1
|
Jyoti TP, Chandel S, Singh R. Unveiling the epigenetic landscape of plants using flow cytometry approach. Cytometry A 2024; 105:231-241. [PMID: 38437027 DOI: 10.1002/cyto.a.24834] [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: 09/23/2023] [Revised: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 03/06/2024]
Abstract
Plants are sessile creatures that have to adapt constantly changing environmental circumstances. Plants are subjected to a range of abiotic stressors as a result of unpredictable climate change. Understanding how stress-responsive genes are regulated can help us better understand how plants can adapt to changing environmental conditions. Epigenetic markers that dynamically change in response to stimuli, such as DNA methylation and histone modifications are known to regulate gene expression. Individual cells or particles' physical and/or chemical properties can be measured using the method known as flow cytometry. It may therefore be used to evaluate changes in DNA methylation, histone modifications, and other epigenetic markers, making it a potent tool for researching epigenetics in plants. We explore the use of flow cytometry as a technique for examining epigenetic traits in this thorough discussion. The separation of cell nuclei and their subsequent labeling with fluorescent antibodies, offering information on the epigenetic mechanisms in plants when utilizing flow cytometry. We also go through the use of high-throughput data analysis methods to unravel the complex epigenetic processes occurring inside plant systems.
Collapse
Affiliation(s)
- Thakur Prava Jyoti
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Shivani Chandel
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| |
Collapse
|
2
|
Kamat K, Lao Z, Qi Y, Wang Y, Ma J, Zhang B. Compartmentalization with nuclear landmarks yields random, yet precise, genome organization. Biophys J 2023; 122:1376-1389. [PMID: 36871158 PMCID: PMC10111368 DOI: 10.1016/j.bpj.2023.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 02/19/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
The 3D organization of eukaryotic genomes plays an important role in genome function. While significant progress has been made in deciphering the folding mechanisms of individual chromosomes, the principles of the dynamic large-scale spatial arrangement of all chromosomes inside the nucleus are poorly understood. We use polymer simulations to model the diploid human genome compartmentalization relative to nuclear bodies such as nuclear lamina, nucleoli, and speckles. We show that a self-organization process based on a cophase separation between chromosomes and nuclear bodies can capture various features of genome organization, including the formation of chromosome territories, phase separation of A/B compartments, and the liquid property of nuclear bodies. The simulated 3D structures quantitatively reproduce both sequencing-based genomic mapping and imaging assays that probe chromatin interaction with nuclear bodies. Importantly, our model captures the heterogeneous distribution of chromosome positioning across cells while simultaneously producing well-defined distances between active chromatin and nuclear speckles. Such heterogeneity and preciseness of genome organization can coexist due to the nonspecificity of phase separation and the slow chromosome dynamics. Together, our work reveals that the cophase separation provides a robust mechanism for us to produce functionally important 3D contacts without requiring thermodynamic equilibration that can be difficult to achieve.
Collapse
Affiliation(s)
- Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Zhuohan Lao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
| |
Collapse
|
3
|
Silveira PP, Meaney MJ. Examining the biological mechanisms of human mental disorders resulting from gene-environment interdependence using novel functional genomic approaches. Neurobiol Dis 2023; 178:106008. [PMID: 36690304 DOI: 10.1016/j.nbd.2023.106008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/30/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
We explore how functional genomics approaches that integrate datasets from human and non-human model systems can improve our understanding of the effect of gene-environment interplay on the risk for mental disorders. We start by briefly defining the G-E paradigm and its challenges and then discuss the different levels of regulation of gene expression and the corresponding data existing in humans (genome wide genotyping, transcriptomics, DNA methylation, chromatin modifications, chromosome conformational changes, non-coding RNAs, proteomics and metabolomics), discussing novel approaches to the application of these data in the study of the origins of mental health. Finally, we discuss the multilevel integration of diverse types of data. Advance in the use of functional genomics in the context of a G-E perspective improves the detection of vulnerabilities, informing the development of preventive and therapeutic interventions.
Collapse
Affiliation(s)
- Patrícia Pelufo Silveira
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada.
| | - Michael J Meaney
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Translational Neuroscience Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), Singapore; Brain - Body Initiative, Agency for Science, Technology and Research (ASTAR), Singapore.
| |
Collapse
|
4
|
Chanou A, Hamperl S. Single-Molecule Techniques to Study Chromatin. Front Cell Dev Biol 2021; 9:699771. [PMID: 34291054 PMCID: PMC8287188 DOI: 10.3389/fcell.2021.699771] [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: 04/24/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Besides the basic organization in nucleosome core particles (NCPs), eukaryotic chromatin is further packed through interactions with numerous protein complexes including transcription factors, chromatin remodeling and modifying enzymes. This nucleoprotein complex provides the template for many important biological processes, such as DNA replication, transcription, and DNA repair. Thus, to understand the molecular basis of these DNA transactions, it is critical to define individual changes of the chromatin structure at precise genomic regions where these machineries assemble and drive biological reactions. Single-molecule approaches provide the only possible solution to overcome the heterogenous nature of chromatin and monitor the behavior of individual chromatin transactions in real-time. In this review, we will give an overview of currently available single-molecule methods to obtain mechanistic insights into nucleosome positioning, histone modifications and DNA replication and transcription analysis-previously unattainable with population-based assays.
Collapse
Affiliation(s)
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| |
Collapse
|
5
|
García-Giménez JL, Garcés C, Romá-Mateo C, Pallardó FV. Oxidative stress-mediated alterations in histone post-translational modifications. Free Radic Biol Med 2021; 170:6-18. [PMID: 33689846 DOI: 10.1016/j.freeradbiomed.2021.02.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022]
Abstract
Epigenetic regulation of gene expression provides a finely tuned response capacity for cells when undergoing environmental changes. However, in the context of human physiology or disease, any cellular imbalance that modulates homeostasis has the potential to trigger molecular changes that result either in physiological adaptation to a new situation or pathological conditions. These effects are partly due to alterations in the functionality of epigenetic regulators, which cause long-term and often heritable changes in cell lineages. As such, free radicals resulting from unbalanced/extended oxidative stress have been proved to act as modulators of epigenetic agents, resulting in alterations of the epigenetic landscape. In the present review we will focus on the particular effect that oxidative stress and free radicals produce in histone post-translational modifications that contribute to altering the histone code and, consequently, gene expression. The pathological consequences of the changes in this epigenetic layer of regulation of gene expression are thoroughly evidenced by data gathered in many physiological adaptive processes and in human diseases that range from age-related neurodegenerative pathologies to cancer, and that include respiratory syndromes, infertility, and systemic inflammatory conditions like sepsis.
Collapse
Affiliation(s)
- José-Luis García-Giménez
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Concepción Garcés
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain
| | - Carlos Romá-Mateo
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Federico V Pallardó
- Department of Physiology, Faculty of Medicine and Dentistry. University of Valencia- INCLIVA, Valencia, 46010, Spain; Associated Unit for Rare Diseases INCLIVA-CIPF, Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| |
Collapse
|
6
|
Noubissi FK, McBride AA, Leppert HG, Millet LJ, Wang X, Davern SM. Detection and quantification of γ-H2AX using a dissociation enhanced lanthanide fluorescence immunoassay. Sci Rep 2021; 11:8945. [PMID: 33903655 PMCID: PMC8076281 DOI: 10.1038/s41598-021-88296-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/30/2021] [Indexed: 11/09/2022] Open
Abstract
Phosphorylation of the histone protein H2AX to form γ-H2AX foci directly represents DNA double-strand break formation. Traditional γ-H2AX detection involves counting individual foci within individual nuclei. The novelty of this work is the application of a time-resolved fluorescence assay using dissociation-enhanced lanthanide fluorescence immunoassay for quantitative measurements of γ-H2AX. For comparison, standard fluorescence detection was employed and analyzed either by bulk fluorescent measurements or by direct foci counting using BioTek Spot Count algorithm and Gen 5 software. Etoposide induced DNA damage in A549 carcinoma cells was compared across all test platforms. Time resolved fluorescence detection of europium as a chelated complex enabled quantitative measurement of γ-H2AX foci with nanomolar resolution. Comparative bulk fluorescent signals achieved only micromolar sensitivity. Lanthanide based immunodetection of γ-H2AX offers superior detection and a user-friendly workflow. These approaches have the potential to improve screening of compounds that either enhance DNA damage or protect against its deleterious effects.
Collapse
Affiliation(s)
| | - Amber A McBride
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Hannah G Leppert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Larry J Millet
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - Xiaofei Wang
- Department of Biological Sciences, Tennessee State University, Nashville, TN, USA
| | - Sandra M Davern
- Radioisotope Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| |
Collapse
|
7
|
Smith MT, Guyton KZ, Kleinstreuer N, Borrel A, Cardenas A, Chiu WA, Felsher DW, Gibbons CF, Goodson WH, Houck KA, Kane AB, La Merrill MA, Lebrec H, Lowe L, McHale CM, Minocherhomji S, Rieswijk L, Sandy MS, Sone H, Wang A, Zhang L, Zeise L, Fielden M. The Key Characteristics of Carcinogens: Relationship to the Hallmarks of Cancer, Relevant Biomarkers, and Assays to Measure Them. Cancer Epidemiol Biomarkers Prev 2020; 29:1887-1903. [PMID: 32152214 PMCID: PMC7483401 DOI: 10.1158/1055-9965.epi-19-1346] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/15/2020] [Accepted: 03/04/2020] [Indexed: 12/21/2022] Open
Abstract
The key characteristics (KC) of human carcinogens provide a uniform approach to evaluating mechanistic evidence in cancer hazard identification. Refinements to the approach were requested by organizations and individuals applying the KCs. We assembled an expert committee with knowledge of carcinogenesis and experience in applying the KCs in cancer hazard identification. We leveraged this expertise and examined the literature to more clearly describe each KC, identify current and emerging assays and in vivo biomarkers that can be used to measure them, and make recommendations for future assay development. We found that the KCs are clearly distinct from the Hallmarks of Cancer, that interrelationships among the KCs can be leveraged to strengthen the KC approach (and an understanding of environmental carcinogenesis), and that the KC approach is applicable to the systematic evaluation of a broad range of potential cancer hazards in vivo and in vitro We identified gaps in coverage of the KCs by current assays. Future efforts should expand the breadth, specificity, and sensitivity of validated assays and biomarkers that can measure the 10 KCs. Refinement of the KC approach will enhance and accelerate carcinogen identification, a first step in cancer prevention.See all articles in this CEBP Focus section, "Environmental Carcinogenesis: Pathways to Prevention."
Collapse
Affiliation(s)
- Martyn T Smith
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, Berkeley, California.
| | - Kathryn Z Guyton
- Monographs Programme, International Agency for Research on Cancer, Lyon, France
| | - Nicole Kleinstreuer
- Division of Intramural Research, Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, North Carolina
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Alexandre Borrel
- Division of Intramural Research, Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, North Carolina
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, Berkeley, California
| | - Weihsueh A Chiu
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas
| | - Dean W Felsher
- Division of Oncology, Departments of Medicine and Pathology, Stanford University School of Medicine, Stanford, California
| | - Catherine F Gibbons
- Office of Research and Development, US Environmental Protection Agency, Washington, D.C
| | - William H Goodson
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Keith A Houck
- Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Agnes B Kane
- Department of Pathology and Laboratory Medicine, Alpert Medical School, Brown University, Providence, Rhode Island
| | - Michele A La Merrill
- Department of Environmental Toxicology, University of California, Davis, California
| | - Herve Lebrec
- Comparative Biology & Safety Sciences, Amgen Research, Amgen Inc., Thousand Oaks, California
| | - Leroy Lowe
- Getting to Know Cancer, Truro, Nova Scotia, Canada
| | - Cliona M McHale
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, Berkeley, California
| | - Sheroy Minocherhomji
- Comparative Biology & Safety Sciences, Amgen Research, Amgen Inc., Thousand Oaks, California
| | - Linda Rieswijk
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, Berkeley, California
- Institute of Data Science, Maastricht University, Maastricht, the Netherlands
| | - Martha S Sandy
- Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Oakland, California
| | - Hideko Sone
- Yokohama University of Pharmacy and National Institute for Environmental Studies, Tsukuba Ibaraki, Japan
| | - Amy Wang
- Office of the Report on Carcinogens, Division of National Toxicology Program, The National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Luoping Zhang
- Division of Environmental Health Sciences, School of Public Health, University of California Berkeley, Berkeley, California
| | - Lauren Zeise
- Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Oakland, California
| | - Mark Fielden
- Expansion Therapeutics Inc, San Diego, California
| |
Collapse
|
8
|
Hayashi-Takanaka Y, Kina Y, Nakamura F, Becking LE, Nakao Y, Nagase T, Nozaki N, Kimura H. Histone modification dynamics as revealed by multicolor immunofluorescence-based single-cell analysis. J Cell Sci 2020; 133:jcs243444. [PMID: 32576661 PMCID: PMC7390643 DOI: 10.1242/jcs.243444] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/08/2020] [Indexed: 01/02/2023] Open
Abstract
Post-translational modifications on histones can be stable epigenetic marks or transient signals that can occur in response to internal and external stimuli. Levels of histone modifications fluctuate during the cell cycle and vary among different cell types. Here, we describe a simple system to monitor the levels of multiple histone modifications in single cells by multicolor immunofluorescence using directly labeled modification-specific antibodies. We analyzed histone H3 and H4 modifications during the cell cycle. Levels of active marks, such as acetylation and H3K4 methylation, were increased during the S phase, in association with chromatin duplication. By contrast, levels of some repressive modifications gradually increased during G2 and the next G1 phases. We applied this method to validate the target modifications of various histone demethylases in cells using a transient overexpression system. In extracts of marine organisms, we also screened chemical compounds that affect histone modifications and identified psammaplin A, which was previously reported to inhibit histone deacetylases. Thus, the method presented here is a powerful and convenient tool for analyzing the changes in histone modifications.
Collapse
Affiliation(s)
- Yoko Hayashi-Takanaka
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-3, Yamadaoka, Suita 565-0871, Japan
| | - Yuto Kina
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Fumiaki Nakamura
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Leontine E Becking
- Marine Animal Ecology Group, Wageningen University & Research, PO Box 338, Bode 36, 6700 AH Wageningen, The Netherlands
| | - Yoichi Nakao
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | | | | | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| |
Collapse
|
9
|
García-Giménez JL, Romá-Mateo C, Pallardó FV. Oxidative post-translational modifications in histones. Biofactors 2019; 45:641-650. [PMID: 31185139 DOI: 10.1002/biof.1532] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/12/2019] [Indexed: 01/12/2023]
Abstract
Epigenetic regulation is attracting much attention because it explains many of the effects that the external environment induces in organisms. Changes in the cellular redox status and even more specifically in its nuclear redox compartment is one of these examples. Redox changes can induce modulation of the epigenetic regulation in cells. Here we present a few cases where reactive oxygen or nitrogen species induces epigenetic marks in histones. Posttranslational modification of these proteins like histone nitrosylation, carbonylation, or glutathionylation together with other mechanisms not reviewed here are the cornerstones of redox-related epigenetic regulation. We currently face a new field of research with potential important consequences for the treatment of many pathologies.
Collapse
Affiliation(s)
- José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Carlos Romá-Mateo
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, Universitat de València (UV), Valencia, Spain
| |
Collapse
|
10
|
Profiling of Epigenetic Features in Clinical Samples Reveals Novel Widespread Changes in Cancer. Cancers (Basel) 2019; 11:cancers11050723. [PMID: 31137727 PMCID: PMC6562406 DOI: 10.3390/cancers11050723] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/09/2019] [Accepted: 05/20/2019] [Indexed: 12/31/2022] Open
Abstract
Aberrations in histone post-translational modifications (PTMs), as well as in the histone modifying enzymes (HMEs) that catalyze their deposition and removal, have been reported in many tumors and many epigenetic inhibitors are currently under investigation for cancer treatment. Therefore, profiling epigenetic features in cancer could have important implications for the discovery of both biomarkers for patient stratification and novel epigenetic targets. In this study, we employed mass spectrometry-based approaches to comprehensively profile histone H3 PTMs in a panel of normal and tumoral tissues for different cancer types, identifying various changes, some of which appear to be a consequence of the increased proliferation rate of tumors, while others are cell-cycle independent. Histone PTM changes found in tumors partially correlate with alterations of the gene expression profiles of HMEs obtained from publicly available data and are generally lost in culture conditions. Through this analysis, we identified tumor- and subtype-specific histone PTM changes, but also widespread changes in the levels of histone H3 K9me3 and K14ac marks. In particular, H3K14ac showed a cell-cycle independent decrease in all the seven tumor/tumor subtype models tested and could represent a novel epigenetic hallmark of cancer. .
Collapse
|
11
|
Jevtić P, Schibler AC, Wesley CC, Pegoraro G, Misteli T, Levy DL. The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity. EMBO Rep 2019; 20:embr.201847283. [PMID: 31085625 DOI: 10.15252/embr.201847283] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
How intracellular organelles acquire their characteristic sizes is a fundamental question in cell biology. Given stereotypical changes in nuclear size in cancer, it is important to understand the mechanisms that control nuclear size in human cells. Using a high-throughput imaging RNAi screen, we identify and mechanistically characterize ELYS, a nucleoporin required for post-mitotic nuclear pore complex (NPC) assembly, as a determinant of nuclear size in mammalian cells. ELYS knockdown results in small nuclei, reduced nuclear lamin B2 localization, lower NPC density, and decreased nuclear import. Increasing nuclear import by importin α overexpression rescues nuclear size and lamin B2 import, while inhibiting importin α/β-mediated nuclear import decreases nuclear size. Conversely, ELYS overexpression increases nuclear size, enriches nuclear lamin B2 at the nuclear periphery, and elevates NPC density and nuclear import. Consistent with these observations, knockdown or inhibition of exportin 1 increases nuclear size. Thus, we identify ELYS as a novel positive effector of mammalian nuclear size and propose that nuclear size is sensitive to NPC density and nuclear import capacity.
Collapse
Affiliation(s)
- Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | | | - Chase C Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Gianluca Pegoraro
- High Throughput Imaging Facility (HiTIF), National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| |
Collapse
|
12
|
Abstract
In the epigenetics field, large-scale functional genomics datasets of ever-increasing size and complexity have been produced using experimental techniques based on high-throughput sequencing. In particular, the study of the 3D organization of chromatin has raised increasing interest, thanks to the development of advanced experimental techniques. In this context, Hi-C has been widely adopted as a high-throughput method to measure pairwise contacts between virtually any pair of genomic loci, thus yielding unprecedented challenges for analyzing and handling the resulting complex datasets. In this review, we focus on the increasing complexity of available Hi-C datasets, which parallels the adoption of novel protocol variants. We also review the complexity of the multiple data analysis steps required to preprocess Hi-C sequencing reads and extract biologically meaningful information. Finally, we discuss solutions for handling and visualizing such large genomics datasets.
Collapse
|
13
|
Shao X, Wang X, Guan S, Lin H, Yan G, Gao M, Deng C, Zhang X. Integrated Proteome Analysis Device for Fast Single-Cell Protein Profiling. Anal Chem 2018; 90:14003-14010. [PMID: 30375851 DOI: 10.1021/acs.analchem.8b03692] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In our previous work, we have demonstrated an integrated proteome analysis device (iPAD-100) to analyze proteomes from 100 cells. (1) In this work, for the first time, a novel integrated device for single-cell analysis (iPAD-1) was developed to profile proteins in a single cell within 1 h. In the iPAD-1, a selected single cell was directly sucked into a 22 μm i.d. capillary. Then the cell lysis and protein digestion were simultaneously accomplished in the capillary in a 2 nL volume, which could prevent protein loss and excessive dilution. Digestion was accelerated by using elevated temperature with ultrasonication. The whole time of cell treatment was 30 min. After that, single-cell digest peptides were transferred into an LC column directly through a true zero dead volume union, to minimize protein transfer loss. A homemade 22 μm i.d. nano-LC packing column with 3 μm i.d. ESI tip was used in the device to achieve ultrasensitive detection. A 30 min elution program was applied to analysis of the single-cell proteome. Therefore, the total time needed for a single-cell analysis was only 1 h. In an analysis of 10 single HeLa cells, a maximum of 328 proteins were identified in one cell by using an Orbitrap Fusion Tribrid MS instrument, and the detection limit was estimated at around 1.7-170 zmol. Such a sensitivity of the iPAD-1 was ∼120-fold higher than that of our previously developed iPAD-100 system. (1) Prominent cellular heterogeneity in protein expressive profiling was observed. Furthermore, we roughly estimated the phases of the cell cycle of tested HeLa cells by the amount of core histone proteins.
Collapse
Affiliation(s)
- Xi Shao
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Xuantang Wang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Sheng Guan
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Haizhu Lin
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| |
Collapse
|
14
|
Jowhar Z, Shachar S, Gudla PR, Wangsa D, Torres E, Russ JL, Pegoraro G, Ried T, Raznahan A, Misteli T. Effects of human sex chromosome dosage on spatial chromosome organization. Mol Biol Cell 2018; 29:2458-2469. [PMID: 30091656 PMCID: PMC6233059 DOI: 10.1091/mbc.e18-06-0359] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/25/2018] [Accepted: 08/01/2018] [Indexed: 01/08/2023] Open
Abstract
Sex chromosome aneuploidies (SCAs) are common genetic syndromes characterized by the presence of an aberrant number of X and Y chromosomes due to meiotic defects. These conditions impact the structure and function of diverse tissues, but the proximal effects of SCAs on genome organization are unknown. Here, to determine the consequences of SCAs on global genome organization, we have analyzed multiple architectural features of chromosome organization in a comprehensive set of primary cells from SCA patients with various ratios of X and Y chromosomes by use of imaging-based high-throughput chromosome territory mapping (HiCTMap). We find that X chromosome supernumeracy does not affect the size, volume, or nuclear position of the Y chromosome or an autosomal chromosome. In contrast, the active X chromosome undergoes architectural changes as a function of increasing X copy number as measured by a decrease in size and an increase in circularity, which is indicative of chromatin compaction. In Y chromosome supernumeracy, Y chromosome size is reduced suggesting higher chromatin condensation. The radial positioning of chromosomes is unaffected in SCA karyotypes. Taken together, these observations document changes in genome architecture in response to alterations in sex chromosome numbers and point to trans-effects of dosage compensation on chromosome organization.
Collapse
Affiliation(s)
- Ziad Jowhar
- Cell Biology of Genomes Group, National Institutes of Health, Bethesda, MD 20892
| | - Sigal Shachar
- Cell Biology of Genomes Group, National Institutes of Health, Bethesda, MD 20892
| | - Prabhakar R. Gudla
- High-Throughput Imaging Facility, National Institutes of Health, Bethesda, MD 20892
| | - Darawalee Wangsa
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Erin Torres
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Jill L. Russ
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Institutes of Health, Bethesda, MD 20892
| | - Thomas Ried
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Armin Raznahan
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Tom Misteli
- Cell Biology of Genomes Group, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|