1
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Mairaville C, Broyon M, Maurel M, Chentouf M, Chiavarina B, Turtoi A, Pirot N, Martineau P. Identification of monoclonal antibodies from naive antibody phage-display libraries for protein detection in formalin-fixed paraffin-embedded tissues. J Immunol Methods 2024; 532:113730. [PMID: 39059744 DOI: 10.1016/j.jim.2024.113730] [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: 04/08/2024] [Revised: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Most antibodies used in immunohistochemistry (IHC) have been developed by animal immunization. We wanted to explore naive antibody repertoires displayed on filamentous phages as a source of full-length antibodies for IHC on Formalin-Fixed and Paraffin-Embedded (FFPE) tissues. We used two isogenic mouse fibroblast cell lines that express or not human HER2 to generate positive and negative FFPE pseudo-tissue respectively. Using these pseudo-tissues and previously described approaches based on differential panning, we isolated very efficient antibody clones, but not against HER2. To optimize HER2 targeting and tissue specificity, we first performed 3-4 rounds of in vitro panning using recombinant HER2 extracellular domain (ECD) to enrich the phage library in HER2 binders, followed by one panning round using the two FFPE pseudo-tissues to retain binders for IHC conditions. We then analyzed the bound phages using next-generation sequencing to identify antibody sequences specifically associated with the HER2-positive pseudo-tissue. Using this approach, the top-ranked clone identified by sequencing was specific to the HER2-positive pseudo-tissue and showed a staining pattern similar to that of the antibody used for the clinical diagnosis of HER2-positive breast cancer. However, we could not optimize staining on other tissues, showing that specificity was restricted to the tissue used for selection and screening. Therefore, future optimized protocols must consider tissue diversity early during the selection by panning using a wide collection of tissue types.
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Affiliation(s)
| | - Morgane Broyon
- BCM, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Margaux Maurel
- IRCM, Univ. Montpellier, ICM, INSERM, Montpellier, France
| | | | | | - Andrei Turtoi
- IRCM, Univ. Montpellier, ICM, INSERM, Montpellier, France
| | - Nelly Pirot
- IRCM, Univ. Montpellier, ICM, INSERM, Montpellier, France; BCM, Univ. Montpellier, CNRS, INSERM, Montpellier, France
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2
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Du J, Liu W, Li M, Li Z, Li X, Dai Y, Liu G, Wang X, Zhu P, Gladyshev VN, Zhou X. Comparative time-series multi-omics analyses suggest H1.2 involvement in anoxic adaptation and cancer resistance. PLoS Biol 2024; 22:e3002778. [PMID: 39178313 PMCID: PMC11376556 DOI: 10.1371/journal.pbio.3002778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/05/2024] [Accepted: 07/31/2024] [Indexed: 08/25/2024] Open
Abstract
The naked mole rat (NMR), Heterocephalus glaber, is known as the longest-lived rodent and is extraordinarily resistant to hypoxia and cancer. Here, both NMR embryonic fibroblasts (NEFs) and their mouse counterparts (MEFs) were subjected to anoxic conditions (0% O2, 5% CO2). A combination of comparative transcriptomics and proteomics was then employed to identify differentially expressed genes (DEGs). Notably, we observed distinct levels of histone H1.2 (encoded by HIST1H1C) accumulation between NEFs and MEFs. Subsequent mechanistic analyses showed that higher H1.2 expression in NEFs was associated with the lower expression of its inhibitor, PARP1. Additionally, we discovered that H1.2 can directly interact with HIF-1α PAS domains, thereby promoting the expression of HIF-1α through facilitating the dimerization with HIF-1β. The overexpression of H1.2 was also found to trigger autophagy and to suppress the migration of cancer cells, as well as the formation of xenograft tumors, via the NRF2/P62 signaling pathway. Moreover, an engineered H1.2 knock-in mouse model exhibited significantly extended survival in hypoxic conditions (4% O2) and showed a reduced rate of tumor formation. Collectively, our results indicate a potential mechanistic link between H1.2 and the dual phenomena of anoxic adaptation and cancer resistance.
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Affiliation(s)
- Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yichen Dai
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
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3
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Polito MP, Marini G, Fabrizi A, Sercia L, Enzo E, De Luca M. Biochemical role of FOXM1-dependent histone linker H1B in human epidermal stem cells. Cell Death Dis 2024; 15:508. [PMID: 39019868 PMCID: PMC11255229 DOI: 10.1038/s41419-024-06905-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
Epidermal stem cells orchestrate epidermal renewal and timely wound repair through a tight regulation of self-renewal, proliferation, and differentiation. In culture, human epidermal stem cells generate a clonal type referred to as holoclone, which give rise to transient amplifying progenitors (meroclone and paraclone-forming cells) eventually generating terminally differentiated cells. Leveraging single-cell transcriptomic data, we explored the FOXM1-dependent biochemical signals controlling self-renewal and differentiation in epidermal stem cells aimed at improving regenerative medicine applications. We report that the expression of H1 linker histone subtypes decrease during serial cultivation. At clonal level we observed that H1B is the most expressed isoform, particularly in epidermal stem cells, as compared to transient amplifying progenitors. Indeed, its expression decreases in primary epithelial culture where stem cells are exhausted due to FOXM1 downregulation. Conversely, H1B expression increases when the stem cells compartment is sustained by enforced FOXM1 expression, both in primary epithelial cultures derived from healthy donors and JEB patient. Moreover, we demonstrated that FOXM1 binds the promotorial region of H1B, hence regulates its expression. We also show that H1B is bound to the promotorial region of differentiation-related genes and negatively regulates their expression in epidermal stem cells. We propose a novel mechanism wherein the H1B acts downstream of FOXM1, contributing to the fine interplay between self-renewal and differentiation in human epidermal stem cells. These findings further define the networks that sustain self-renewal along the previously identified YAP-FOXM1 axis.
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Affiliation(s)
- Maria Pia Polito
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Grazia Marini
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandra Fabrizi
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Laura Sercia
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Elena Enzo
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy.
| | - Michele De Luca
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy.
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4
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Zeng Z, Chen L, Luo H, Xiao H, Gao S, Zeng Y. Progress on H2B as a multifunctional protein related to pathogens. Life Sci 2024; 347:122654. [PMID: 38657835 DOI: 10.1016/j.lfs.2024.122654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/06/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Histone H2B is a member of the core histones, which together with other histones form the nucleosome, the basic structural unit of chromosomes. As scientists delve deeper into histones, researchers gradually realize that histone H2B is not only an important part of nucleosomes, but also plays a momentous role in regulating gene transcription, acting as a receptor and antimicrobial action outside the nucleus. There are a variety of epigenetically modified sites in the H2B tail rich in arginine and lysine, which can occur in ubiquitination, phosphorylation, methylation, acetylation, etc. When stimulated by foreign factors such as bacteria, viruses or parasites, histone H2B can act as a receptor for the recognition of these pathogens, and induce an intrinsic immune response to enhance host defense. In addition, the extrachromosomal histone H2B is also an important anti-microorganism agent, which may be the key to the development of antibiotics in the future. This review aims to summarize the interaction between histone H2B and etiological agents and explore the role of H2B in epigenetic modifications, receptors and antimicrobial activity.
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Affiliation(s)
- Zhuo Zeng
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China
| | - Li Chen
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China
| | - Haodang Luo
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China; The Laboratory Department, The affiliated Nanhua Hospital, University of South China, Hengyang City, Hunan Province 421001, PR China.
| | - Hua Xiao
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China
| | - Siqi Gao
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China
| | - Yanhua Zeng
- Institute of Pathogenic Biology, Basic Medicine School, Hengyang Medical College, University of South China, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hengyang City, Hunan Province 421001, PR China.
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5
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Kim RK, Truby NL, Silva GM, Picone JA, Miller CS, Baldwin AN, Neve RL, Cui X, Hamilton PJ. Histone H1x in mouse ventral hippocampus associates with, but does not cause behavioral adaptations to stress. Transl Psychiatry 2024; 14:239. [PMID: 38834575 PMCID: PMC11150540 DOI: 10.1038/s41398-024-02931-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/06/2024] Open
Abstract
Prior research has identified differential protein expression levels of linker histone H1x within the ventral hippocampus (vHipp) of stress-susceptible versus stress-resilient mice. These mice are behaviorally classified based on their divergent responses to chronic social stress. Here, we sought to determine whether elevated vHipp H1x protein levels directly contribute to these diverging behavioral adaptations to stress. First, we demonstrated that stress-susceptible mice uniquely express elevated vHipp H1x protein levels following chronic stress. Given that linker histones coordinate heterochromatin compaction, we hypothesize that elevated levels of H1x in the vHipp may impede pro-resilience transcriptional adaptations and prevent development of the resilient phenotype following social stress. To test this, 8-10-week-old male C57BL/6 J mice were randomly assigned to groups undergoing 10 days of chronic social defeat stress (CSDS) or single housing, respectively. Following CSDS, mice were classified as susceptible versus resilient based on their social interaction behaviors. We synthesized a viral overexpression (OE) vector for H1x and transduced all stressed and single housed mice with either H1x or control GFP within vHipp. Following viral delivery, we conducted social, anxiety-like, and memory-reliant behavior tests on distinct cohorts of mice. We found no behavioral adaptations following H1x OE compared to GFP controls in susceptible, resilient, or single housed mice. In sum, although we confirm elevated vHipp protein levels of H1x associate with susceptibility to social stress, we observe no significant behavioral consequence of H1x OE. Thus, we conclude elevated levels of H1x are associated with, but are not singularly sufficient to drive development of behavioral adaptations to stress.
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Affiliation(s)
- R Kijoon Kim
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Natalie L Truby
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Gabriella M Silva
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Joseph A Picone
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Cary S Miller
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Amber N Baldwin
- Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Rachael L Neve
- Gene Delivery Technology Core, Massachusetts General Hospital, Cambridge, MA, USA
| | - Xiaohong Cui
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Peter J Hamilton
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA.
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6
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Abu Alhaija AA, Lone IN, Sekeroglu EO, Batur T, Angelov D, Dimitrov S, Hamiche A, Firat Karalar EN, Ercan ME, Yagci T, Alotaibi H, Diril MK. Development of a mouse embryonic stem cell model for investigating the functions of the linker histone H1-4. FEBS Open Bio 2024; 14:309-321. [PMID: 38098212 PMCID: PMC10839353 DOI: 10.1002/2211-5463.13750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/11/2023] [Accepted: 12/13/2023] [Indexed: 01/13/2024] Open
Abstract
The linker histone H1 C-terminal domain (CTD) plays a pivotal role in chromatin condensation. De novo frameshift mutations within the CTD coding region of H1.4 have recently been reported to be associated with Rahman syndrome, a neurological disease that causes intellectual disability and overgrowth. To investigate the mechanisms and pathogenesis of Rahman syndrome, we developed a cellular model using murine embryonic stem cells (mESCs) and CRISPR/Cas9 genome engineering. Our engineered mES cells facilitate detailed investigations, such as H1-4 dynamics, immunoprecipitation, and nuclear localization; in addition, we tagged the mutant H1-4 with a photoactivatable GFP (PA-GFP) and an HA tag to facilitate pulldown assays. We anticipate that these engineered cells could also be used for the development of a mouse model to study the in vivo role of the H1-4 protein.
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Affiliation(s)
- Abed Alkarem Abu Alhaija
- Department of Molecular Biology and Genetics, Faculty of Basic SciencesGebze Technical UniversityTurkey
- Izmir Biomedicine and Genome CenterTurkey
| | | | - Esin Ozkuru Sekeroglu
- Izmir Biomedicine and Genome CenterTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTurkey
| | | | - Dimitar Angelov
- Izmir Biomedicine and Genome CenterTurkey
- Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239Université de Lyon, Ecole Normale Supérieure de LyonFrance
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome CenterTurkey
- Roumen Tsanev Institute of Molecular BiologyBulgarian Academy of SciencesSofiaBulgaria
- Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309Université Grenoble AlpesFrance
| | - Ali Hamiche
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)UdS, CNRS, INSERMStrasbourgFrance
| | | | | | - Tamer Yagci
- Department of Molecular Biology and Genetics, Faculty of Basic SciencesGebze Technical UniversityTurkey
| | - Hani Alotaibi
- Izmir Biomedicine and Genome CenterTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTurkey
| | - Muhammed Kasim Diril
- Izmir Biomedicine and Genome CenterTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylül UniversityIzmirTurkey
- Department of Medical Biology, Faculty of MedicineDokuz Eylül UniversityIzmirTurkey
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7
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Schmidt A, Zhang H, Schmitt S, Rausch C, Popp O, Chen J, Cmarko D, Butter F, Dittmar G, Lermyte F, Cardoso MC. The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues. Cells 2024; 13:139. [PMID: 38247831 PMCID: PMC10814525 DOI: 10.3390/cells13020139] [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: 11/01/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Pericentric heterochromatin (PCH) forms spatio-temporarily distinct compartments and affects chromosome organization and stability. Albeit some of its components are known, an elucidation of its proteome and how it differs between tissues in vivo is lacking. Here, we find that PCH compartments are dynamically organized in a tissue-specific manner, possibly reflecting compositional differences. As the mouse brain and liver exhibit very different PCH architecture, we isolated native PCH fractions from these tissues, analyzed their protein compositions using quantitative mass spectrometry, and compared them to identify common and tissue-specific PCH proteins. In addition to heterochromatin-enriched proteins, the PCH proteome includes RNA/transcription and membrane-related proteins, which showed lower abundance than PCH-enriched proteins. Thus, we applied a cut-off of PCH-unspecific candidates based on their abundance and validated PCH-enriched proteins. Amongst the hits, MeCP2 was classified into brain PCH-enriched proteins, while linker histone H1 was not. We found that H1 and MeCP2 compete to bind to PCH and regulate PCH organization in opposite ways. Altogether, our workflow of unbiased PCH isolation, quantitative mass spectrometry, and validation-based analysis allowed the identification of proteins that are common and tissue-specifically enriched at PCH. Further investigation of selected hits revealed their opposing role in heterochromatin higher-order architecture in vivo.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Stephanie Schmitt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Oliver Popp
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Jiaxuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Dusan Cmarko
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Gunnar Dittmar
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Frederik Lermyte
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
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8
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Capelle CM, Ciré S, Hedin F, Hansen M, Pavelka L, Grzyb K, Kyriakis D, Hunewald O, Konstantinou M, Revets D, Tslaf V, Marques TM, Gomes CPC, Baron A, Domingues O, Gomez M, Zeng N, Betsou F, May P, Skupin A, Cosma A, Balling R, Krüger R, Ollert M, Hefeng FQ. Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females. Nat Commun 2023; 14:7461. [PMID: 37985656 PMCID: PMC10662447 DOI: 10.1038/s41467-023-43053-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Neuroinflammation in the brain contributes to the pathogenesis of Parkinson's disease (PD), but the potential dysregulation of peripheral immunity has not been systematically investigated for idiopathic PD (iPD). Here we showed an elevated peripheral cytotoxic immune milieu, with more terminally-differentiated effector memory (TEMRA) CD8 T, CD8+ NKT cells and circulating cytotoxic molecules in fresh blood of patients with early-to-mid iPD, especially females, after analyzing > 700 innate and adaptive immune features. This profile, also reflected by fewer CD8+FOXP3+ T cells, was confirmed in another subcohort. Co-expression between cytotoxic molecules was selectively enhanced in CD8 TEMRA and effector memory (TEM) cells. Single-cell RNA-sequencing analysis demonstrated the accelerated differentiation within CD8 compartments, enhanced cytotoxic pathways in CD8 TEMRA and TEM cells, while CD8 central memory (TCM) and naïve cells were already more-active and transcriptionally-reprogrammed. Our work provides a comprehensive map of dysregulated peripheral immunity in iPD, proposing candidates for early diagnosis and treatments.
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Affiliation(s)
- Christophe M Capelle
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Av. de Université, L-4365, Esch-sur-Alzette, Luxembourg
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8049, Zurich, Switzerland
| | - Séverine Ciré
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
- Eligo Bioscience, 111 Av. de France, 75013, Paris, France
| | - Fanny Hedin
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Maxime Hansen
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), 4 Rue Nicolas Ernest Barblé, L-1210, Luxembourg, Luxembourg
| | - Lukas Pavelka
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), 4 Rue Nicolas Ernest Barblé, L-1210, Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
| | - Dimitrios Kyriakis
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029-5674, USA
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Maria Konstantinou
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Dominique Revets
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Vera Tslaf
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Av. de Université, L-4365, Esch-sur-Alzette, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Tainá M Marques
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Clarissa P C Gomes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
| | - Alexandre Baron
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Olivia Domingues
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Mario Gomez
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Ni Zeng
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Av. de Université, L-4365, Esch-sur-Alzette, Luxembourg
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), 1 Rue Louis Rech, L-3555, Dudelange, Luxembourg
- CRBIP, Institut Pasteur, Université Paris Cité, Paris, France
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Department of Physics and Material Science, University of Luxembourg, 162a Av. de la Faïencerie, L-1511, Luxembourg, Luxembourg
- Department of Neurosciences, University California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093-0662, USA
| | - Antonio Cosma
- National Cytometry Platform, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Institute of Molecular Psychiatry, University of Bonn, Venusberg-Campus 1, D-53127, Bonn, Germany
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Av. du Swing, L-4367, Belvaux, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), 4 Rue Nicolas Ernest Barblé, L-1210, Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg.
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis (ORCA), University of Southern Denmark, Odense, 5000C, Denmark.
| | - Feng Q Hefeng
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg.
- Data Integration and Analysis Unit, Luxembourg Institute of Health (LIH), L-1445, Strassen, Luxembourg.
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9
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Kim RK, Truby NL, Silva GM, Picone JA, Miller CS, Neve RL, Cui X, Hamilton PJ. Histone H1x in mouse ventral hippocampus correlates with, but does not cause behavioral adaptations to stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.06.565881. [PMID: 37986938 PMCID: PMC10659322 DOI: 10.1101/2023.11.06.565881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Prior research has identified differential protein expression levels of linker histone H1x within the ventral hippocampus (vHipp) of stress-susceptible versus stress-resilient mice. These mice are behaviorally classified based on their divergent responses to chronic social stress. Here, we sought to determine whether elevated vHipp H1x protein levels directly contribute to these diverging behavioral adaptations to stress. First, we demonstrate that stress-susceptible mice uniquely express elevated vHipp H1x protein levels following chronic stress. Given that linker histones coordinate heterochromatin compaction, we hypothesize that elevated levels of H1x in the vHipp may impede pro-resilience transcriptional adaptations and prevent development of the resilient phenotype following social stress. To test this, 8-10-week-old male C57BL/6J mice were randomly assigned to stressed and unstressed groups undergoing 10 days of chronic social defeat stress (CSDS) or single housing respectively. Following CSDS, mice were classified as susceptible versus resilient based on their social interaction behaviors. We synthesized a viral overexpression (OE) vector for H1x and transduced experimental mice with either H1x or control GFP within vHipp. Following viral delivery, we conducted social, anxiety-like, and memory-reliant behavior tests on distinct cohorts of mice. We found no behavioral adaptations following H1x OE compared to GFP controls in susceptible, resilient, or unstressed mice. In sum, although we confirm vHipp protein levels of H1x correlate with susceptibility to social stress, we observe no significant behavioral consequence of H1x OE. Thus, we conclude elevated levels of H1x are correlated with, but are not singularly sufficient to drive development of behavioral adaptations to stress.
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10
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Pascal C, Zonszain J, Hameiri O, Gargi-Levi C, Lev-Maor G, Tammer L, Levy T, Tarabeih A, Roy VR, Ben-Salmon S, Elbaz L, Eid M, Hakim T, Abu Rabe'a S, Shalev N, Jordan A, Meshorer E, Ast G. Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation. Mol Cell 2023; 83:3801-3817.e8. [PMID: 37922872 DOI: 10.1016/j.molcel.2023.10.003] [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: 03/21/2023] [Revised: 08/17/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to the high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA-processing machineries have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors, including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. H1s are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation of RNA polymerase II (RNAPII). Thus, H1 variants determine splicing fate by modulating RNAPII elongation.
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Affiliation(s)
- Corina Pascal
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan Zonszain
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ofir Hameiri
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Gargi-Levi
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Luna Tammer
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Levy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anan Tarabeih
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vanessa Rachel Roy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stav Ben-Salmon
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liraz Elbaz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mireille Eid
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Hakim
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Salima Abu Rabe'a
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nana Shalev
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Albert Jordan
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel; Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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11
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Das SK, Kumar A, Hao F, Cutter DiPiazza AR, Fang H, Lee TH, Hayes JJ. Histone H3 Tail Modifications Alter Structure and Dynamics of the H1 C-Terminal Domain Within Nucleosomes. J Mol Biol 2023; 435:168242. [PMID: 37619707 PMCID: PMC10530611 DOI: 10.1016/j.jmb.2023.168242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
The highly positively charged and intrinsically disordered H1 C-terminal domain (CTD) undergoes extensive condensation upon binding to nucleosomes, and stabilizes nucleosomes and higher-order chromatin structures but its interactions in chromatin are not well defined. Using single-molecule FRET we found that about half of the H1 CTDs in H1-nucleosome complexes exhibit well-defined FRET values indicative of distinct, static conformations, while the remainder of the population exhibits exchange between multiple defined FRET structures. Moreover, crosslinking studies indicate that the first 30 residues of the H1 CTD participate in relatively localized contacts with the first ∼25 bp of linker DNA, and that two separate regions in the CTD contribute to H1-dependent organization of linker DNA. Finally, we show that acetylation mimetics within the histone H3 tail markedly reduce the overall extent of H1 CTD condensation and significantly increase the fraction of H1 CTDs undergoing dynamic exchange between FRET states. Our results indicate the nucleosome-bound H1 CTD adopts loosely defined structures that exhibit significantly enhanced dynamics and decondensation upon epigenetic acetylation within the H3 tail.
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Affiliation(s)
- Subhra Kanti Das
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Ashok Kumar
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States
| | - Fanfan Hao
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States
| | - Amber R Cutter DiPiazza
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States
| | - He Fang
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States.
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, Rochester University Medical Center, Rochester, NY 14625, United States.
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12
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Li Z, Portillo-Ledesma S, Schlick T. Brownian dynamics simulations of mesoscale chromatin fibers. Biophys J 2023; 122:2884-2897. [PMID: 36116007 PMCID: PMC10397810 DOI: 10.1016/j.bpj.2022.09.013] [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: 05/31/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
The relationship between chromatin architecture and function defines a central problem in biology and medicine. Many computational chromatin models with atomic, coarse-grained, mesoscale, and polymer resolution have been used to shed light onto the mechanisms that dictate genome folding and regulation of gene expression. The associated simulation techniques range from Monte Carlo to molecular, Brownian, and Langevin dynamics. Here, we present an efficient Compute Unified Device Architecture (CUDA) implementation of Brownian dynamics (BD) to simulate chromatin fibers at the nucleosome resolution with our chromatin mesoscale model. With the CUDA implementation for computer architectures with graphic processing units (GPUs), we significantly accelerate compute-intensive hydrodynamic tensor calculations in the BD simulations by massive parallelization, boosting the performance a hundred-fold compared with central processing unit calculations. We validate our BD simulation approach by reproducing experimental trends on fiber diffusion and structure as a function of salt, linker histone binding, and histone-tail composition, as well as Monte Carlo equilibrium sampling results. Our approach proves to be physically accurate with performance that makes feasible the study of chromatin fibers in the range of kb or hundreds of nucleosomes (small gene). Such simulations are essential to advance the study of biological processes such as gene regulation and aberrant genome-structure related diseases.
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Affiliation(s)
- Zilong Li
- Department of Chemistry, New York University, New York, New York
| | | | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York; Courant Institute of Mathematical Sciences, New York University, New York, New York; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, China; Simons Center for Computational Physical Chemistry, New York University, New York, New York.
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13
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Yuan Y, Fan Y, Zhou Y, Qiu R, Kang W, Liu Y, Chen Y, Wang C, Shi J, Liu C, Li Y, Wu M, Huang K, Liu Y, Zheng L. Linker histone variant H1.2 is a brake on white adipose tissue browning. Nat Commun 2023; 14:3982. [PMID: 37414781 PMCID: PMC10325996 DOI: 10.1038/s41467-023-39713-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
Adipose-tissue is a central metabolic organ for whole-body energy homeostasis. Here, we find that highly expressed H1.2, a linker histone variant, senses thermogenic stimuli in beige and brown adipocytes. Adipocyte H1.2 regulates thermogenic genes in inguinal white-adipose-tissue (iWAT) and affects energy expenditure. Adipocyte H1.2 deletion (H1.2AKO) male mice show promoted iWAT browning and improved cold tolerance; while overexpressing H1.2 shows opposite effects. Mechanistically, H1.2 binds to the promoter of Il10rα, which encodes an Il10 receptor, and positively regulates its expression to suppress thermogenesis in a beige cell autonomous manner. Il10rα overexpression in iWAT negates cold-enhanced browning of H1.2AKO male mice. Increased H1.2 level is also found in WAT of obese humans and male mice. H1.2AKO male mice show alleviated fat accumulation and glucose intolerance in long-term normal chow-fed and high fat diet-fed conditions; while Il10rα overexpression abolishes these effects. Here, we show a metabolic function of H1.2-Il10rα axis in iWAT.
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Affiliation(s)
- Yangmian Yuan
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Yu Fan
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Yihao Zhou
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Rong Qiu
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Wei Kang
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Yu Liu
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Yuchen Chen
- School of Pharmacy, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Chenyu Wang
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Jiajian Shi
- School of Pharmacy, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Chengyu Liu
- Department of Transfusion Medicine, Wuhan Hospital of Traditional Chinese and Western Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Yangkai Li
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Min Wu
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Kun Huang
- School of Pharmacy, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Yong Liu
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Ling Zheng
- Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, College of Life Sciences, Wuhan University, 430072, Wuhan, China.
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14
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Das SK, Kumar A, Hao F, DiPiazza ARC, Lee TH, Hayes JJ. Histone H3 tail modifications regulate structure and dynamics of the H1 C-terminal domain within nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540398. [PMID: 37214834 PMCID: PMC10197648 DOI: 10.1101/2023.05.11.540398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Despite their importance, how linker histone H1s interact in chromatin and especially how the highly positively charged and intrinsically disordered H1 C-terminal domain (CTD) binds and stabilizes nucleosomes and higher-order chromatin structures remains unclear. Using single-molecule FRET we found that about half of the H1 CTDs in H1-nucleosome complexes exhibit well-defined FRET values indicative of distinct, static conformations, while the remainder of the population exhibits dynamically changing values, similar to that observed for H1 in the absence of nucleosomes. We also find that the first 30 residues of the CTD participate in relatively localized interactions with the first ∼20 bp of linker DNA, and that two separate regions in the CTD contribute to H1-dependent organization of linker DNA, consistent with some non-random CTD-linker DNA interactions. Finally, our data show that acetylation mimetics within the histone H3 tail induce decondensation and enhanced dynamics of the nucleosome-bound H1 CTD. (148 words).
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15
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Joseph FM, Young NL. Histone variant-specific post-translational modifications. Semin Cell Dev Biol 2023; 135:73-84. [PMID: 35277331 PMCID: PMC9458767 DOI: 10.1016/j.semcdb.2022.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 01/12/2023]
Abstract
Post-translational modifications (PTMs) of histones play a key role in DNA-based processes and contribute to cell differentiation and gene function by adding an extra layer of regulation. Variations in histone sequences within each family of histones expands the chromatin repertoire and provide further mechanisms for regulation and signaling. While variants are known to be present in certain genomic loci and carry out important functions, much remains unknown about variant-specific PTMs and their role in regulating chromatin. This ambiguity is in part due to the limited technologies and appropriate reagents to identify and quantitate variant-specific PTMs. Nonetheless, histone variants are an integral portion of the chromatin system and the understanding of their modifications and resolving how PTMs function differently on specific variants is paramount to the advancement of the field. Here we review the current knowledge on post-translational modifications specific to histone variants, with an emphasis on well-characterized PTMs of known function. While not every possible PTM is addressed, we present key variant-specific PTMs and what is known about their function and mechanisms in convenient reference tables.
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Affiliation(s)
- Faith M Joseph
- Translational Biology and Molecular Medicine Graduate Program, USA
| | - Nicolas L Young
- Translational Biology and Molecular Medicine Graduate Program, USA; Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
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16
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Prothymosin α Plays Role as a Brain Guardian through Ecto-F 1 ATPase-P2Y 12 Complex and TLR4/MD2. Cells 2023; 12:cells12030496. [PMID: 36766838 PMCID: PMC9914670 DOI: 10.3390/cells12030496] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Prothymosin alpha (ProTα) was discovered to be a necrosis inhibitor from the conditioned medium of a primary culture of rat cortical neurons under starved conditions. This protein carries out a neuronal cell-death-mode switch from necrosis to apoptosis, which is, in turn, suppressed by a variety of neurotrophic factors (NTFs). This type of NTF-assisted survival action of ProTα is reproduced in cerebral and retinal ischemia-reperfusion models. Further studies that used a retinal ischemia-reperfusion model revealed that ProTα protects retinal cells via ecto-F1 ATPase coupled with the Gi-coupled P2Y12 receptor and Toll-like receptor 4 (TLR4)/MD2 coupled with a Toll-IL-1 receptor domain-containing adaptor inducing IFN-β (TRIF). In cerebral ischemia-reperfusion models, ProTα has additional survival mechanisms via an inhibition of matrix metalloproteases in microglia and vascular endothelial cells. Heterozygous or conditional ProTα knockout mice show phenotypes of anxiety, memory learning impairment, and a loss of neurogenesis. There are many reports that ProTα has multiple intracellular functions for cell survival and proliferation through a variety of protein-protein interactions. Overall, it is suggested that ProTα plays a key role as a brain guardian against ischemia stress through a cell-death-mode switch assisted by NTFs and a role of neurogenesis.
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17
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Kumar A, Maurya P, Hayes JJ. Post-Translation Modifications and Mutations of Human Linker Histone Subtypes: Their Manifestation in Disease. Int J Mol Sci 2023; 24:ijms24021463. [PMID: 36674981 PMCID: PMC9860689 DOI: 10.3390/ijms24021463] [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: 11/07/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Linker histones (LH) are a critical component of chromatin in addition to the canonical histones (H2A, H2B, H3, and H4). In humans, 11 subtypes (7 somatic and 4 germinal) of linker histones have been identified, and their diverse cellular functions in chromatin structure, DNA replication, DNA repair, transcription, and apoptosis have been explored, especially for the somatic subtypes. Delineating the unique role of human linker histone (hLH) and their subtypes is highly tedious given their high homology and overlapping expression patterns. However, recent advancements in mass spectrometry combined with HPLC have helped in identifying the post-translational modifications (PTMs) found on the different LH subtypes. However, while a number of PTMs have been identified and their potential nuclear and non-nuclear functions explored in cellular processes, there are very few studies delineating the direct relevance of these PTMs in diseases. In addition, recent whole-genome sequencing of clinical samples from cancer patients and individuals afflicted with Rahman syndrome have identified high-frequency mutations and therefore broadened the perspective of the linker histone mutations in diseases. In this review, we compile the identified PTMs of hLH subtypes, current knowledge of the relevance of hLH PTMs in human diseases, and the correlation of PTMs coinciding with mutations mapped in diseases.
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Affiliation(s)
- Ashok Kumar
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
- Correspondence:
| | - Preeti Maurya
- Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY 14642, USA
| | - Jeffrey J. Hayes
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
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18
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Song L, Soomro MA, Wang L, Song Y, Hu G. Identification and functional analysis of histone 1.2-like in red sea bream (Pagrus major). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 138:104529. [PMID: 36087785 DOI: 10.1016/j.dci.2022.104529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Histone H1 acts as an essential chromatin component and participates in the formation of higher chromatin structures together with core histones. In addition, H1 also has important functions in physiological processes such as gene expression regulation, DNA repair, and the immune response. In this study, the histone homologous protein Pm-H1.2-like was identified from the transcriptome database of Pagrus major we studied previously. Conservatism of evolution was investigated by sequence alignment and phylogenetic analysis. Transcripts of Pm-H1.2-like were detected in P. major tissues. The highest expression level was found in gill and skin tissues. Consistent with the data from the transcriptome database, we observed that the expression of Pm-H1.2-like was rapidly induced in nonspecific cytotoxic cells (NCCs) infected with inactivated Vibrio anguillarum. Gene silencing of Pm-H1.2-like by RNAi significantly suppressed the expression of NK-lysin and GZMB in NCCs at 12 h after pathogen stimulation, but had no significant effect on IFN-γ expression. Next, we obtained the fusion proteins rPm-H1.2-like and rPm-H1.2-like (36-80) through prokaryotic expression. ELISA showed that rPm-H1.2-like bound to oligonucleotide (ODN) in a concentration-dependent manner, while no binding activity of rPm-H1.2-like (36-80) with ODN was observed. This study confirmed that Pm-H1.2-like actively participates in the immune response of NCCs to bacterial infection, deepening the understanding of the immune features of histone H1 in fish.
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Affiliation(s)
- Lianfei Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Maqsood Ahmed Soomro
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Lingshu Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Yuting Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Guobin Hu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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19
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The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14:genes14010112. [PMID: 36672853 PMCID: PMC9859207 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
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20
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HAT- and HDAC-Targeted Protein Acetylation in the Occurrence and Treatment of Epilepsy. Biomedicines 2022; 11:biomedicines11010088. [PMID: 36672596 PMCID: PMC9856006 DOI: 10.3390/biomedicines11010088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/12/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023] Open
Abstract
Epilepsy is a common and severe chronic neurological disorder. Recently, post-translational modification (PTM) mechanisms, especially protein acetylation modifications, have been widely studied in various epilepsy models or patients. Acetylation is regulated by two classes of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs). HATs catalyze the transfer of the acetyl group to a lysine residue, while HDACs catalyze acetyl group removal. The expression of many genes related to epilepsy is regulated by histone acetylation and deacetylation. Moreover, the acetylation modification of some non-histone substrates is also associated with epilepsy. Various molecules have been developed as HDAC inhibitors (HDACi), which have become potential antiepileptic drugs for epilepsy treatment. In this review, we summarize the changes in acetylation modification in epileptogenesis and the applications of HDACi in the treatment of epilepsy as well as the mechanisms involved. As most of the published research has focused on the differential expression of proteins that are known to be acetylated and the knowledge of whole acetylome changes in epilepsy is still minimal, a further understanding of acetylation regulation will help us explore the pathological mechanism of epilepsy and provide novel ideas for treating epilepsy.
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21
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Previously Unidentified Histone H1-Like Protein Is Involved in Cell Division and Ribosome Biosynthesis in Toxoplasma gondii. mSphere 2022; 7:e0040322. [PMID: 36468865 PMCID: PMC9769792 DOI: 10.1128/msphere.00403-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromatin dynamics can regulate all DNA-dependent processes. Access to DNA within chromatin is orchestrated mainly by histones and their posttranslational modifications (PTMs). Like other eukaryotes, the apicomplexan parasite Toxoplasma gondii encodes four canonical histones and five histone variants. In contrast, the linker histone (H1) has never been identified in apicomplexan parasites. In other eukaryotes, histone H1 compacts the chromatin by linking the nucleosome and increasing the DNA compaction. H1 is a multifunctional protein and can be involved in different steps of DNA metabolism or associated with protein complexes related to distinct biological processes. We have identified a novel protein in T. gondii ("TgH1-like") that, although lacking the globular domain of mammalian H1, is remarkably like the H1-like proteins of bacteria and trypanosomatids. Our results demonstrate that TgH1-like is a nuclear protein associated with chromatin and other histones. Curiously, TgH1-like is also in the nucleolus and associated with ribosomal proteins, indicating a versatile function in this parasite. Although knockout of the tgh1-like gene does not affect the cell cycle, it causes endopolygeny and asynchronous division. Interestingly, mutation of posttranslationally modified amino acids results in defects in cell division like those in the Δtgh1-like mutant, showing that these sites are important for protein function. Furthermore, in the bradyzoite stage, this protein is expressed only in dividing parasites, reinforcing its importance in cell division. Indeed, the absence of TgH1-like decreases compaction of peripheral chromatin, confirming its role in the chromatin modulation in T. gondii. IMPORTANCE Histone H1, or linker histone, is an important protein that binds to the nucleosome, aiding chromatin compaction. Here, we characterize for the first time a linker histone in T. gondii, named TgH1-like. It is a small and basic protein that corresponds only to the C-terminal portion of the human H1 but is similar to histone H1 from trypanosomatids and bacteria. TgH1-like is located in the nucleus, interacts with nucleosome histones, and acts in chromatin structure and cell division. Our findings show for the first time the presence of a histone H1 protein in an apicomplexan parasite and will provide new insights into cell division and chromatin dynamics in T. gondii and related parasites.
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22
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Feng H, Zhou BR, Schwieters CD, Bai Y. Structural Mechanism of TAF-Iβ Chaperone Function on Linker Histone H1.10. J Mol Biol 2022; 434:167755. [PMID: 35870650 PMCID: PMC9489631 DOI: 10.1016/j.jmb.2022.167755] [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: 05/10/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022]
Abstract
Linker histone H1, facilitated by its chaperones, plays an essential role in regulating gene expression by maintaining chromatin's higher-order structure and epigenetic state. However, we know little about the structural mechanism of how the chaperones recognize linker histones and conduct their function. Here, we used biophysical and biochemical methods to investigate the recognition of human linker histone isoform H1.10 by the TAF-Iβ chaperone. Both H1.10 and TAF-Iβ proteins consist of folded cores and disordered tails. We found that H1.10 formed a complex with TAF-Iβ in a 2:2 stoichiometry. Using distance restraints obtained from methyl-TROSY NMR and spin labels, we built a structural model for the core region of the complex. In the model, the TAF-Iβ core interacts with the globular domain of H1.10 mainly through electrostatic interactions. We confirmed the interactions by measuring the effects of mutations on the binding affinity. A comparison of our structural model with the chromatosome structure shows that TAF-Iβ blocks the DNA binding sites of H1.10. Our study provides insights into the structural mechanism whereby TAF-Iβ functions as a chaperone by preventing H1.10 from interacting with DNA directly.
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Affiliation(s)
- Haniqao Feng
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles D Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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23
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Takizawa Y, Kurumizaka H. Chromatin structure meets cryo-EM: Dynamic building blocks of the functional architecture. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194851. [PMID: 35952957 DOI: 10.1016/j.bbagrm.2022.194851] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Chromatin is a dynamic molecular complex composed of DNA and proteins that package the DNA in the nucleus of eukaryotic cells. The basic structural unit of chromatin is the nucleosome core particle, composed of ~150 base pairs of genomic DNA wrapped around a histone octamer containing two copies each of four histones, H2A, H2B, H3, and H4. Individual nucleosome core particles are connected by short linker DNAs, forming a nucleosome array known as a beads-on-a-string fiber. Higher-order structures of chromatin are closely linked to nuclear events such as replication, transcription, recombination, and repair. Recently, a variety of chromatin structures have been determined by single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), and their structural details have provided clues about the chromatin architecture functions in the cell. In this review, we highlight recent cryo-EM structural studies of a fundamental chromatin unit to clarify the functions of chromatin.
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Affiliation(s)
- Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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24
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Portillo-Ledesma S, Wagley M, Schlick T. Chromatin transitions triggered by LH density as epigenetic regulators of the genome. Nucleic Acids Res 2022; 50:10328-10342. [PMID: 36130289 PMCID: PMC9561278 DOI: 10.1093/nar/gkac757] [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: 05/31/2022] [Revised: 07/26/2022] [Accepted: 09/02/2022] [Indexed: 11/14/2022] Open
Abstract
Motivated by experiments connecting linker histone (LH) deficiency to lymphoma progression and retinal disorders, we study by mesoscale chromatin modeling how LH density (ρ) induces gradual, as well sudden, changes in chromatin architecture and how the process depends on DNA linker length, LH binding dynamics and binding mode, salt concentration, tail modifications, and combinations of ρ and linker DNA length. We show that ρ tightly regulates the overall shape and compaction of the fiber, triggering a transition from an irregular disordered state to a compact and ordered structure. Such a structural transition, resembling B to A compartment transition connected with lymphoma of B cells, appears to occur around ρ = 0.5. The associated mechanism is DNA stem formation by LH binding, which is optimal when the lengths of the DNA linker and LH C-terminal domain are similar. Chromatin internal and external parameters are key regulators, promoting or impeding the transition. The LH density thus emerges as a critical tunable variable in controlling cellular functions through structural transitions of the genome.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Meghna Wagley
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai 200062, China.,Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, NY 10012, USA.,Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003 USA
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25
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Zhang H, Huo QY, Gao YQ. DNA Sequence-Dependent Binding of Linker Histone gH1 Regulates Nucleosome Conformations. J Phys Chem B 2022; 126:6771-6779. [PMID: 36062461 DOI: 10.1021/acs.jpcb.2c03785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence-dependent binding between DNA and proteins in chromatin is an essential part of gene expression. Linker histone H1 is an important protein in the regulation of chromatin compartmentalization and compaction, and its binding with the nucleosome is sensitive to the DNA sequence. Although the interactions of H1 and DNA have been widely investigated, the mechanism of nucleosome conformation changes induced by the DNA-sequence-dependent binding with gH1 (globular H1.0) remains largely unclear at the atomic level. In the present molecular dynamics simulations, both linker and dyad DNAs were mutated to investigate the conformational changes of the nucleosome induced by the sequence-dependent binding of gH1 based on the on-dyad binding mode. Our results indicate that gH1 is insensitive to the DNA sequence of the dyad DNA but presents an apparent preference to linker DNA with an AT-rich sequence. Moreover, this specific binding induces the entry/exit region of a nucleosome to a tight conformation and regulates the accessibility of core histones. Considering that the entry/exit region of the nucleosome is a crucial binding site for many functional proteins related to gene expression, the conformational change at this region could represent an important gene regulation signal.
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Affiliation(s)
- Hong Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qin Yuan Huo
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
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26
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Maity S, Abbaspour R, Nahabedian D, Connor SA. Norepinephrine, beyond the Synapse: Coordinating Epigenetic Codes for Memory. Int J Mol Sci 2022; 23:ijms23179916. [PMID: 36077313 PMCID: PMC9456295 DOI: 10.3390/ijms23179916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/16/2022] Open
Abstract
The noradrenergic system is implicated in neuropathologies contributing to major disorders of the memory, including post-traumatic stress disorder and Alzheimer’s disease. Determining the impact of norepinephrine on cellular function and plasticity is thus essential for making inroads into our understanding of these brain conditions, while expanding our capacity for treating them. Norepinephrine is a neuromodulator within the mammalian central nervous system which plays important roles in cognition and associated synaptic plasticity. Specifically, norepinephrine regulates the formation of memory through the stimulation of β-ARs, increasing the dynamic range of synaptic modifiability. The mechanisms through which NE influences neural circuit function have been extended to the level of the epigenome. This review focuses on recent insights into how the noradrenergic recruitment of epigenetic modifications, including DNA methylation and post-translational modification of histones, contribute to homo- and heterosynaptic plasticity. These advances will be placed in the context of synaptic changes associated with memory formation and linked to brain disorders and neurotherapeutic applications.
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Affiliation(s)
- Sabyasachi Maity
- Department of Physiology, Neuroscience, and Behavioral Sciences, St. George’s University School of Medicine, True Blue FZ818, Grenada
| | - Raman Abbaspour
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - David Nahabedian
- The Center for Biomedical Visualization, Department of Anatomical Sciences, St. George’s University School of Medicine, True Blue FZ818, Grenada
| | - Steven A. Connor
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
- Correspondence: ; Tel.: +1-(416)-736-2100 (ext. 33803)
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27
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Li S, Shi Y, Dang Y, Hu B, Xiao L, Zhao P, Wang S, Zhang K. Linker histone H1FOO is required for bovine preimplantation development by regulating lineage specification and chromatin structure. Biol Reprod 2022; 107:1425-1438. [PMID: 36001353 DOI: 10.1093/biolre/ioac167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/11/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Linker histone H1 binds to the nucleosome and is implicated in the regulation of the chromatin structure and function. The H1 variant H1FOO is heavily expressed in oocytes and early embryos. However, given the poor homology of H1FOO among mammals, the functional role of H1FOO during preimplantation embryonic development remains largely unknown, especially in domestic animals. Here, we find that H1FOO is not only expressed in oocytes and preimplantation embryos but granulosa cells and spermatids in cattle. We then demonstrate that the interference of H1FOO results in preimplantation embryonic developmental arrest in cattle using either RNA editing or Trim-Away approach. H1FOO depletion leads to a compromised expression of critical lineage-specific genes at the morula stage and affects the establishment of cell polarity. Interestingly, H1FOO depletion causes a significant increase in the expression of genes encoding other linker H1 and core histones. Concurrently, there is an increase of H3K9me3 and H3K27me3, two markers of repressive chromatin and a decrease of H4K16ac, a marker of open chromatin. Importantly, overexpression of bovine H1FOO results in severe embryonic developmental defects. In sum, we propose that H1FOO controls the proper chromatin structure that is crucial for the fidelity of cell polarization and lineage specification during bovine preimplantation development.
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Affiliation(s)
- Shuang Li
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Shi
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yanna Dang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Bingjie Hu
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lieying Xiao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Panpan Zhao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohua Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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28
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Mauceri D. Role of Epigenetic Mechanisms in Chronic Pain. Cells 2022; 11:cells11162613. [PMID: 36010687 PMCID: PMC9406853 DOI: 10.3390/cells11162613] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 12/11/2022] Open
Abstract
Pain is an unpleasant but essential-to-life sensation, usually resulting from tissue damage. When pain persists long after the injury has resolved, it becomes pathological. The precise molecular and cellular mechanisms causing the transition from acute to chronic pain are not fully understood. A key aspect of pain chronicity is that several plasticity events happen along the neural pathways involved in pain. These long-lasting adaptive changes are enabled by alteration in the expression of relevant genes. Among the different modulators of gene transcription in adaptive processes in the nervous system, epigenetic mechanisms play a pivotal role. In this review, I will first outline the main classes of epigenetic mediators and then discuss their implications in chronic pain.
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Affiliation(s)
- Daniela Mauceri
- Department of Neurobiology, Interdisciplinary Centre for Neurosciences (IZN), Heidelberg University, 69120 Heidelberg, Germany
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29
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Solovyev VI, Dubatolov VV, Vavilova VY, Kosterin OE. Estimating range disjunction time of the Palearctic Admirals (Limenitis L.) with COI and histone H1 genes. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00565-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Kohli A, Huang S, Chang T, Chao CC, Sun N. H1.0 induces paclitaxel‐resistance genes expression in ovarian cancer cells by recruiting GCN5 and androgen receptor. Cancer Sci 2022; 113:2616-2626. [PMID: 35639349 PMCID: PMC9357662 DOI: 10.1111/cas.15448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/16/2022] [Accepted: 05/27/2022] [Indexed: 12/05/2022] Open
Abstract
More than 90% of ovarian cancer deaths are due to relapse following development of chemoresistance. Our main objective is to better understand the molecular mechanism underlying paclitaxel resistance (taxol resistance, Txr) in ovarian cancer. Here, we observed that the linker histone H1.0 is upregulated in paclitaxel‐resistant ovarian cancer cells. Knockdown of H1.0 significantly downregulates the androgen receptor (AR) and sensitizes paclitaxel‐resistant SKOV3/Txr and 2774/Txr cell lines to paclitaxel. Conversely, ectopic expression of H1.0 upregulates AR and increases Txr in parental SKOV3 and MDAH2774 cells. Notably, H1.0 upregulation is associated with disease recurrence and poor survival in a subset of ovarian cancer subjects. Inhibition of PI3K significantly reduces H1.0 mRNA and protein levels in paclitaxel‐resistant cells, suggesting the involvement of the PI3K/AKT signaling pathway. Knockdown of H1.0 and AR also downregulates the Txr genes ABCB1 and ABCG2 in paclitaxel‐resistant cells. Our data show that H1.0 induces GCN5 expression and histone acetylation, thereby enhancing Txr gene transactivation. These findings suggest that Txr in ovarian cancer involves the PI3K/AKT pathway and leads to upregulation of histone H1.0, recruitment of GCN5 and AR, followed by upregulation of a subgroup of Txr genes that include ABCB1 and ABCG2. This study is the first report describing the relationship between histone H1.0 and GCN5 that cooperate to induce AR‐dependent Txr in ovarian cancer cells.
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Affiliation(s)
- Abhidha Kohli
- Graduate Institute of Biomedical Sciences Department of Biochemistry and Molecular Biology College of Medicine Chang Gung University Taoyuan Taiwan, Republic of China
| | - Shang‐Lang Huang
- Division of Biomedical Sciences Chang Gung University of Science and Technology Taoyuan Taiwan, Republic of China
- Research Center for Chinese Herbal Medicine Chang Gung University of Science and Technology Taoyuan Taiwan, Republic of China
| | - Ting‐Chang Chang
- Department of Obstetrics and Gynaecology Chang Gung Memorial Hospital Linkou Medical Centre Taoyuan Taiwan, Republic of China
| | - Chuck C.‐K. Chao
- Graduate Institute of Biomedical Sciences Department of Biochemistry and Molecular Biology College of Medicine Chang Gung University Taoyuan Taiwan, Republic of China
| | - Nian‐Kang Sun
- Division of Biomedical Sciences Chang Gung University of Science and Technology Taoyuan Taiwan, Republic of China
- Research Center for Chinese Herbal Medicine Chang Gung University of Science and Technology Taoyuan Taiwan, Republic of China
- Department of Obstetrics and Gynaecology Chang Gung Memorial Hospital Linkou Medical Centre Taoyuan Taiwan, Republic of China
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31
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The Highest Density of Phosphorylated Histone H1 Appeared in Prophase and Prometaphase in Parallel with Reduced H3K9me3, and HDAC1 Depletion Increased H1.2/H1.3 and H1.4 Serine 38 Phosphorylation. Life (Basel) 2022; 12:life12060798. [PMID: 35743829 PMCID: PMC9224986 DOI: 10.3390/life12060798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 01/10/2023] Open
Abstract
Background: Variants of linker histone H1 are tissue-specific and are responsible for chromatin compaction accompanying cell differentiation, mitotic chromosome condensation, and apoptosis. Heterochromatinization, as the main feature of these processes, is also associated with pronounced trimethylation of histones H3 at the lysine 9 position (H3K9me3). Methods: By confocal microscopy, we analyzed cell cycle-dependent levels and distribution of phosphorylated histone H1 (H1ph) and H3K9me3. By mass spectrometry, we studied post-translational modifications of linker histones. Results: Phosphorylated histone H1, similarly to H3K9me3, has a comparable level in the G1, S, and G2 phases of the cell cycle. A high density of phosphorylated H1 was inside nucleoli of mouse embryonic stem cells (ESCs). H1ph was also abundant in prophase and prometaphase, while H1ph was absent in anaphase and telophase. H3K9me3 surrounded chromosomal DNA in telophase. This histone modification was barely detectable in the early phases of mitosis. Mass spectrometry revealed several ESC-specific phosphorylation sites of H1. HDAC1 depletion did not change H1 acetylation but potentiated phosphorylation of H1.2/H1.3 and H1.4 at serine 38 positions. Conclusions: Differences in the level and distribution of H1ph and H3K9me3 were revealed during mitotic phases. ESC-specific phosphorylation sites were identified in a linker histone.
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32
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Bosire R, Fadel L, Mocsár G, Nánási P, Sen P, Sharma AK, Naseem MU, Kovács A, Kugel J, Kroemer G, Vámosi G, Szabó G. Doxorubicin impacts chromatin binding of HMGB1, Histone H1 and retinoic acid receptor. Sci Rep 2022; 12:8087. [PMID: 35577872 PMCID: PMC9110345 DOI: 10.1038/s41598-022-11994-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Doxorubicin (Dox), a widely used anticancer DNA-binding drug, affects chromatin in multiple ways, and these effects contribute to both its efficacy and its dose-limiting side effects, especially cardiotoxicity. Here, we studied the effects of Dox on the chromatin binding of the architectural proteins high mobility group B1 (HMGB1) and the linker histone H1, and the transcription factor retinoic acid receptor (RARα) by fluorescence recovery after photobleaching (FRAP) and fluorescence correlation spectroscopy (FCS) in live cells. At lower doses, Dox increased the binding of HMGB1 to DNA while decreasing the binding of the linker histone H1. At higher doses that correspond to the peak plasma concentrations achieved during chemotherapy, Dox reduced the binding of HMGB1 as well. This biphasic effect is interpreted in terms of a hierarchy of competition between the ligands involved and Dox-induced local conformational changes of nucleosome-free DNA. Combined, FRAP and FCS mobility data suggest that Dox decreases the overall binding of RARα to DNA, an effect that was only partially overcome by agonist binding. The intertwined interactions described are likely to contribute to both the effects and side effects of Dox.
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Affiliation(s)
- Rosevalentine Bosire
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Lina Fadel
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Mocsár
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Nánási
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Pialy Sen
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Anshu Kumar Sharma
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Muhammad Umair Naseem
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Kovács
- Department of Radiation Therapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jennifer Kugel
- Department of Biochemistry, University of Colorado, Boulder, USA
| | - Guido Kroemer
- Centre de Recherche Des Cordeliers, Equipe Labellisée Par La Ligue Contre Le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - György Vámosi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Gábor Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
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33
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Hou X, Wang Z, Shi L, Wang L, Zhao F, Liu X, Gao H, Shi L, Yan H, Wang L, Zhang L. Identification of imprinted genes in the skeletal muscle of newborn piglets by high-throughput sequencing. Anim Genet 2022; 53:479-486. [PMID: 35481679 DOI: 10.1111/age.13212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/01/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Imprinted genes - exhibiting parent-specific transcription - play essential roles in the process of mammalian development and growth. Skeletal muscle growth is crucial for meat production. To further understand the role of imprinted genes during the porcine skeletal muscle growth, DNA-seq and RNA-seq were used to explore the characteristics of imprinted genes from porcine reciprocal crosses. A total of 584 545 single-nucleotide variations were discovered in the DNA-seq data of F0 parents, heterozygous in two pig breeds (Yorkshire and Min pigs) but homozygous in each breed. These single-nucleotide variations were used to determine the allelic-specific expression in F1 individuals. Finally, eight paternal expression sites and three maternal expression sites were detected, whereas two paternally expressed imprinted genes (NDN and IGF2) and one maternally expressed imprinted gene (H1-3) were validated by Sanger sequencing. DNA methylation regulates the expression of imprinted genes, and all of the identified imprinted genes in this study were predicted to possess CpG islands. PBX1 and YY1 binding motifs were discovered in the promoter regions of all three imprinted genes, which were candidate elements regulating the transcription of imprinted genes. For these identified imprinted genes, IGF2 and NDN promoted muscle growth whereas H1-3 inhibited cell proliferation, corroborating the 'parental conflict' theory that paternally expressed imprinted genes assisted descendants' growth whereas maternally expressed imprinted genes inhibited it. This study discovered porcine imprinted genes in skeletal muscle and was the first to reveal that H1-3 was expressed by the maternal allele to our knowledge. Our findings provided valuable resources for the potential utilization of imprinted genes in pig breeding.
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Affiliation(s)
- Xinhua Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zishuai Wang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Liangyu Shi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Ligang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fuping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongmei Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijun Shi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua Yan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Neuroprotective Effects of PARP Inhibitors in Drosophila Models of Alzheimer’s Disease. Cells 2022; 11:cells11081284. [PMID: 35455964 PMCID: PMC9027574 DOI: 10.3390/cells11081284] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 12/10/2022] Open
Abstract
Alzheimer’s disease (AD) is an irreversible age-related neurodegenerative disorder clinically characterized by severe memory impairment, language deficits and cognitive decline. The major neuropathological hallmarks of AD include extracellular deposits of the β-amyloid (Aβ) peptides and cytoplasmic neurofibrillary tangles (NFTs) of hyperphosphorylated tau protein. The accumulation of plaques and tangles in the brain triggers a cascade of molecular events that culminate in neuronal damage and cell death. Despite extensive research, our understanding of the molecular basis of AD pathogenesis remains incomplete and a cure for this devastating disease is still not available. A growing body of evidence in different experimental models suggests that poly(ADP-ribose) polymerase-1 (PARP-1) overactivation might be a crucial component of the molecular network of interactions responsible for AD pathogenesis. In this work, we combined genetic, molecular and biochemical approaches to investigate the effects of two different PARP-1 inhibitors (olaparib and MC2050) in Drosophila models of Alzheimer’s disease by exploring their neuroprotective and therapeutic potential in vivo. We found that both pharmacological inhibition and genetic inactivation of PARP-1 significantly extend lifespan and improve the climbing ability of transgenic AD flies. Consistently, PARP-1 inhibitors lead to a significant decrease of Aβ42 aggregates and partially rescue the epigenetic alterations associated with AD in the brain. Interestingly, olaparib and MC2050 also suppress the AD-associated aberrant activation of transposable elements in neuronal tissues of AD flies.
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35
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Serna-Pujol N, Salinas-Pena M, Mugianesi F, Le Dily F, Marti-Renom MA, Jordan A. Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion. Nucleic Acids Res 2022; 50:3892-3910. [PMID: 35380694 PMCID: PMC9023279 DOI: 10.1093/nar/gkac226] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022] Open
Abstract
Up to seven members of the histone H1 family may contribute to chromatin compaction and its regulation in human somatic cells. In breast cancer cells, knock-down of multiple H1 variants deregulates many genes, promotes the appearance of genome-wide accessibility sites and triggers an interferon response via activation of heterochromatic repeats. However, how these changes in the expression profile relate to the re-distribution of H1 variants as well as to genome conformational changes have not been yet studied. Here, we combined ChIP-seq of five endogenous H1 variants with Chromosome Conformation Capture analysis in wild-type and H1.2/H1.4 knock-down T47D cells. The results indicate that H1 variants coexist in the genome in two large groups depending on the local GC content and that their distribution is robust with respect to H1 depletion. Despite the small changes in H1 variants distribution, knock-down of H1 translated into more isolated but de-compacted chromatin structures at the scale of topologically associating domains (TADs). Such changes in TAD structure correlated with a coordinated gene expression response of their resident genes. This is the first report describing simultaneous profiling of five endogenous H1 variants and giving functional evidence of genome topology alterations upon H1 depletion in human cancer cells.
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Affiliation(s)
- Núria Serna-Pujol
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
| | - Mónica Salinas-Pena
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
| | - Francesca Mugianesi
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain
| | - François Le Dily
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.,Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona 08003, Spain.,Pompeu Fabra University, Doctor Aiguader 88, Barcelona 08003, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028 Spain
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36
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Loers G, Kleene R, Girbes Minguez M, Schachner M. The Cell Adhesion Molecule L1 Interacts with Methyl CpG Binding Protein 2 via Its Intracellular Domain. Int J Mol Sci 2022; 23:ijms23073554. [PMID: 35408913 PMCID: PMC8998178 DOI: 10.3390/ijms23073554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Cell adhesion molecule L1 regulates multiple cell functions, and L1 deficiency is linked to several neural diseases. Recently, we have identified methyl CpG binding protein 2 (MeCP2) as a potential binding partner of the intracellular L1 domain. By ELISA we show here that L1's intracellular domain binds directly to MeCP2 via the sequence motif KDET. Proximity ligation assay with cultured cerebellar and cortical neurons suggests a close association between L1 and MeCP2 in nuclei of neurons. Immunoprecipitation using MeCP2 antibodies and nuclear mouse brain extracts indicates that MeCP2 interacts with an L1 fragment of ~55 kDa (L1-55). Proximity ligation assay indicates that metalloproteases, β-site of amyloid precursor protein cleaving enzyme (BACE1) and ɣ-secretase, are involved in the generation of L1-55. Reduction in MeCP2 expression by siRNA decreases L1-dependent neurite outgrowth from cultured cortical neurons as well as the migration of L1-expressing HEK293 cells. Moreover, L1 siRNA, MeCP2 siRNA, or a cell-penetrating KDET-containing L1 peptide leads to reduced levels of myocyte enhancer factor 2C (Mef2c) mRNA and protein in cortical neurons, suggesting that the MeCP2/L1 interaction regulates Mef2c expression. Altogether, the present findings indicate that the interaction of the novel fragment L1-55 with MeCP2 affects L1-dependent functions, such as neurite outgrowth and neuronal migration.
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Affiliation(s)
- Gabriele Loers
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany; (G.L.); (R.K.); (M.G.M.)
| | - Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany; (G.L.); (R.K.); (M.G.M.)
| | - Maria Girbes Minguez
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany; (G.L.); (R.K.); (M.G.M.)
| | - Melitta Schachner
- Keck Center for Collaborative Neuroscience, Department of Cell Biology and Neuroscience, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, USA
- Correspondence: ; Tel.: +1-848-445-1780
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37
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Phillips EO, Gunjan A. Histone Variants: The Unsung Guardians of the Genome. DNA Repair (Amst) 2022; 112:103301. [DOI: 10.1016/j.dnarep.2022.103301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/01/2022] [Accepted: 02/12/2022] [Indexed: 12/15/2022]
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38
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Shukla S, Agarwal P, Kumar A. Disordered regions tune order in chromatin organization and function. Biophys Chem 2022; 281:106716. [PMID: 34844028 DOI: 10.1016/j.bpc.2021.106716] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins or hybrid proteins with ordered domains and disordered regions (both collectively designated as IDP(R)s) defy the well-established structure-function paradigm due to their ability to perform multiple biological functions even in the absence of a well-defined 3D structure. IDP(R)s have a unique ability to exist as a functional heterogeneous ensemble, where they adopt multiple thermodynamically stable conformations with low energy barriers between states. The resultant structural plasticity or conformational adaptability provides them with a high functional diversity and ease of regulation. Hence, IDP(R)s are highly efficient biological machinery to mediate intricate cellular functions such as signaling, gene expression, and assembly of complex structures. One such structure is the nucleoprotein complex known as Chromatin. Interestingly, the proteins involved in shaping up the structure and function of chromatin are abundant in disordered regions, which serve more than just as mere flexible linkers. The disordered regions are involved in crucial processes such as gene expression regulation, chromatin architecture maintenance, and liquid-liquid phase separation initiation. This review is an attempt to explore the advantages and the functional and regulatory roles of intrinsic disorder in several Chromatin Associated Proteins from a mechanistic standpoint.
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Affiliation(s)
- Shivangi Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Prakhar Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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39
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Lai S, Jia J, Cao X, Zhou PK, Gao S. Molecular and Cellular Functions of the Linker Histone H1.2. Front Cell Dev Biol 2022; 9:773195. [PMID: 35087830 PMCID: PMC8786799 DOI: 10.3389/fcell.2021.773195] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 01/14/2023] Open
Abstract
Linker histone H1.2, which belongs to the linker histone family H1, plays a crucial role in the maintenance of the stable higher-order structures of chromatin and nucleosomes. As a critical part of chromatin structure, H1.2 has an important function in regulating chromatin dynamics and participates in multiple other cellular processes as well. Recent work has also shown that linker histone H1.2 regulates the transcription levels of certain target genes and affects different processes as well, such as cancer cell growth and migration, DNA duplication and DNA repair. The present work briefly summarizes the current knowledge of linker histone H1.2 modifications. Further, we also discuss the roles of linker histone H1.2 in the maintenance of genome stability, apoptosis, cell cycle regulation, and its association with disease.
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Affiliation(s)
- Shuting Lai
- Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, China.,Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jin Jia
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China.,School of Medicine, University of South China, Hengyang, China
| | - Xiaoyu Cao
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China.,School of Life Sciences, Hebei University, Baoding, China
| | - Ping-Kun Zhou
- Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, China.,Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Shanshan Gao
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, Beijing, China
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40
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Wootton J, Soutoglou E. Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity. Front Genet 2022; 12:773426. [PMID: 34970302 PMCID: PMC8712883 DOI: 10.3389/fgene.2021.773426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.
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Affiliation(s)
- Jack Wootton
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Evi Soutoglou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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41
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Epigenetic Mechanisms in Memory and Cognitive Decline Associated with Aging and Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms222212280. [PMID: 34830163 PMCID: PMC8618067 DOI: 10.3390/ijms222212280] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/21/2022] Open
Abstract
Epigenetic mechanisms, which include DNA methylation, a variety of post-translational modifications of histone proteins (acetylation, phosphorylation, methylation, ubiquitination, sumoylation, serotonylation, dopaminylation), chromatin remodeling enzymes, and long non-coding RNAs, are robust regulators of activity-dependent changes in gene transcription. In the brain, many of these epigenetic modifications have been widely implicated in synaptic plasticity and memory formation. Dysregulation of epigenetic mechanisms has been reported in the aged brain and is associated with or contributes to memory decline across the lifespan. Furthermore, alterations in the epigenome have been reported in neurodegenerative disorders, including Alzheimer’s disease. Here, we review the diverse types of epigenetic modifications and their role in activity- and learning-dependent synaptic plasticity. We then discuss how these mechanisms become dysregulated across the lifespan and contribute to memory loss with age and in Alzheimer’s disease. Collectively, the evidence reviewed here strongly supports a role for diverse epigenetic mechanisms in memory formation, aging, and neurodegeneration in the brain.
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42
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Höllmüller E, Greiner K, Kienle SM, Scheffner M, Marx A, Stengel F. Interactome of Site-Specifically Acetylated Linker Histone H1. J Proteome Res 2021; 20:4443-4451. [PMID: 34351766 DOI: 10.1021/acs.jproteome.1c00396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Linker histone H1 plays a key role in chromatin organization and maintenance, yet our knowledge of the regulation of H1 functions by post-translational modifications is rather limited. In this study, we report on the generation of site-specifically mono- and di-acetylated linker histone H1.2 by genetic code expansion. We used these modified histones to identify and characterize the acetylation-dependent cellular interactome of H1.2 by affinity purification mass spectrometry and show that site-specific acetylation results in overlapping but distinct groups of interacting partners. Among these, we find multiple translational initiation factors and transcriptional regulators such as the NAD+-dependent deacetylase SIRT1, which we demonstrate to act on acetylated H1.2. Taken together, our data suggest that site-specific acetylation of H1.2 plays a role in modulating protein-protein interactions.
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43
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Saha A, Dalal Y. A glitch in the snitch: the role of linker histone H1 in shaping the epigenome in normal and diseased cells. Open Biol 2021; 11:210124. [PMID: 34343462 PMCID: PMC8331230 DOI: 10.1098/rsob.210124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Histone H1s or the linker histones are a family of dynamic chromatin compacting proteins that are essential for higher-order chromatin organization. These highly positively charged proteins were previously thought to function solely as repressors of transcription. However, over the last decade, there is a growing interest in understanding this multi-protein family, finding that not all variants act as repressors. Indeed, the H1 family members appear to have distinct affinities for chromatin and may potentially affect distinct functions. This would suggest a more nuanced contribution of H1 to chromatin organization. The advent of new technologies to probe H1 dynamics in vivo, combined with powerful computational biology, and in vitro imaging tools have greatly enhanced our knowledge of the mechanisms by which H1 interacts with chromatin. This family of proteins can be metaphorically compared to the Golden Snitch from the Harry Potter series, buzzing on and off several regions of the chromatin, in combat with competing transcription factors and chromatin remodellers, thereby critical to the epigenetic endgame on short and long temporal scales in the life of the nucleus. Here, we summarize recent efforts spanning structural, computational, genomic and genetic experiments which examine the linker histone as an unseen architect of chromatin fibre in normal and diseased cells and explore unanswered fundamental questions in the field.
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Affiliation(s)
- Ankita Saha
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yamini Dalal
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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44
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Yuan L, Sun B, Xu L, Chen L, Ou W. The Updating of Biological Functions of Methyltransferase SETDB1 and Its Relevance in Lung Cancer and Mesothelioma. Int J Mol Sci 2021; 22:ijms22147416. [PMID: 34299035 PMCID: PMC8306223 DOI: 10.3390/ijms22147416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/11/2022] Open
Abstract
SET domain bifurcated 1 (SETDB1) is a histone H3 lysine 9 (H3K9) methyltransferase that exerts important effects on epigenetic gene regulation. SETDB1 complexes (SETDB1-KRAB-KAP1, SETDB1-DNMT3A, SETDB1-PML, SETDB1-ATF7IP-MBD1) play crucial roles in the processes of histone methylation, transcriptional suppression and chromatin remodelling. Therefore, aberrant trimethylation at H3K9 due to amplification, mutation or deletion of SETDB1 may lead to transcriptional repression of various tumour-suppressing genes and other related genes in cancer cells. Lung cancer is the most common type of cancer worldwide in which SETDB1 amplification and H3K9 hypermethylation have been indicated as potential tumourigenesis markers. In contrast, frequent inactivation mutations of SETDB1 have been revealed in mesothelioma, an asbestos-associated, locally aggressive, highly lethal, and notoriously chemotherapy-resistant cancer. Above all, the different statuses of SETDB1 indicate that it may have different biological functions and be a potential diagnostic biomarker and therapeutic target in lung cancer and mesothelioma.
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Affiliation(s)
| | | | | | | | - Wenbin Ou
- Correspondence: ; Tel./Fax: +86-571-86843303
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45
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Unraveling linker histone interactions in nucleosomes. Curr Opin Struct Biol 2021; 71:87-93. [PMID: 34246862 DOI: 10.1016/j.sbi.2021.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 11/23/2022]
Abstract
Considerable progress has been made recently in defining the interactions of linker histones (H1s) within nucleosomes. Major advancements include atomic resolution structures of the globular domain of full-length H1s in the context of nucleosomes containing full-length linker DNA. Although these studies have led to a detailed understanding of the interactions and dynamics of H1 globular domains in the canonical on-dyad nucleosome binding pocket, more information regarding the intrinsically disordered N-terminal and C-terminal domains is needed. In this review, we highlight studies supporting our current understanding of the structures and interactions of the N-terminal, globular, and C-terminal domains of linker histones within the nucleosome.
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46
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Initial proteomic characterization of IMMODIN, commercially available dialysable leukocytes extract. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-020-01467-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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47
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Amatori S, Tavolaro S, Gambardella S, Fanelli M. The dark side of histones: genomic organization and role of oncohistones in cancer. Clin Epigenetics 2021; 13:71. [PMID: 33827674 PMCID: PMC8025322 DOI: 10.1186/s13148-021-01057-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Background The oncogenic role of histone mutations is one of the most relevant discovery in cancer epigenetics. Recurrent mutations targeting histone genes have been described in pediatric brain tumors, chondroblastoma, giant cell tumor of bone and other tumor types. The demonstration that mutant histones can be oncogenic and drive the tumorigenesis in pediatric tumors, led to the coining of the term “oncohistones.” The first identified histone mutations were localized at or near residues normally targeted by post-translational modifications (PTMs) in the histone N-terminal tails and suggested a possible interference with histone PTMs regulation and reading. Main body In this review, we describe the peculiar organization of the multiple genes that encode histone proteins, and the latter advances in both the identification and the biological role of histone mutations in cancer. Recent works show that recurrent somatic mutations target both N-terminal tails and globular histone fold domain in diverse tumor types. Oncohistones are often dominant-negative and occur at higher frequencies in tumors affecting children and adolescents. Notably, in many cases the mutations target selectively only some of the genes coding the same histone protein and are frequently associated with specific tumor types or, as documented for histone variant H3.3 in pediatric glioma, with peculiar tumors arising from specific anatomic locations. Conclusion The overview of the most recent advances suggests that the oncogenic potential of histone mutations can be exerted, together with the alteration of histone PTMs, through the destabilization of nucleosome and DNA–nucleosome interactions, as well as through the disruption of higher-order chromatin structure. However, further studies are necessary to fully elucidate the mechanism of action of oncohistones, as well as to evaluate their possible application to cancer classification, prognosis and to the identification of new therapies.
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Affiliation(s)
- Stefano Amatori
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
| | - Simona Tavolaro
- Fredis Associazione, Via Edoardo Jenner 30, 00151, Rome, Italy
| | - Stefano Gambardella
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.,IRCCS Neuromed, Via Atinense 18, 86077, Pozzilli, IS, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
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48
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Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome. Sci Rep 2021; 11:380. [PMID: 33432055 PMCID: PMC7801413 DOI: 10.1038/s41598-020-79654-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023] Open
Abstract
Linker histones play essential roles in the regulation and maintenance of the dynamic chromatin structure of higher eukaryotes. The influence of human histone H1.0 on the nucleosome structure and biophysical properties of the resulting chromatosome were investigated and compared with the 177-bp nucleosome using Cryo-EM and SAXS. The 4.5 Å Cryo-EM chromatosome structure showed that the linker histone binds at the nucleosome dyad interacting with both linker DNA arms but in a tilted manner leaning towards one of the linker sides. The chromatosome is laterally compacted and rigid in the dyad and linker DNA area, in comparison with the nucleosome where linker DNA region is more flexible and displays structural variability. In solution, the chromatosomes appear slightly larger than the nucleosomes, with the volume increase compared to the bound linker histone, according to solution SAXS measurements. SAXS X-ray diffraction characterisation of Mg-precipitated samples showed that the different shapes of the 177 chromatosome enabled the formation of a highly ordered lamello-columnar phase when precipitated by Mg2+, indicating the influence of linker histone on the nucleosome stacking. The biological significance of linker histone, therefore, may be affected by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in comparison to nucleosomes.
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49
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Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y. Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Mol Cell 2021; 81:166-182.e6. [PMID: 33238161 PMCID: PMC7796963 DOI: 10.1016/j.molcel.2020.10.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/21/2020] [Accepted: 10/27/2020] [Indexed: 12/21/2022]
Abstract
The repeating structural unit of metazoan chromatin is the chromatosome, a nucleosome bound to a linker histone, H1. There are 11 human H1 isoforms with diverse cellular functions, but how they interact with the nucleosome remains elusive. Here, we determined the cryoelectron microscopy (cryo-EM) structures of chromatosomes containing 197 bp DNA and three different human H1 isoforms, respectively. The globular domains of all three H1 isoforms bound to the nucleosome dyad. However, the flanking/linker DNAs displayed substantial distinct dynamic conformations. Nuclear magnetic resonance (NMR) and H1 tail-swapping cryo-EM experiments revealed that the C-terminal tails of the H1 isoforms mainly controlled the flanking DNA orientations. We also observed partial ordering of the core histone H2A C-terminal and H3 N-terminal tails in the chromatosomes. Our results provide insights into the structures and dynamics of the chromatosomes and have implications for the structure and function of chromatin.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - Tara Fox
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Htet Khant
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Natalia de Val
- Center of Macromolecular Microscopy, National Cancer Institute, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Lyubitelev AV, Kirpichnikov MP, Studitsky VM. The Role of Linker Histones in Carcinogenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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