1
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Nakao M, Sato Y, Aizawa A, Kimura H. Mode of SUV420H2 heterochromatin localization through multiple HP1 binding motifs in the heterochromatic targeting module. Genes Cells 2024; 29:361-379. [PMID: 38403935 DOI: 10.1111/gtc.13109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024]
Abstract
Constitutive heterochromatin is transcriptionally repressed and densely packed chromatin, typically harboring histone H3 Lys9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1). SUV420H2, a histone H4 Lys20 methyltransferase, is recruited to heterochromatin by binding to HP1 through its Heterochromatic Targeting Module (HTM). Here, we have identified three HP1 binding motifs within the HTM. Both the full-length HTM and its N-terminal region (HTM-N), which contains the first and second motifs, stabilized HP1 on heterochromatin. The intervening region between the first and second HP1 binding motifs in HTM-N was also crucial for HP1 binding. In contrast, the C-terminal region of HTM (HTM-C), containing the third motif, destabilized HP1 on chromatin. An HTM V374D mutant, featuring a Val374 to Asp substitution in the second HP1 binding motif, localizes to heterochromatin without affecting HP1 stability. These data suggest that the second HP1 binding motif in the SUV420H2 HTM is critical for locking HP1 on H3K9me3-enriched heterochromatin. HTM V374D, tagged with a fluorescent protein, can serve as a live-cell probe to visualize HP1-bound heterochromatin.
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Affiliation(s)
- Masaru Nakao
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Arisa Aizawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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2
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Scelfo A, Barra V, Abdennur N, Spracklin G, Busato F, Salinas-Luypaert C, Bonaiti E, Velasco G, Bonhomme F, Chipont A, Tijhuis AE, Spierings DC, Guérin C, Arimondo P, Francastel C, Foijer F, Tost J, Mirny L, Fachinetti D. Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization. J Cell Biol 2024; 223:e202307026. [PMID: 38376465 PMCID: PMC10876481 DOI: 10.1083/jcb.202307026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/20/2023] [Accepted: 01/15/2024] [Indexed: 02/21/2024] Open
Abstract
DNA methylation (DNAme) is a key epigenetic mark that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present cell models that allow inducible and reversible DNAme modulation through DNMT1 depletion. By dynamically assessing whole genome and locus-specific effects of induced passive demethylation through cell divisions, we reveal a cooperative activity between DNMT1 and DNMT3B, but not of DNMT3A, to maintain and control DNAme. We show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin, compartmentalization, and peripheral localization. DNA methylation loss coincides with a gradual reduction of cell fitness due to G1 arrest, with minor levels of mitotic failure. Altogether, this system allows DNMTs and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNAme dysfunction and human disease.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
| | - Viviana Barra
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Nezar Abdennur
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Department of Systems Biology, UMass Chan Medical School, Worcester, MA, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George Spracklin
- Department of Systems Biology, UMass Chan Medical School, Worcester, MA, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Florence Busato
- Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay, Evry, France
| | | | - Elena Bonaiti
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
| | | | - Frédéric Bonhomme
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR n°3523 Chem4Life, Université Paris Cité, Paris, France
| | - Anna Chipont
- Cytometry Platform, Institut Curie, Paris, France
| | - Andréa E. Tijhuis
- European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Coralie Guérin
- Cytometry Platform, Institut Curie, Paris, France
- Université Paris Cité, INSERM, Paris, France
| | - Paola Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR n°3523 Chem4Life, Université Paris Cité, Paris, France
| | | | - Floris Foijer
- European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jӧrg Tost
- Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay, Evry, France
| | - Leonid Mirny
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
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3
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Vargas-López V, Prada LF, Alméciga-Díaz CJ. Evidence of epigenetic landscape shifts in mucopolysaccharidosis IIIB and IVA. Sci Rep 2024; 14:3961. [PMID: 38368436 PMCID: PMC10874391 DOI: 10.1038/s41598-024-54626-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/14/2024] [Indexed: 02/19/2024] Open
Abstract
Lysosomal storage diseases (LSDs) are a group of monogenic diseases characterized by mutations in genes coding for proteins associated with the lysosomal function. Despite the monogenic nature, LSDs patients exhibit variable and heterogeneous clinical manifestations, prompting investigations into epigenetic factors underlying this phenotypic diversity. In this study, we focused on the potential role of epigenetic mechanisms in the pathogenesis of mucopolysaccharidosis IIIB (MPS IIIB) and mucopolysaccharidosis IVA (MPS IVA). We analyzed DNA methylation (5mC) and histone modifications (H3K14 acetylation and H3K9 trimethylation) in MPS IIIB and MPS IVA patients' fibroblasts and healthy controls. The findings revealed that global DNA hypomethylation is present in cell lines for both diseases. At the same time, histone acetylation was increased in MPS IIIB and MPS IVA cells in a donor-dependent way, further indicating a shift towards relaxed open chromatin in these MPS. Finally, the constitutive heterochromatin marker, histone H3K9 trimethylation, only showed reduced clustering in MPS IIIB cells, suggesting limited alterations in heterochromatin organization. These findings collectively emphasize the significance of epigenetic mechanisms in modulating the phenotypic variations observed in LSDs. While global DNA hypomethylation could contribute to the MPS pathogenesis, the study also highlights individual-specific epigenetic responses that might contribute to phenotypic heterogeneity. Further research into the specific genes and pathways affected by these epigenetic changes could provide insights into potential therapeutic interventions for these MPS and other LSDs.
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Affiliation(s)
- Viviana Vargas-López
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Cra. 7 No. 43-82 Edificio 54, Laboratorio 305A, Bogotá D.C., 110231, Colombia
| | - Luisa F Prada
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Cra. 7 No. 43-82 Edificio 54, Laboratorio 305A, Bogotá D.C., 110231, Colombia
| | - Carlos J Alméciga-Díaz
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Cra. 7 No. 43-82 Edificio 54, Laboratorio 305A, Bogotá D.C., 110231, Colombia.
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4
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Stepanov AI, Zhurlova PA, Shuvaeva AA, Sokolinskaya EL, Gurskaya NG, Lukyanov KA, Putlyaeva LV. Optogenetics for sensors: On-demand fluorescent labeling of histone epigenetics. Biochem Biophys Res Commun 2023; 687:149174. [PMID: 37939505 DOI: 10.1016/j.bbrc.2023.149174] [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: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
Post-translational modifications of histones to a large extent determine the functional state of chromatin loci. Dynamic visualization of histone modifications with genetically encoded fluorescent sensors makes it possible to monitor changes in the epigenetic state of a single living cell. At the same time, the sensors can potentially compete with endogenous factors recognizing these modifications. Thus, prolonged binding of the sensors to chromatin can affect normal epigenetic regulation. Here, we report an optogenetic sensor for live-cell visualization of histone H3 methylated at lysine-9 (H3K9me3) named MPP8-LAMS (MPP8-based light-activated modification sensor). MPP8-LAMS consists of several fusion protein parts (from N- to C-terminus): i) nuclear export signal (NES), ii) far-red fluorescent protein Katushka, iii) H3K9me3-binding reader domain of the human M phase phosphoprotein 8 (MPP8), iv) the light-responsive AsLOV2 domain, which exposes a nuclear localization signal (NLS) upon blue light stimulation. In the dark, due to the NES, MPP8-LAMS is localized in the cytosol. Under blue light illumination, MPP8-LAMS underwent an efficient translocation from cytosol to nucleus, enabling visualization of H3K9me3-enriched loci. Such an on-demand visualization minimizes potential impact on cell physiology as most of the time the sensor is separated from its target. In general, the present work extends the application of optogenetics to the area of advanced use of genetically encoded sensors.
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Affiliation(s)
- Afanasii I Stepanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Polina A Zhurlova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia
| | - Alexandra A Shuvaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, 141701 Dolgoprudny, Russia
| | - Elena L Sokolinskaya
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia
| | - Nadya G Gurskaya
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Lidia V Putlyaeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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5
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Haynes KA, Priode JH. Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering. Methods Mol Biol 2023; 2599:191-214. [PMID: 36427151 DOI: 10.1007/978-1-0716-2847-8_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chromatin is the nucleoprotein complex that organizes genomic DNA in the nuclei of eukaryotic cells. Chromatin-modifying enzymes and chromatin-binding regulators generate chromatin states that affect DNA compaction, repair, gene expression, and ultimately cell phenotype. Many natural chromatin mediators contain subdomains that can be isolated and recombined to build synthetic regulators and probes. Engineered chromatin proteins make up a growing collection of new tools for cell engineering and can help deepen our understanding of the mechanism by which chromatin features, such as modifications of histones and DNA, contribute to the epigenetic states that govern DNA-templated processes. To support efficient exploration of the large combinatorial design space of synthetic chromatin proteins, we have developed a Golden Gate assembly method for one-step construction of protein-encoding recombinant DNA. A set of standard 2-amino acid linkers allows facile assembly of any combination of up to four protein modules, obviating the need to design different compatible overhangs to ligate different modules. Beginning with the identification of protein modules of interest, a synthetic chromatin protein can be built and expressed in vitro or in cells in under 2 weeks.
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Affiliation(s)
- Karmella A Haynes
- W. H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA.
| | - J Harrison Priode
- W. H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA
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6
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Matveevsky S, Bakloushinskaya I, Tambovtseva V, Atsaeva M, Grishaeva T, Bogdanov A, Kolomiets O. Nonhomologous Chromosome Interactions in Prophase I: Dynamics of Bizarre Meiotic Contacts in the Alay Mole Vole Ellobius alaicus (Mammalia, Rodentia). Genes (Basel) 2022; 13:genes13122196. [PMID: 36553461 PMCID: PMC9778597 DOI: 10.3390/genes13122196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Nonhomologous chromosome interactions take place in both somatic and meiotic cells. Prior to this study, we had discovered special contacts through the SYCP3 (synaptonemal complex protein 3) filament between the short arms of nonhomologous acrocentrics at the pachytene stage in the Alay mole vole, and these contacts demonstrate several patterns from proximity to the complete fusion stage. Here, we investigated the nonhomologous chromosome contacts in meiotic prophase I. It turned out that such contacts do not introduce changes into the classic distribution of DNA double-strand breaks. It is noteworthy that not all meiotic contacts were localized in the H3k9me3-positive heterochromatic environment. Both in the mid zygotene and in the early-mid diplotene, three types of contacts (proximity, touching, and anchoring/tethering) were observed, whereas fusion seems to be characteristic only for pachytene. The number of contacts in the mid pachytene is significantly higher than that in the zygotene, and the distance between centromeres in nonhomologous contacts is also the smallest in mid pachytene for all types of contacts. Thus, this work provides a new insight into the behavior of meiotic contacts during prophase I and points to avenues of further research.
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Affiliation(s)
- Sergey Matveevsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence:
| | - Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Maret Atsaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- Department of Cell Biology, Morphology and Microbiology, Chechen State University, 364024 Grozny, Russia
| | - Tatiana Grishaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Aleksey Bogdanov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Oxana Kolomiets
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
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7
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Stepanov AI, Besedovskaia ZV, Moshareva MA, Lukyanov KA, Putlyaeva LV. Studying Chromatin Epigenetics with Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms23168988. [PMID: 36012253 PMCID: PMC9409072 DOI: 10.3390/ijms23168988] [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: 07/04/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Epigenetic modifications of histones (methylation, acetylation, phosphorylation, etc.) are of great importance in determining the functional state of chromatin. Changes in epigenome underlay all basic biological processes, such as cell division, differentiation, aging, and cancerous transformation. Post-translational histone modifications are mainly studied by immunoprecipitation with high-throughput sequencing (ChIP-Seq). It enables an accurate profiling of target modifications along the genome, but suffers from the high cost of analysis and the inability to work with living cells. Fluorescence microscopy represents an attractive complementary approach to characterize epigenetics. It can be applied to both live and fixed cells, easily compatible with high-throughput screening, and provide access to rich spatial information down to the single cell level. In this review, we discuss various fluorescent probes for histone modification detection. Various types of live-cell imaging epigenetic sensors suitable for conventional as well as super-resolution fluorescence microscopy are described. We also focus on problems and future perspectives in the development of fluorescent probes for epigenetics.
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Affiliation(s)
- Afanasii I. Stepanov
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
| | - Zlata V. Besedovskaia
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
| | - Maria A. Moshareva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklay St. 16/10, 117997 Moscow, Russia
| | - Konstantin A. Lukyanov
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
- Correspondence: (K.A.L.); (L.V.P.)
| | - Lidia V. Putlyaeva
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
- Correspondence: (K.A.L.); (L.V.P.)
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8
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Liu W, Padhi A, Zhang X, Narendran J, Anastasio MA, Nain AS, Irudayaraj J. Dynamic Heterochromatin States in Anisotropic Nuclei of Cells on Aligned Nanofibers. ACS NANO 2022; 16:10754-10767. [PMID: 35803582 PMCID: PMC9332347 DOI: 10.1021/acsnano.2c02660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The cancer cell nucleus deforms as it invades the interstitial spaces in tissues and the tumor microenvironment. While alteration of the chromatin structure in a deformed nucleus is expected and documented, the chromatin structure in the nuclei of cells on aligned matrices has not been elucidated. In this work we elucidate the spatiotemporal organization of heterochromatin in the elongated nuclei of cells on aligned nanofibers with stimulated emission depletion nanoscopy and fluorescence correlation spectroscopy. We show that the anisotropy of nuclei is sufficient to drive H3K9me3-heterochromatin alterations, with enhanced H3K9me3 nanocluster compaction and aggregation states that otherwise are indistinguishable from diffraction-limited microscopy. We interrogated the higher-order heterochromatin structures within major chromatin compartments in anisotropic nuclei and discovered a wider spatial dispersion of nanodomain clusters in the nucleoplasm and condensed larger nanoclusters near the periphery and pericentromeric heterochromatin. Upon examining the spatiotemporal dynamics of heterochromatin in anisotropic nuclei, we observed reduced mobility of the constitutive heterochromatin mark H3K9me3 and the associated heterochromatin protein 1 (HP1α) at the nucleoplasm and periphery regions, correlating with increased viscosity and changes in gene expression. Since heterochromatin remodeling is crucial to genome integrity, our results reveal an unconventional H3K9me3 heterochromatin distribution, providing cues to an altered chromatin state due to perturbations of the nuclei in aligned fiber configurations.
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Affiliation(s)
- Wenjie Liu
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Cancer Center at Illinois,
Micro and Nanotechnology Laboratory, Beckman
Institute, Carl Woese Institute for Genomic Biology, Urbana, Illinois 61801, United States
| | - Abinash Padhi
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Xiaohui Zhang
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Jairaj Narendran
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Mark A. Anastasio
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
| | - Amrinder S. Nain
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Joseph Irudayaraj
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, 1102 Everitt Lab, 1406 W. Green Street, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Cancer Center at Illinois,
Micro and Nanotechnology Laboratory, Beckman
Institute, Carl Woese Institute for Genomic Biology, Urbana, Illinois 61801, United States
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9
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Locatelli M, Lawrimore J, Lin H, Sanaullah S, Seitz C, Segall D, Kefer P, Salvador Moreno N, Lietz B, Anderson R, Holmes J, Yuan C, Holzwarth G, Bloom KS, Liu J, Bonin K, Vidi PA. DNA damage reduces heterogeneity and coherence of chromatin motions. Proc Natl Acad Sci U S A 2022; 119:e2205166119. [PMID: 35858349 PMCID: PMC9304018 DOI: 10.1073/pnas.2205166119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/07/2022] [Indexed: 01/14/2023] Open
Abstract
Chromatin motions depend on and may regulate genome functions, in particular the DNA damage response. In yeast, DNA double-strand breaks (DSBs) globally increase chromatin diffusion, whereas in higher eukaryotes the impact of DSBs on chromatin dynamics is more nuanced. We mapped the motions of chromatin microdomains in mammalian cells using diffractive optics and photoactivatable chromatin probes and found a high level of spatial heterogeneity. DNA damage reduces heterogeneity and imposes spatially defined shifts in motions: Distal to DNA breaks, chromatin motions are globally reduced, whereas chromatin retains higher mobility at break sites. These effects are driven by context-dependent changes in chromatin compaction. Photoactivated lattices of chromatin microdomains are ideal to quantify microscale coupling of chromatin motion. We measured correlation distances up to 2 µm in the cell nucleus, spanning chromosome territories, and speculate that this correlation distance between chromatin microdomains corresponds to the physical separation of A and B compartments identified in chromosome conformation capture experiments. After DNA damage, chromatin motions become less correlated, a phenomenon driven by phase separation at DSBs. Our data indicate tight spatial control of chromatin motions after genomic insults, which may facilitate repair at the break sites and prevent deleterious contacts of DSBs, thereby reducing the risk of genomic rearrangements.
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Affiliation(s)
- Maëlle Locatelli
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Hua Lin
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
| | - Sarvath Sanaullah
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Clayton Seitz
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
| | - Dave Segall
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Paul Kefer
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Naike Salvador Moreno
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Benton Lietz
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Rebecca Anderson
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Julia Holmes
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907
| | - George Holzwarth
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Kerry S. Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jing Liu
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202
- Center for Computational Biology and Bioinformatics, Indiana University, Indianapolis, IN 46202
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157
| | - Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157
- Laboratoire InGenO, Institut de Cancérologie de l’Ouest, 49055 Angers, France
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10
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SWI/SNF chromatin remodeler complex within the reward pathway is required for behavioral adaptations to stress. Nat Commun 2022; 13:1807. [PMID: 35379786 PMCID: PMC8980038 DOI: 10.1038/s41467-022-29380-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 02/22/2022] [Indexed: 01/01/2023] Open
Abstract
Enduring behavioral changes upon stress exposure involve changes in gene expression sustained by epigenetic modifications in brain circuits, including the mesocorticolimbic pathway. Brahma (BRM) and Brahma Related Gene 1 (BRG1) are ATPase subunits of the SWI/SNF complexes involved in chromatin remodeling, a process essential to enduring plastic changes in gene expression. Here, we show that in mice, social defeat induces changes in BRG1 nuclear distribution. The inactivation of the Brg1/Smarca4 gene within dopamine-innervated regions or the constitutive inactivation of the Brm/Smarca2 gene leads to resilience to repeated social defeat and decreases the behavioral responses to cocaine without impacting midbrain dopamine neurons activity. Within striatal medium spiny neurons, Brg1 gene inactivation reduces the expression of stress- and cocaine-induced immediate early genes, increases levels of heterochromatin and at a global scale decreases chromatin accessibility. Altogether these data demonstrate the pivotal function of SWI/SNF complexes in behavioral and transcriptional adaptations to salient environmental challenges. Repeated exposure to social stressors in rodents results in behavioural changes. Here the authors show that behavioural adaptations to stress are associated with nuclear organization changes through SWI/SNF chromatin remodeler in specific neuronal populations of the mesolimbic system.
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11
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Zhao H, Lin LF, Hahn J, Xie J, Holman HF, Yuan C. Single-Cell Image-Based Analysis Reveals Chromatin Changes during the Acquisition of Tamoxifen Drug Resistance. Life (Basel) 2022; 12:life12030438. [PMID: 35330189 PMCID: PMC8950147 DOI: 10.3390/life12030438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer drug resistance is the leading cause of cancer related deaths. The development of drug resistance can be partially contributed to tumor heterogeneity and epigenetic plasticity. However, the detailed molecular mechanism underlying epigenetic modulated drug resistance remains elusive. In this work, we systematically analyzed epigenetic changes in tamoxifen (Tam) responsive and resistant breast cancer cell line MCF7, and adopted a data-driven approach to identify key epigenetic features distinguishing between these two cell types. Significantly, we revealed that DNA methylation and H3K9me3 marks that constitute the heterochromatin are distinctively different between Tam-resistant and -responsive cells. We then performed time-lapse imaging of 5mC and H3K9me3 features using engineered probes. After Tam treatment, we observed a slow transition of MCF7 cells from a drug-responsive to -resistant population based on DNA methylation features. A similar trend was not observed using H3K9me3 probes. Collectively, our results suggest that DNA methylation changes partake in the establishment of Tam-resistant breast cancer cell lines. Instead of global changes in the DNA methylation level, the distribution of DNA methylation features inside the nucleus can be one of the drivers that facilitates the establishment of a drug resistant phenotype in MCF7.
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Affiliation(s)
- Han Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA; (H.Z.); (L.F.L.); (J.H.); (J.X.); (H.F.H.)
| | - Li F. Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA; (H.Z.); (L.F.L.); (J.H.); (J.X.); (H.F.H.)
| | - Joshua Hahn
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA; (H.Z.); (L.F.L.); (J.H.); (J.X.); (H.F.H.)
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA; (H.Z.); (L.F.L.); (J.H.); (J.X.); (H.F.H.)
| | - Harvey F. Holman
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA; (H.Z.); (L.F.L.); (J.H.); (J.X.); (H.F.H.)
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA; (H.Z.); (L.F.L.); (J.H.); (J.X.); (H.F.H.)
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47906, USA
- Correspondence: ; Tel.: +1-765-494-5824; Fax: +1-765-494-0805
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12
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Suraritdechachai S, Lakkanasirorat B, Uttamapinant C. Molecular probes for cellular imaging of post-translational proteoforms. RSC Chem Biol 2022; 3:201-219. [PMID: 35360891 PMCID: PMC8826509 DOI: 10.1039/d1cb00190f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However, it is not trivial to visualize post-translational modifications in a protein- and site-specific manner, especially in a living-cell context. Herein, we review recent advances in the development of molecular imaging tools to detect diverse classes of post-translational proteoforms in individual cells, and their applications in studying precise roles of PTMs in regulating the function of cellular proteins.
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Affiliation(s)
- Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Benya Lakkanasirorat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
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13
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Mendonca A, Sánchez O, Zhao H, Lin L, Min A, Yuan C. Development and application of novel BiFC probes for cell sorting based on epigenetic modification. Cytometry A 2022; 101:339-350. [PMID: 35001539 DOI: 10.1002/cyto.a.24530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022]
Abstract
The epigenetic signature of cancer cells varies with disease progression and drug treatment, necessitating the study of these modifications with single cell resolution over time. The rapid detection and sorting of cells based on their underlying epigenetic modifications by flow cytometry can enable single cell measurement and tracking to understand tumor heterogeneity and progression warranting the development of a live-cell compatible epigenome probes. In this work, we developed epigenetic probes based on bimolecular fluorescence complementation (BiFC) and demonstrated their capabilities in quantifying and sorting cells based on their epigenetic modification contents. The sorted cells are viable and exhibit distinctive responses to chemo-therapy drugs. Notably, subpopulations of MCF7 cells with higher H3K9me3 levels are more likely to develop resistance to Doxorubicin. Subpopulations with higher 5mC levels, on the other hand, tend to be more responsive. Overall, we report for the first time, the application of novel split probes in flow cytometry application and elucidated the potential role of 5mC and H3K9me3 in determining drug responses.
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Affiliation(s)
- Agnes Mendonca
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Oscar Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Han Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Li Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Alan Min
- Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Center for Cancer Research, West Lafayette, Indiana, USA
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14
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Sánchez OF, Lin LF, Xie J, Freeman JL, Yuan C. Lead exposure induces dysregulation of constitutive heterochromatin hallmarks in live cells. Curr Res Toxicol 2021; 3:100061. [PMID: 35005634 PMCID: PMC8717252 DOI: 10.1016/j.crtox.2021.12.001] [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: 08/26/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/28/2022] Open
Abstract
Lead (Pb) is a heavy metal contaminant commonly found in air, soil, and drinking water due to legacy uses. Excretion of ingested Pb can result in extensive kidney damages due to elevated oxidative stress. Epigenetic alterations induced by exposure to Pb have also been implied but remain poorly understood. In this work, we assessed changes in repressive epigenetic marks, namely DNA methylation (meCpG) and histone 3 lysine 9 tri-methylation (H3K9me3) after exposure to Pb. Live cell epigenetic probes coupled to bimolecular fluorescence complementation (BiFC) were used to monitor changes in the selected epigenetic marks. Exposure to Pb significantly lowered meCpG and H3K9me3 levels in HEK293T cells suggesting global changes in constitutive heterochromatin. A heterodimeric pair of probes that tags chromatin regions enriched in both meCpG and H3K9me3 further confirmed our findings. The observed epigenetic changes can be partially attributed to aberrant transcriptional changes induced by Pb, such as overexpression of TET1 after Pb exposure. Lastly, we monitored changes in selected heterochromatin marks after removal of Pb and found that changes in these markers do not immediately recover to their original level suggesting potential long-term damages to chromatin structure.
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Affiliation(s)
- Oscar F. Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Li F. Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Jennifer L. Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center of Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center of Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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15
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Zhao H, Ma D, Xie J, Sanchez O, Huang F, Yuan C. Live-Cell Probe for In Situ Single-Cell Monitoring of Mitochondrial DNA Methylation. ACS Sens 2021; 6:3575-3586. [PMID: 34586782 DOI: 10.1021/acssensors.1c00731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mitochondria, as the center of energy production, play an important role in cell homeostasis by regulating the cellular metabolism and mediating the cellular response to stress. Epigenetic changes such as DNA and histone methylation have been increasingly recognized to play a significant role in homeostasis and stress response. The cross-talking between the metabolome and the epigenome has attracted significant attention in recent years but with a major focus on how metabolism contributes to epigenomic changes. Few studies have focused on how epigenetic modifications may alter the mitochondrial composition and activity. In this work, we designed a novel probe targeting methylated CpGs of mitochondrial DNA (mtDNA). We demonstrated the capability of our probe to reveal the spatial distribution of methylated mtDNA and capture the mtDNA methylation changes at a single-cell level. We were also able to track single-cell mtDNA and nDNA methylation simultaneously and discovered the unsynchronized dynamics of the nucleus and mitochondria. Our tool offers a unique opportunity to understand the epigenetic regulation of mtDNA and its dynamic response to the microenvironment and cellular changes.
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Affiliation(s)
- Han Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Donghan Ma
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Oscar Sanchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue University Center for Cancer Research, West Lafayette, Indiana 47907, United States
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue University Center for Cancer Research, West Lafayette, Indiana 47907, United States
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16
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Sato Y, Nakao M, Kimura H. Live-Cell Imaging Probes to Track Chromatin Modification Dynamics. Microscopy (Oxf) 2021; 70:415-422. [PMID: 34329472 PMCID: PMC8491620 DOI: 10.1093/jmicro/dfab030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
The spatiotemporal organization of chromatin is regulated at different levels in the nucleus. Epigenetic modifications such as DNA methylation and histone modifications are involved in chromatin regulation and play fundamental roles in genome function. While the one-dimensional epigenomic landscape in many cell types has been revealed by chromatin immunoprecipitation and sequencing, the dynamic changes of chromatin modifications and their relevance to chromatin organization and genome function remain elusive. Live-cell probes to visualize chromatin and its modifications have become powerful tools to monitor dynamic chromatin regulation. Bulk chromatin can be visualized by both small fluorescent dyes and fluorescent proteins, and specific endogenous genomic loci have been detected by adapting genome-editing tools. To track chromatin modifications in living cells, various types of probes have been developed. Protein domains that bind weakly to specific modifications, such as chromodomains for histone methylation, can be repeated to create a tighter binding probe that can then be tagged with a fluorescent protein. It has also been demonstrated that antigen-binding fragments and single-chain variable fragments from modification-specific antibodies can serve as binding probes without disturbing cell division, development and differentiation. These modification-binding modules are used in modification sensors based on fluorescence/Förster resonance energy transfer to measure the intramolecular conformational changes triggered by modifications. Other probes can be created using a bivalent binding system, such as fluorescence complementation or luciferase chemiluminescence. Live-cell chromatin modification imaging using these probes will address dynamic chromatin regulation and will be useful for assaying and screening effective epigenome drugs in cells and organisms.
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Affiliation(s)
- Yuko Sato
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Masaru Nakao
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
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17
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Mendonca A, Sánchez OF, Xie J, Carneiro A, Lin L, Yuan C. Identifying distinct heterochromatin regions using combinatorial epigenetic probes in live cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194725. [PMID: 34174495 DOI: 10.1016/j.bbagrm.2021.194725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
The 3D spatial organization of the genome controls gene expression and cell functionality. Heterochromatin (HC), which is the densely compacted and largely silenced part of the chromatin, is the driver for the formation and maintenance of nuclear organization in the mammalian nucleus. It is functionally divided into highly compact constitutive heterochromatin (cHC) and transcriptionally poised facultative heterochromatin (fHC). Long regarded as a static structure, the highly dynamic nature of the heterochromatin is being slowly understood and studied. These changes in HC occur on various temporal scales during the cell cycle and differentiation processes. Most methods that capture information about the heterochromatin are static techniques that cannot provide a readout of how the HC organization evolves with time. The delineation of specific areas such as fHC are also rendered difficult due to its diffusive nature and lack of specific features. Another degree of complexity in characterizing changes in heterochromatin occurs due to the heterogeneity in the HC organization of individual cells, necessitating single cell studies. Overall, there is a need for live cell compatible tools that can stably track the heterochromatin as it undergoes re-organization. In this work, we present an approach to track cHC and fHC based on the epigenetic hallmarks associated with them. Unlike conventional immunostaining approaches, we use small recombinant protein probes that allow us to dynamically monitor the HC by binding to modifications specific to the cHC and fHC, such as H3K9me3, DNA methylation and H3K27me3. We demonstrate the use of the probes to follow the changes in HC induced by drug perturbations at the single cell level. We also use the probe sets combinatorically to simultaneously track chromatin regions enriched in two selected epigenetic modifications using a FRET based approach that enabled us tracking distinctive chromatin features in situ.
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Affiliation(s)
- Agnes Mendonca
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Oscar F Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Ana Carneiro
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Li Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47906, USA.
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18
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Xie J, Lin L, Sánchez OF, Bryan C, Freeman JL, Yuan C. Pre-differentiation exposure to low-dose of atrazine results in persistent phenotypic changes in human neuronal cell lines. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116379. [PMID: 33388679 DOI: 10.1016/j.envpol.2020.116379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/04/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Exposures to organic pesticides, particularly during a developmental window, have been associated with various neurodegenerative diseases later in life. Atrazine (ATZ), one of the most used pesticides in the U.S., is suspected to be associated with increased neurodegeneration later in life but few studies assessed the neurotoxicity of developmental ATZ exposure using human neuronal cells. Here, we exposed human SH-SY5Y cells to 0.3, 3, and 30 ppb of ATZ prior to differentiating them into dopaminergic-like neurons in ATZ-free medium to mimic developmental exposure. The differentiated neurons exhibit altered neurite outgrowth and SNCA pathology depending on the ATZ treatment doses. Epigenome changes, such as decreases in 5mC (for 0.3 ppb only), H3K9me3, and H3K27me3 were observed immediately after exposure. These alterations persist in a compensatory manner in differentiated neurons. Specifically, we observed significant reductions in 5mC and H3K9me3, as well as, an increase in H3K27me3 in ATZ-exposed cells after differentiation, suggesting substantial chromatin rearrangements after developmental ATZ exposure. Transcriptional changes of relevant epigenetic enzymes were also quantified but found to only partially explain the observed epigenome alteration. Our results thus collectively suggest that exposure to low-dose of ATZ prior to differentiation can result in long-lasting changes in epigenome and increase risks of SNCA-related Parkinson's Disease.
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Affiliation(s)
- Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Li Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Oscar F Sánchez
- Department of Nutrition and Biochemistry, Pontificia Universidad Javeriana, Bogotá, 110231, Colombia
| | - Chris Bryan
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA.
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19
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Lin LF, Xie J, Sánchez OF, Bryan C, Freeman JL, Yuan C. Low dose lead exposure induces alterations on heterochromatin hallmarks persisting through SH-SY5Y cell differentiation. CHEMOSPHERE 2021; 264:128486. [PMID: 33032221 DOI: 10.1016/j.chemosphere.2020.128486] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 06/11/2023]
Abstract
Lead (Pb) is a commonly found heavy metal due to its historical applications. Recent studies have associated early-life Pb exposure with the onset of various neurodegenerative disease. The molecular mechanisms of Pb conferring long-term neurotoxicity, however, is yet to be elucidated. In this study, we explored the persistency of alteration in epigenetic marks that arise from exposure to low dose of Pb using a combination of image-based and gene expression analysis. Using SH-SY5Y as a model cell line, we observed significant alterations in global 5-methycytosine (5 mC) and histone 3 lysine 27 tri-methylation (H3K27me3) and histone 3 lysine 9 tri-methylation (H3K9me3) levels in a dose-dependent manner immediately after Pb exposure. The changes are partially associated with alterations in epigenetic enzyme expression levels. Long term culturing (14 days) after cease of exposure revealed persistent changes in 5 mC, partial recovery in H3K9me3 and overcompensation in H3K27me3 levels. The observed alterations in H3K9me3 and H3K27me3 are reversed after neuronal differentiation, while reduction in 5 mC levels are amplified with significant changes in patterns as identified via texture clustering analysis. Moreover, correlation analysis demonstrates a strong positive correlation between trends of 5 mC alteration after differentiation and neuronal morphology. Collectively, our results suggest that exposure to low dose of Pb prior to differentiation can result in persistent epigenome alterations that can potentially be responsible for the observed phenotypic changes. Our work reveals that Pb induced changes in epigenetic repressive marks can persist through neuron differentiation, which provides a plausible mechanism underlying long-term neurotoxicity associated with developmental Pb-exposure.
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Affiliation(s)
- Li F Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Oscar F Sánchez
- Department of Nutrition and Biochemistry, Pontificia Universidad Javeriana, Bogotá, 110231, Colombia
| | - Chris Bryan
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA.
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20
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Xie J, Wettschurack K, Yuan C. Review: In vitro Cell Platform for Understanding Developmental Toxicity. Front Genet 2020; 11:623117. [PMID: 33424939 PMCID: PMC7785584 DOI: 10.3389/fgene.2020.623117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/03/2020] [Indexed: 12/30/2022] Open
Abstract
Developmental toxicity and its affiliation to long-term health, particularly neurodegenerative disease (ND) has attracted significant attentions in recent years. There is, however, a significant gap in current models to track longitudinal changes arising from developmental toxicity. The advent of induced pluripotent stem cell (iPSC) derived neuronal culture has allowed for more complex and functionally active in vitro neuronal models. Coupled with recent progress in the detection of ND biomarkers, we are equipped with promising new tools to understand neurotoxicity arising from developmental exposure. This review provides a brief overview of current progress in neuronal culture derived from iPSC and in ND markers.
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Affiliation(s)
- Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, United States
| | - Kyle Wettschurack
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, United States
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, United States
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
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21
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22
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Sánchez OF, Lin L, Bryan CJ, Xie J, Freeman JL, Yuan C. Profiling epigenetic changes in human cell line induced by atrazine exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113712. [PMID: 31875570 DOI: 10.1016/j.envpol.2019.113712] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/12/2019] [Accepted: 11/30/2019] [Indexed: 05/24/2023]
Abstract
How environmental chemicals can affect and exert their toxic effect at a molecular level has gained significant interest in recent years, not only for understanding their immediate health implications over exposed individuals, but also for their subsequent progeny. Atrazine (ATZ) is a commonly used herbicide in the U.S. and a long-suspected endocrine disrupting chemical. The molecular mechanism conferring long-term adverse health outcomes, however, remain elusive. Here, we explored changes in epigenetic marks that arise after exposure to ATZ at selected doses using image-based analysis coupled with data clustering. Significant decreases in methylated CpG (meCpG) and histone 3 lysine 9 tri-methylated (H3K9me3) were observed in the selected human cell line with a clear spatial preference. Treating cells with ATZ leads to the loss of a subpopulation of cells with high meCpG levels as identified in our clustering and histogram analysis. A similar trend was observed in H3K9me3 potentially attributing to the cross-talking between meCpG and H3K9me3. Changes in meCpG are likely to be associated with alterations in epigenetic enzyme expression levels regulating meCpG and persist after the removal of ATZ source which collectively provide a plausible mechanism for long-term ATZ-induced toxicity.
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Affiliation(s)
- Oscar F Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA; Department of Nutrition and Biochemistry, Pontificia Universidad Javeriana, Bogotá, 110231, Colombia
| | - Li Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Chris J Bryan
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA.
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