; 16:21-34. [PMID: 36446341 DOI: 10.1159/000528011] [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: 06/29/2022] [Accepted: 11/06/2022] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Our daily intake of food provides nutrients for the maintenance of health, growth, and development. The field of nutrigenomics aims to link dietary intake/nutrients to changes in epigenetic status and gene expression. SUMMARY Although the relationship between our diet and our genes in under intense investigation, there is still a significant aspect of our genome that has received little attention with regard to this. In the past 15 years, the importance of genome organization has become increasingly evident, with research identifying small-scale local changes to large segments of the genome dynamically repositioning within the nucleus in response to/or mediating change in gene expression. The discovery of these dynamic processes and organization maybe as significant as dynamic plate tectonics is to geology, there is little information tying genome organization to specific nutrients or dietary intake. KEY MESSAGES Here, we detail key principles of genome organization and structure, with emphasis on genome folding and organization, and link how these contribute to our future understand of nutrigenomics.
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Affiliation(s)
- Morgan Fleming
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Fina Nelson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- 21st Street Brewery Inc., Saskatoon, Saskatchewan, Canada
| | - Iain Wallace
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Proxima Research and Development, Saskatoon, Saskatchewan, Canada
| | - Christopher H Eskiw
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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20
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Nair SJ, Suter T, Wang S, Yang L, Yang F, Rosenfeld MG. Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures. Trends Genet 2022; 38:1019-1047. [PMID: 35811173 PMCID: PMC9474616 DOI: 10.1016/j.tig.2022.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023]
Abstract
Gene regulation by transcriptional enhancers is the dominant mechanism driving cell type- and signal-specific transcriptional diversity in metazoans. However, over four decades since the original discovery, how enhancers operate in the nuclear space remains largely enigmatic. Recent multidisciplinary efforts combining real-time imaging, genome sequencing, and biophysical strategies provide insightful but conflicting models of enhancer-mediated gene control. Here, we review the discovery and progress in enhancer biology, emphasizing the recent findings that acutely activated enhancers assemble regulatory machinery as mesoscale architectural structures with distinct physical properties. These findings help formulate novel models that explain several mysterious features of the assembly of transcriptional enhancers and the mechanisms of spatial control of gene expression.
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Affiliation(s)
- Sreejith J Nair
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.
| | - Tom Suter
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Wang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Cellular and Molecular Medicine Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lu Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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21
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Currey ML, Kandula V, Biggs R, Marko JF, Stephens AD. A Versatile Micromanipulation Apparatus for Biophysical Assays of the Cell Nucleus. Cell Mol Bioeng 2022; 15:303-312. [PMID: 36119136 PMCID: PMC9474788 DOI: 10.1007/s12195-022-00734-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022] Open
Abstract
Intro Force measurements of the nucleus, the strongest organelle, have propelled the field of mechanobiology to understand the basic mechanical components of the nucleus and how these components properly support nuclear morphology and function. Micromanipulation force measurement provides separation of the relative roles of nuclear mechanical components chromatin and lamin A. Methods To provide access to this technique, we have developed a universal micromanipulation apparatus for inverted microscopes. We outline how to engineer and utilize this apparatus through dual micromanipulators, fashion and calibrate micropipettes, and flow systems to isolate a nucleus and provide force vs. extensions measurements. This force measurement approach provides the unique ability to measure the separate contributions of chromatin at short extensions and lamin A strain stiffening at long extensions. We then investigated the apparatus’ controllable and programmable micromanipulators through compression, isolation, and extension in conjunction with fluorescence to develop new assays for nuclear mechanobiology. Results Using this methodology, we provide the first rebuilding of the micromanipulation setup outside of its lab of origin and recapitulate many key findings including spring constant of the nucleus and strain stiffening across many cell types. Furthermore, we have developed new micromanipulation-based techniques to compress nuclei inducing nuclear deformation and/or rupture, track nuclear shape post-isolation, and fluorescence imaging during micromanipulation force measurements. Conclusion We provide the workflow to build and use a micromanipulation apparatus with any inverted microscope to perform nucleus isolation, force measurements, and various other biophysical techniques. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-022-00734-y.
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Affiliation(s)
| | - Viswajit Kandula
- Department of Molecular Biosciences and Department of Physics & Astronomy, Northwestern University, Evanston, USA
- Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Ronald Biggs
- Department of Molecular Biosciences and Department of Physics & Astronomy, Northwestern University, Evanston, USA
| | - John F. Marko
- Department of Molecular Biosciences and Department of Physics & Astronomy, Northwestern University, Evanston, USA
| | - Andrew D. Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, USA
- Molecular and Cellular Biosciences, University of Massachusetts Amherst, Amherst, USA
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22
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Keizer VIP, Grosse-Holz S, Woringer M, Zambon L, Aizel K, Bongaerts M, Delille F, Kolar-Znika L, Scolari VF, Hoffmann S, Banigan EJ, Mirny LA, Dahan M, Fachinetti D, Coulon A. Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics. Science 2022; 377:489-495. [PMID: 35901134 DOI: 10.1126/science.abi9810] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Our understanding of the physical principles organizing the genome in the nucleus is limited by the lack of tools to directly exert and measure forces on interphase chromosomes in vivo and probe their material nature. Here, we introduce an approach to actively manipulate a genomic locus using controlled magnetic forces inside the nucleus of a living human cell. We observed viscoelastic displacements over micrometers within minutes in response to near-piconewton forces, which are consistent with a Rouse polymer model. Our results highlight the fluidity of chromatin, with a moderate contribution of the surrounding material, revealing minor roles for cross-links and topological effects and challenging the view that interphase chromatin is a gel-like material. Our technology opens avenues for future research in areas from chromosome mechanics to genome functions.
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Affiliation(s)
- Veer I P Keizer
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France.,Institut Curie, PSL Research University, CNRS UMR144, Laboratoire Biologie Cellulaire et Cancer, 75005 Paris, France
| | - Simon Grosse-Holz
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France.,Department of Physics and Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maxime Woringer
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Laura Zambon
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France.,Institut Curie, PSL Research University, CNRS UMR144, Laboratoire Biologie Cellulaire et Cancer, 75005 Paris, France
| | - Koceila Aizel
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Maud Bongaerts
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Fanny Delille
- ESPCI Paris, PSL Research University, Sorbonne Université, CNRS UMR8213, Laboratoire de Physique et d'Étude des Matériaux, 75005 Paris, France
| | - Lorena Kolar-Znika
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Vittore F Scolari
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Sebastian Hoffmann
- Institut Curie, PSL Research University, CNRS UMR144, Laboratoire Biologie Cellulaire et Cancer, 75005 Paris, France
| | - Edward J Banigan
- Department of Physics and Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leonid A Mirny
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Department of Physics and Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maxime Dahan
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS UMR144, Laboratoire Biologie Cellulaire et Cancer, 75005 Paris, France
| | - Antoine Coulon
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.,Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
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23
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Deng W, Wang H. Efficient cell chatting between embryo and uterus ensures embryo implantation. Biol Reprod 2022; 107:339-348. [PMID: 35774025 PMCID: PMC9310511 DOI: 10.1093/biolre/ioac135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/12/2022] Open
Abstract
Embryo implantation is one of the hottest topics during female reproduction since it is the first dialogue between maternal uterus and developing embryo whose disruption will contribute to adverse pregnancy outcome. Numerous achievements have been made to decipher the underlying mechanism of embryo implantation by genetic and molecular approaches accompanied with emerging technological advances. In recent decades, raising concepts incite insightful understanding on the mechanism of reciprocal communication between implantation competent embryos and receptive uterus. Enlightened by these gratifying evolvements, we aim to summarize and revisit current progress on the critical determinants of mutual communication between maternal uterus and embryonic signaling on the perspective of embryo implantation to alleviate infertility, enhance fetal health, and improve contraceptive design.
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Affiliation(s)
- Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
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24
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Gerhardt LMS, McMahon AP. Multi-omic approaches to acute kidney injury and repair. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 20:100344. [PMID: 35005326 PMCID: PMC8740908 DOI: 10.1016/j.cobme.2021.100344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The kidney has a remarkable regenerative capacity. In response to ischemic or toxic injury, proximal tubule cells can proliferate to rebuild damaged tubules and restore kidney function. However, severe acute kidney injury (AKI) or recurrent AKI events can lead to maladaptive repair and disease progression from AKI to chronic kidney disease (CKD). The application of single cell technologies has identified injured proximal tubule cell states weeks after AKI, distinguished by a pro-inflammatory senescent molecular signature. Epigenetic studies highlighted dynamic changes in the chromatin landscape of the kidney following AKI and described key transcription factors linked to the AKI response. The integration of multi-omic technologies opens new possibilities to improve our understanding of AKI and the driving forces behind the AKI-to-CKD transition, with the ultimate goal of designing tailored diagnostic and therapeutic strategies to improve AKI outcomes and prevent kidney disease progression.
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Affiliation(s)
- Louisa M. S. Gerhardt
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
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25
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Abstract
At fifteen different genomic locations, the expansion of a CAG/CTG repeat causes a neurodegenerative or neuromuscular disease, the most common being Huntington's disease and myotonic dystrophy type 1. These disorders are characterized by germline and somatic instability of the causative CAG/CTG repeat mutations. Repeat lengthening, or expansion, in the germline leads to an earlier age of onset or more severe symptoms in the next generation. In somatic cells, repeat expansion is thought to precipitate the rate of disease. The mechanisms underlying repeat instability are not well understood. Here we review the mammalian model systems that have been used to study CAG/CTG repeat instability, and the modifiers identified in these systems. Mouse models have demonstrated prominent roles for proteins in the mismatch repair pathway as critical drivers of CAG/CTG instability, which is also suggested by recent genome-wide association studies in humans. We draw attention to a network of connections between modifiers identified across several systems that might indicate pathway crosstalk in the context of repeat instability, and which could provide hypotheses for further validation or discovery. Overall, the data indicate that repeat dynamics might be modulated by altering the levels of DNA metabolic proteins, their regulation, their interaction with chromatin, or by direct perturbation of the repeat tract. Applying novel methodologies and technologies to this exciting area of research will be needed to gain deeper mechanistic insight that can be harnessed for therapies aimed at preventing repeat expansion or promoting repeat contraction.
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Affiliation(s)
- Vanessa C. Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA,Department of Neurology, Harvard Medical School, Boston, MA, USA,Correspondence to: Vanessa C. Wheeler, Center for Genomic Medicine, Massachusetts Hospital, Boston MAA 02115, USA. E-mail: . and Vincent Dion, UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK. E-mail:
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, UK,Correspondence to: Vanessa C. Wheeler, Center for Genomic Medicine, Massachusetts Hospital, Boston MAA 02115, USA. E-mail: . and Vincent Dion, UK Dementia Research Institute at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK. E-mail:
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26
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Zhang Y, Mao Q, Xia Q, Cheng J, Huang Z, Li Y, Chen P, Yang J, Fan X, Liang Y, Lin H. Noncoding RNAs link metabolic reprogramming to immune microenvironment in cancers. J Hematol Oncol 2021; 14:169. [PMID: 34654454 PMCID: PMC8518176 DOI: 10.1186/s13045-021-01179-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/27/2021] [Indexed: 02/08/2023] Open
Abstract
Altered metabolic patterns in tumor cells not only meet their own growth requirements but also shape an immunosuppressive microenvironment through multiple mechanisms. Noncoding RNAs constitute approximately 60% of the transcriptional output of human cells and have been shown to regulate numerous cellular processes under developmental and pathological conditions. Given their extensive action mechanisms based on motif recognition patterns, noncoding RNAs may serve as hinges bridging metabolic activity and immune responses. Indeed, recent studies have shown that microRNAs, long noncoding RNAs and circRNAs are widely involved in tumor metabolic rewiring, immune cell infiltration and function. Hence, we summarized existing knowledge of the role of noncoding RNAs in the remodeling of tumor metabolism and the immune microenvironment, and notably, we established the TIMELnc manual, which is a free and public manual for researchers to identify pivotal lncRNAs that are simultaneously correlated with tumor metabolism and immune cell infiltration based on a bioinformatic approach.
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Affiliation(s)
- Yiyin Zhang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Qijiang Mao
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Qiming Xia
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Jiaxi Cheng
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Zhengze Huang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Yirun Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Peng Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Jing Yang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Xiaoxiao Fan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
- State Key Laboratory of Modern Optical Instrumentations, Centre for Optical and Electromagnetic Research, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, 310058, China.
| | - Yuelong Liang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
| | - Hui Lin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
- Zhejiang Engineering Research Center of Cognitive Healthcare, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
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27
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Abstract
Nuclei are central hubs for information processing in eukaryotic cells. The need to fit large genomes into small nuclei imposes severe restrictions on genome organization and the mechanisms that drive genome-wide regulatory processes. How a disordered polymer such as chromatin, which has vast heterogeneity in its DNA and histone modification profiles, folds into discernibly consistent patterns is a fundamental question in biology. Outstanding questions include how genomes are spatially and temporally organized to regulate cellular processes with high precision and whether genome organization is causally linked to transcription regulation. The advent of next-generation sequencing, super-resolution imaging, multiplexed fluorescent in situ hybridization, and single-molecule imaging in individual living cells has caused a resurgence in efforts to understand the spatiotemporal organization of the genome. In this review, we discuss structural and mechanistic properties of genome organization at different length scales and examine changes in higher-order chromatin organization during important developmental transitions.
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Affiliation(s)
- Rajarshi P Ghosh
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; ,
| | - Barbara J Meyer
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; ,
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28
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Single-particle diffusional fingerprinting: A machine-learning framework for quantitative analysis of heterogeneous diffusion. Proc Natl Acad Sci U S A 2021; 118:2104624118. [PMID: 34321355 PMCID: PMC8346862 DOI: 10.1073/pnas.2104624118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Single-particle tracking (SPT) analysis of individual biomolecules is an indispensable tool for extracting quantitative information from dynamic biological processes, but often requires some a priori knowledge of the system. Here we present “single-particle diffusional fingerprinting,” a more general approach for extraction of diffusional patterns in SPT independently of the biological system. This method extracts a set of descriptive features for each SPT trajectory, which are ranked upon classification to yield mechanistic insights for the species under comparison. We demonstrate its capacity to yield a dictionary of diffusional traits across multiple systems (e.g., lipases hydrolyzing fat, transcription factors diffusing in cells, and nanoparticles in mucus), supporting its use on multiple biological phenomena (e.g., drug delivery, receptor dynamics, and virology). Single-particle tracking (SPT) is a key tool for quantitative analysis of dynamic biological processes and has provided unprecedented insights into a wide range of systems such as receptor localization, enzyme propulsion, bacteria motility, and drug nanocarrier delivery. The inherently complex diffusion in such biological systems can vary drastically both in time and across systems, consequently imposing considerable analytical challenges, and currently requires an a priori knowledge of the system. Here we introduce a method for SPT data analysis, processing, and classification, which we term “diffusional fingerprinting.” This method allows for dissecting the features that underlie diffusional behavior and establishing molecular identity, regardless of the underlying diffusion type. The method operates by isolating 17 descriptive features for each observed motion trajectory and generating a diffusional map of all features for each type of particle. Precise classification of the diffusing particle identity is then obtained by training a simple logistic regression model. A linear discriminant analysis generates a feature ranking that outputs the main differences among diffusional features, providing key mechanistic insights. Fingerprinting operates by both training on and predicting experimental data, without the need for pretraining on simulated data. We found this approach to work across a wide range of simulated and experimentally diverse systems, such as tracked lipases on fat substrates, transcription factors diffusing in cells, and nanoparticles diffusing in mucus. This flexibility ultimately supports diffusional fingerprinting’s utility as a universal paradigm for SPT diffusional analysis and prediction.
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29
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Brown K, Andrianakos H, Ingersoll S, Ren X. Single-molecule imaging of epigenetic complexes in living cells: insights from studies on Polycomb group proteins. Nucleic Acids Res 2021; 49:6621-6637. [PMID: 34009336 PMCID: PMC8266577 DOI: 10.1093/nar/gkab304] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/30/2022] Open
Abstract
Chromatin-associated factors must locate, bind to, and assemble on specific chromatin regions to execute chromatin-templated functions. These dynamic processes are essential for understanding how chromatin achieves regulation, but direct quantification in living mammalian cells remains challenging. Over the last few years, live-cell single-molecule tracking (SMT) has emerged as a new way to observe trajectories of individual chromatin-associated factors in living mammalian cells, providing new perspectives on chromatin-templated activities. Here, we discuss the relative merits of live-cell SMT techniques currently in use. We provide new insights into how Polycomb group (PcG) proteins, master regulators of development and cell differentiation, decipher genetic and epigenetic information to achieve binding stability and highlight that Polycomb condensates facilitate target-search efficiency. We provide perspectives on liquid-liquid phase separation in organizing Polycomb targets. We suggest that epigenetic complexes integrate genetic and epigenetic information for target binding and localization and achieve target-search efficiency through nuclear organization.
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Affiliation(s)
- Kyle Brown
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | | | - Steven Ingersoll
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
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30
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Chen AN, Luo Y, Yang YH, Fu JT, Geng XM, Shi JP, Yang J. Lactylation, a Novel Metabolic Reprogramming Code: Current Status and Prospects. Front Immunol 2021; 12:688910. [PMID: 34177945 PMCID: PMC8222712 DOI: 10.3389/fimmu.2021.688910] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022] Open
Abstract
Lactate is an end product of glycolysis. As a critical energy source for mitochondrial respiration, lactate also acts as a precursor of gluconeogenesis and a signaling molecule. We briefly summarize emerging concepts regarding lactate metabolism, such as the lactate shuttle, lactate homeostasis, and lactate-microenvironment interaction. Accumulating evidence indicates that lactate-mediated reprogramming of immune cells and enhancement of cellular plasticity contribute to establishing disease-specific immunity status. However, the mechanisms by which changes in lactate states influence the establishment of diverse functional adaptive states are largely uncharacterized. Posttranslational histone modifications create a code that functions as a key sensor of metabolism and are responsible for transducing metabolic changes into stable gene expression patterns. In this review, we describe the recent advances in a novel lactate-induced histone modification, histone lysine lactylation. These observations support the idea that epigenetic reprogramming-linked lactate input is related to disease state outputs, such as cancer progression and drug resistance.
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Affiliation(s)
- An-Na Chen
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Yan Luo
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Yu-Han Yang
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Jian-Tao Fu
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Xiu-Mei Geng
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Jun-Ping Shi
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Jin Yang
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
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31
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Abstract
In eukaryotes, the genome is hierarchically packed inside the nucleus, which facilitates physical contact between cis-regulatory elements (CREs), such as enhancers and promoters. Accumulating evidence highlights the critical role of higher-order chromatin structure in precise regulation of spatiotemporal gene expression under diverse biological contexts including lineage commitment and cell activation by external stimulus. Genomics and imaging-based technologies, such as Hi-C and DNA fluorescence in situ hybridization (FISH), have revealed the key principles of genome folding, while newly developed tools focus on improvement in resolution, throughput and modality at single-cell and population levels, and challenge the knowledge obtained through conventional approaches. In this review, we discuss recent advances in our understanding of principles of higher-order chromosome conformation and technologies to investigate 4D chromatin interactions.
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Affiliation(s)
- Namyoung Jung
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Tae-Kyung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Yonsei University, Seoul 03722, Korea
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32
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Brodie ED, Gregory B, Lisch D, Riddle NC. The epigenome and beyond: How does non-genetic inheritance change our view of evolution? Integr Comp Biol 2021; 61:2199-2207. [PMID: 34028538 DOI: 10.1093/icb/icab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evidence from across the tree of life suggests that epigenetic inheritance is more common than previously thought. If epigenetic inheritance is indeed as common as the data suggest, this finding has potentially important implications for evolutionary theory and our understanding of how evolution and adaptation progress. However, we currently lack an understanding of how common various epigenetic inheritance types are, and how they impact phenotypes. In this perspective, we review the open questions that need to be addressed to fully integrate epigenetic inheritance into evolutionary theory and to develop reliable predictive models for phenotypic evolution. We posit that addressing these challenges will require the collaboration of biologists from different disciplines and a focus on the exploration of data and phenomena without preconceived limits on potential mechanisms or outcomes.
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Affiliation(s)
- Edmund D Brodie
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Brian Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL
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33
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Abstract
Genomic information is encoded on long strands of DNA, which are folded into chromatin and stored in a tiny nucleus. Nuclear chromatin is a negatively charged polymer composed of DNA, histones, and various nonhistone proteins. Because of its highly charged nature, chromatin structure varies greatly depending on the surrounding environment (e.g., cations, molecular crowding, etc.). New technologies to capture chromatin in living cells have been developed over the past 10 years. Our view on chromatin organization has drastically shifted from a regular and static one to a more variable and dynamic one. Chromatin forms numerous compact dynamic domains that act as functional units of the genome in higher eukaryotic cells and locally appear liquid-like. By changing DNA accessibility, these domains can govern various functions. Based on new evidences from versatile genomics and advanced imaging studies, we discuss the physical nature of chromatin in the crowded nuclear environment and how it is regulated.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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34
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Bergo V, Trompouki E. New tools for 'ZEBRA-FISHING'. Brief Funct Genomics 2021:elab001. [PMID: 33605988 DOI: 10.1093/bfgp/elab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 11/14/2022] Open
Abstract
Zebrafish has been established as a classical model for developmental studies, yet in the past years, with the explosion of novel technological methods, the use of zebrafish as a model has expanded. One of the prominent fields that took advantage of zebrafish as a model organism early on is hematopoiesis, the process of blood cell generation from hematopoietic stem and progenitor cells (HSPCs). In zebrafish, HSPCs are born early during development in the aorta-gonad-mesonephros region and then translocate to the caudal hematopoietic tissue, where they expand and finally take residence in the kidney marrow. This journey is tightly regulated at multiple levels from extracellular signals to chromatin. In order to delineate the mechanistic underpinnings of this process, next-generation sequencing techniques could be an important ally. Here, we describe genome-wide approaches that have been undertaken to delineate zebrafish hematopoiesis.
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35
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Melters DP, Dalal Y. Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin. J Mol Biol 2020; 433:166720. [PMID: 33221335 PMCID: PMC8770095 DOI: 10.1016/j.jmb.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/12/2023]
Abstract
Chromatin is the epigenomic platform for diverse nuclear processes such as DNA repair, replication, transcription, telomere, and centromere function. In cancer cells, mutations in key processes result in DNA amplification, chromosome translocations, and chromothripsis, severely distorting the natural chromatin state. In normal and diseased states, dozens of chromatin effectors alter the physical integrity and dynamics of chromatin at the level of both single nucleosomes and arrays of nucleosomes folded into 3-dimensional shapes. Integrating these length scales, from the 10 nm sized nucleosome to mitotic chromosomes, whilst jostling within the crowded environment of the cell, cannot yet be achieved by a single technology. In this review, we discuss tools that have proven powerful in the investigation of nucleosome and chromatin fiber dynamics. We also provide a deeper focus into atomic force microscopy (AFM) applications that can bridge diverse length and time scales. Using time course AFM, we observe that chromatin condensation by H1.5 is dynamic, whereas using nano-indentation force spectroscopy we observe that both histone variants and nucleosome binding partners alter material properties of individual nucleosomes. Finally, we demonstrate how high-speed AFM can visualize plasmid DNA dynamics, intermittent nucleosome-nucleosome contacts, and changes in nucleosome phasing along a contiguous chromatin fiber. Altogether, the development of innovative technologies holds the promise of revealing the secret lives of nucleosomes, potentially bridging the gaps in our understanding of how chromatin works within living cells and tissues.
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Affiliation(s)
- Daniël P Melters
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
| | - Yamini Dalal
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
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36
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Shaban HA, Barth R, Bystricky K. Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription. Genome Biol 2020; 21:278. [PMID: 33203432 PMCID: PMC7670612 DOI: 10.1186/s13059-020-02185-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
The eukaryotic genome is hierarchically structured yet highly dynamic. Regulating transcription in this environment demands a high level of coordination to permit many proteins to interact with chromatin fiber at appropriate sites in a timely manner. We describe how recent advances in quantitative imaging techniques overcome caveats of sequencing-based methods (Hi-C and related) by enabling direct visualization of transcription factors and chromatin at high resolution, from single genes to the whole nucleus. We discuss the contribution of fluorescence imaging to deciphering the principles underlying this coordination within the crowded nuclear space in living cells and discuss challenges ahead.
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Affiliation(s)
- Haitham A Shaban
- Spectroscopy Department, Physics Division, National Research Centre, Dokki, Cairo, 12622, Egypt.
- Current Address: Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Roman Barth
- Department of Bionanoscience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.
- Institut Universitaire de France (IUF), Paris, France.
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