1
|
Maurya D, Rai G, Mandal D, Mondal BC. Transient caspase-mediated activation of caspase-activated DNase causes DNA damage required for phagocytic macrophage differentiation. Cell Rep 2024; 43:114251. [PMID: 38761374 DOI: 10.1016/j.celrep.2024.114251] [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: 12/05/2023] [Revised: 04/04/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
Phagocytic macrophages are crucial for innate immunity and tissue homeostasis. Most tissue-resident macrophages develop from embryonic precursors that populate every organ before birth to lifelong self-renew. However, the mechanisms for versatile macrophage differentiation remain unknown. Here, we use in vivo genetic and cell biological analysis of the Drosophila larval hematopoietic organ, the lymph gland that produces macrophages. We show that the developmentally regulated transient activation of caspase-activated DNase (CAD)-mediated DNA strand breaks in intermediate progenitors is essential for macrophage differentiation. Insulin receptor-mediated PI3K/Akt signaling regulates the apoptosis signal-regulating kinase 1 (Ask1)/c-Jun kinase (JNK) axis to control sublethal levels of caspase activation, causing DNA strand breaks during macrophage development. Furthermore, caspase activity is also required for embryonic-origin macrophage development and efficient phagocytosis. Our study provides insights into developmental signaling and CAD-mediated DNA strand breaks associated with multifunctional and heterogeneous macrophage differentiation.
Collapse
Affiliation(s)
- Deepak Maurya
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Gayatri Rai
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Debleena Mandal
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Bama Charan Mondal
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| |
Collapse
|
2
|
Martin-Blazquez A, Martin-Lorenzo M, Santiago-Hernandez A, Heredero A, Donado A, Lopez JA, Anfaiha-Sanchez M, Ruiz-Jimenez R, Esteban V, Vazquez J, Aldamiz-Echevarria G, Alvarez-Llamas G. Analysis of Vascular Smooth Muscle Cells from Thoracic Aortic Aneurysms Reveals DNA Damage and Cell Cycle Arrest as Hallmarks in Bicuspid Aortic Valve Patients. J Proteome Res 2024. [PMID: 38594816 DOI: 10.1021/acs.jproteome.3c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Thoracic aortic aneurysm (TAA) is mainly sporadic and with higher incidence in the presence of a bicuspid aortic valve (BAV) for unknown reasons. The lack of drug therapy to delay TAA progression lies in the limited knowledge of pathophysiology. We aimed to identify the molecular hallmarks that differentiate the aortic dilatation associated with BAV and tricuspid aortic valve (TAV). Aortic vascular smooth muscle cells (VSMCs) isolated from sporadic TAA patients with BAV or TAV were analyzed by mass spectrometry. DNA oxidative damage assay and cell cycle profiling were performed in three independent cohorts supporting proteomics data. The alteration of secreted proteins was confirmed in plasma. Stress phenotype, oxidative stress, and enhanced DNA damage response (increased S-phase arrest and apoptosis) were found in BAV-TAA patients. The increased levels of plasma C1QTNF5, LAMA2, THSB3, and FAP confirm the enhanced stress in BAV-TAA. Plasma FAP and BGN point to an increased inflammatory condition in TAV. The arterial wall of BAV patients shows a limited capacity to counteract drivers of sporadic TAA. The molecular pathways identified support the need of differential molecular diagnosis and therapeutic approaches for BAV and TAV patients, showing specific markers in plasma which may serve to monitor therapy efficacy.
Collapse
Affiliation(s)
- Ariadna Martin-Blazquez
- Immunology Department, IIS-Fundación Jiménez Díaz, Fundación Jiménez Díaz Hospital-UAM, 28040 Madrid, Spain
| | - Marta Martin-Lorenzo
- Immunology Department, IIS-Fundación Jiménez Díaz, Fundación Jiménez Díaz Hospital-UAM, 28040 Madrid, Spain
| | | | - Angeles Heredero
- Cardiac Surgery Service, Fundación Jiménez Díaz Hospital-UAM, 28040 Madrid, Spain
| | - Alicia Donado
- Cardiac Surgery Service, Fundación Jiménez Díaz Hospital-UAM, 28040 Madrid, Spain
| | - Juan A Lopez
- Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Miriam Anfaiha-Sanchez
- Immunology Department, IIS-Fundación Jiménez Díaz, Fundación Jiménez Díaz Hospital-UAM, 28040 Madrid, Spain
| | - Rocio Ruiz-Jimenez
- Immunology Department, IIS-Fundación Jiménez Díaz, Fundación Jiménez Díaz Hospital-UAM, 28040 Madrid, Spain
| | - Vanesa Esteban
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Fundación Jiménez Díaz Hospital-UAM, 28040 Madrid, Spain
- Faculty of Medicine and Biomedicine, Alfonso X El Sabio University, 28691 Madrid, Spain
| | - Jesus Vazquez
- Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | | | - Gloria Alvarez-Llamas
- Immunology Department, IIS-Fundación Jiménez Díaz, Fundación Jiménez Díaz Hospital-UAM, 28040 Madrid, Spain
- RICORS2040, Fundación Jiménez Díaz, 28040 Madrid, Spain
- Department of Biochemistry and Molecular Biology, Complutense University, 28040 Madrid, Spain
| |
Collapse
|
3
|
Qu R, Cheng X, Sefik E, Stanley Iii JS, Landa B, Strino F, Platt S, Garritano J, Odell ID, Coifman R, Flavell RA, Myung P, Kluger Y. Gene trajectory inference for single-cell data by optimal transport metrics. Nat Biotechnol 2024:10.1038/s41587-024-02186-3. [PMID: 38580861 DOI: 10.1038/s41587-024-02186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/26/2024] [Indexed: 04/07/2024]
Abstract
Single-cell RNA sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies to infer the sequential dynamics of genes in a process typically rely on constructing cell pseudotime through cell trajectory inference. However, the presence of concurrent gene processes in the same group of cells and technical noise can obscure the true progression of the processes studied. To address this challenge, we present GeneTrajectory, an approach that identifies trajectories of genes rather than trajectories of cells. Specifically, optimal transport distances are calculated between gene distributions across the cell-cell graph to extract gene programs and define their gene pseudotemporal order. Here we demonstrate that GeneTrajectory accurately extracts progressive gene dynamics in myeloid lineage maturation. Moreover, we show that GeneTrajectory deconvolves key gene programs underlying mouse skin hair follicle dermal condensate differentiation that could not be resolved by cell trajectory approaches. GeneTrajectory facilitates the discovery of gene programs that control the changes and activities of biological processes.
Collapse
Affiliation(s)
- Rihao Qu
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiuyuan Cheng
- Department of Mathematics, Duke University, Durham, NC, USA
| | - Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Boris Landa
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
| | | | - Sarah Platt
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - James Garritano
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
| | - Ian D Odell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Ronald Coifman
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
- Department of Mathematics, Yale University, New Haven, CT, USA
- Department of Electrical Engineering, Yale University, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Peggy Myung
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
- Program in Applied Mathematics, Yale University, New Haven, CT, USA.
| |
Collapse
|
4
|
Dreyer J, Ricci G, van den Berg J, Bhardwaj V, Funk J, Armstrong C, van Batenburg V, Sine C, VanInsberghe MA, Marsman R, Mandemaker IK, di Sanzo S, Costantini J, Manzo SG, Biran A, Burny C, Völker-Albert M, Groth A, Spencer SL, van Oudenaarden A, Mattiroli F. Acute multi-level response to defective de novo chromatin assembly in S-phase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586291. [PMID: 38585916 PMCID: PMC10996472 DOI: 10.1101/2024.03.22.586291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin of these defects is unknown. Here, we combine acute degradation of Chromatin Assembly Factor 1 (CAF-1), a key player in de novo chromatin assembly, with single-cell genomics, quantitative proteomics, and live-microscopy to uncover these initiating mechanisms in human cells. CAF-1 loss immediately slows down DNA replication speed and renders nascent DNA hyperaccessible. A rapid cellular response, distinct from canonical DNA damage signaling, is triggered and lowers histone mRNAs. As a result, histone variants usage and their modifications are altered, limiting transcriptional fidelity and delaying chromatin maturation within a single S-phase. This multi-level response induces a cell-cycle arrest after mitosis. Our work reveals the immediate consequences of defective de novo chromatin assembly during DNA replication, explaining how at later times the epigenome and cell fate can be altered.
Collapse
Affiliation(s)
- Jan Dreyer
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Giulia Ricci
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jeroen van den Berg
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Vivek Bhardwaj
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Janina Funk
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Claire Armstrong
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Vincent van Batenburg
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Chance Sine
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Michael A. VanInsberghe
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Richard Marsman
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Imke K. Mandemaker
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Simone di Sanzo
- MOLEQLAR Analytics GmbH, Rosenheimer Street 141 h, 81671 Munich, Germany
| | - Juliette Costantini
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Stefano G. Manzo
- Oncode Institute, The Netherlands
- Division of Gene Regulation, Netherlands Cancer Institute, The Netherlands
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Alva Biran
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Claire Burny
- MOLEQLAR Analytics GmbH, Rosenheimer Street 141 h, 81671 Munich, Germany
| | | | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sabrina L. Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Alexander van Oudenaarden
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| |
Collapse
|
5
|
Yang KB, Rasouly A, Epshtein V, Martinez C, Nguyen T, Shamovsky I, Nudler E. Persistence of backtracking by human RNA polymerase II. Mol Cell 2024; 84:897-909.e4. [PMID: 38340716 DOI: 10.1016/j.molcel.2024.01.019] [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: 08/25/2023] [Revised: 11/20/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
RNA polymerase II (RNA Pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome-wide distribution of more persistent backtracking are unknown. Consequently, we developed a method to directly sequence the extruded, "backtracked" 3' RNA. Our data show that RNA Pol II slides backward more than 20 nt in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where RNA Pol II pauses near promoters and intron-exon junctions and is enriched in genes involved in translation, replication, and development, where gene expression is decreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, and the resolution of such events is likely required for timely expression during cell division. These results demonstrate that persistent backtracking can potentially affect diverse gene expression programs.
Collapse
Affiliation(s)
- Kevin B Yang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Aviram Rasouly
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Criseyda Martinez
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Thao Nguyen
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA.
| |
Collapse
|
6
|
Alahmari AA, Chaubey AH, Jonnakuti VS, Tisdale AA, Schwarz CD, Cornwell AC, Maraszek KE, Paterson EJ, Kim M, Venkat S, Gomez EC, Wang J, Gurova KV, Yalamanchili HK, Feigin ME. CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing. RNA (NEW YORK, N.Y.) 2024; 30:281-297. [PMID: 38191171 PMCID: PMC10870380 DOI: 10.1261/rna.079931.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options, potentiating the importance of uncovering novel drug targets. Here, we target cleavage and polyadenylation specificity factor 3 (CPSF3), the 3' endonuclease that catalyzes mRNA cleavage during polyadenylation and histone mRNA processing. We find that CPSF3 is highly expressed in PDAC and is associated with poor prognosis. CPSF3 knockdown blocks PDAC cell proliferation and colony formation in vitro and tumor growth in vivo. Chemical inhibition of CPSF3 by the small molecule JTE-607 also attenuates PDAC cell proliferation and colony formation, while it has no effect on cell proliferation of nontransformed immortalized control pancreatic cells. Mechanistically, JTE-607 induces transcriptional readthrough in replication-dependent histones, reduces core histone expression, destabilizes chromatin structure, and arrests cells in the S-phase of the cell cycle. Therefore, CPSF3 represents a potential therapeutic target for the treatment of PDAC.
Collapse
Affiliation(s)
- Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Aditi H Chaubey
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Venkata S Jonnakuti
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Arwen A Tisdale
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Carla D Schwarz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Abigail C Cornwell
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Kathryn E Maraszek
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Emily J Paterson
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Minsuh Kim
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| |
Collapse
|
7
|
Dubey SK, Dubey R, Kleinman ME. Unraveling Histone Loss in Aging and Senescence. Cells 2024; 13:320. [PMID: 38391933 PMCID: PMC10886805 DOI: 10.3390/cells13040320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
As the global population experiences a notable surge in aging demographics, the need to understand the intricate molecular pathways exacerbated by age-related stresses, including epigenetic dysregulation, becomes a priority. Epigenetic mechanisms play a critical role in driving age-related diseases through altered gene expression, genomic instability, and irregular chromatin remodeling. In this review, we focus on histones, a central component of the epigenome, and consolidate the key findings of histone loss and genome-wide redistribution as fundamental processes contributing to aging and senescence. The review provides insights into novel histone expression profiles, nucleosome occupancy, disruptions in higher-order chromatin architecture, and the emergence of noncanonical histone variants in the aging cellular landscape. Furthermore, we explore the current state of our understanding of the molecular mechanisms of histone deficiency in aging cells. Specific emphasis is placed on highlighting histone degradation pathways in the cell and studies that have explored potential strategies to mitigate histone loss or restore histone levels in aging cells. Finally, in addressing future perspectives, the insights gained from this review hold profound implications for advancing strategies that actively intervene in modulating histone expression profiles in the context of cellular aging and identifying potential therapeutic targets for alleviating a multitude of age-related diseases.
Collapse
Affiliation(s)
| | | | - Mark Ellsworth Kleinman
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA; (S.K.D.); (R.D.)
| |
Collapse
|
8
|
Yang KB, Rasouly A, Epshtein V, Martinez C, Nguyen T, Shamovsky I, Nudler E. Persistence of backtracking by human RNA polymerase II. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571520. [PMID: 38168453 PMCID: PMC10760130 DOI: 10.1101/2023.12.13.571520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
RNA polymerase II (pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome wide distribution of more persistent backtracking is unknown. Consequently, we developed a novel method to directly sequence the extruded, "backtracked" 3' RNA. Our data shows that pol II slides backwards more than 20 nucleotides in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where pol II pauses near promoters and intron-exon junctions, and is enriched in genes involved in translation, replication, and development, where gene expression is decreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, and the resolution of such events is likely required for timely expression during cell division. These results demonstrate that persistent backtracking has the potential to affect diverse gene expression programs.
Collapse
|
9
|
Sereesongsaeng N, Burrows JF, Scott CJ, Brix K, Burden RE. Cathepsin V regulates cell cycle progression and histone stability in the nucleus of breast cancer cells. Front Pharmacol 2023; 14:1271435. [PMID: 38026973 PMCID: PMC10657903 DOI: 10.3389/fphar.2023.1271435] [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: 08/02/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: We previously identified that Cathepsin V (CTSV) expression is associated with poor prognosis in ER+ breast cancer, particularly within the Luminal A subtype. Examination of the molecular role of the protease within Luminal A tumours, revealed that CTSV promotes tumour cell invasion and proliferation, in addition to degradation of the luminal transcription factor, GATA3, via the proteasome. Methods: Cell line models expressing CTSV shRNA or transfected to overexpress CTSV were used to examine the impact of CTSV on cell proliferation by MTT assay and flow cytometry. Western blotting analysis was used to identify the impact of CTSV on histone and chaperone protein expression. Cell fractionation and confocal microscopy was used to illustrate the presence of CTSV in the nuclear compartment. Results: In this work we have identified that CTSV has an impact on breast cancer cell proliferation, with CTSV depleted cells exhibiting delayed progression through the G2/M phase of the cell cycle. Further investigation has revealed that CTSV can control nuclear expression levels of histones H3 and H4 via regulating protein expression of their chaperone sNASP. We have discovered that CTSV is localised to the nuclear compartment in breast tumour cells, mediated by a bipartite nuclear localisation signal (NLS) within the CTSV sequence and that nuclear CTSV is required for cell cycle progression and histone stability in breast tumour cells. Discussion: Collectively these findings support the hypothesis that targeting CTSV may have utility as a novel therapeutic target in ER+ breast cancer by impairing cell cycle progression via manipulating histone stabilisation.
Collapse
Affiliation(s)
| | - James F. Burrows
- School of Pharmacy, Medical Biology Centre, Queen’s University Belfast, Belfast, United Kingdom
| | - Christopher J. Scott
- The Patrick G Johnston Centre for Cancer Research, Medical Biology Centre, Queen’s University Belfast, Belfast, United Kingdom
| | - Klaudia Brix
- School of Science, Constructor University, Bremen, Germany
| | - Roberta E. Burden
- School of Pharmacy, Medical Biology Centre, Queen’s University Belfast, Belfast, United Kingdom
| |
Collapse
|
10
|
Kwon MJ, Jung HS, Kang SM, Lee SH, Park JH. The Protective Effects of Eicosapentaenoic Acid for Stress-induced Accelerated Senescence in Vascular Endothelial Cells. Int J Med Sci 2023; 20:1479-1491. [PMID: 37790848 PMCID: PMC10542193 DOI: 10.7150/ijms.85224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/06/2023] [Indexed: 10/05/2023] Open
Abstract
Background: Eicosapentaenoic acid (EPA) is an omega-3 fatty acid that protects against cardiovascular diseases in patients with hypertriglyceridemia and may have pleotropic effects beyond lowering triglycerides. Many degenerative diseases, such as atherosclerosis and diabetes, are related to cellular senescence as a pathophysiological mechanism. We aimed to examine whether EPA could protect vascular endothelial cells under stress conditions against stress-induced accelerated senescence (SIAS). Methods: Cultured human umbilical vein endothelial cells (HUVECs) were exposed to H2O2 as oxidative stress and a high glucose concentration with palmitate as a glucolipotoxic condition. Changes in cell viability, apoptosis, lactate dehydrogenase release, and cell cycle analysis were measured by cell counting kit-8 assay, annexin V/ propidium iodide staining, and enzyme-linked immunosorbent assay, respectively. EPA was applied in stress conditions. The degree of senescence was measured by senescence-associated beta-galactosidase staining and p16 staining using immunofluorescence. Apoptosis and cellular senescence-related proteins were measured by Western blotting. Results: Cultured HUVECs under oxidative and glucolipotoxic stresses revealed accelerated senescence and increased apoptosis. These changes were markedly reversed by EPA administration, and the expressions of apoptosis and cellular senescence-related proteins were reversed by EPA treatment. Conclusion: EPA effectively protects HUVECs against SIAS, which may be one of its pleotrophic effects.
Collapse
Affiliation(s)
- Min Jeong Kwon
- Department of Internal Medicine, Busan Paik Hospital, College of Medicine, Inje University, Busan, South Korea
| | - Hye Sook Jung
- Paik Institute for Clinical Research, Inje University, Busan, South Korea
| | - Seon Mee Kang
- Department of Internal Medicine, Kangwon National University Hospital, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Soon Hee Lee
- Department of Internal Medicine, Busan Paik Hospital, College of Medicine, Inje University, Busan, South Korea
| | - Jeong Hyun Park
- Department of Internal Medicine, Busan Paik Hospital, College of Medicine, Inje University, Busan, South Korea
- Paik Institute for Clinical Research, Inje University, Busan, South Korea
| |
Collapse
|
11
|
Wooten M, Takushi B, Ahmad K, Henikoff S. Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters. SCIENCE ADVANCES 2023; 9:eadg3257. [PMID: 37315134 DOI: 10.1126/sciadv.adg3257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/08/2023] [Indexed: 06/16/2023]
Abstract
Anthracyclines are a class of widely prescribed anticancer drugs that disrupt chromatin by intercalating into DNA and enhancing nucleosome turnover. To understand the molecular consequences of anthracycline-mediated chromatin disruption, we used Cleavage Under Targets and Tagmentation (CUT&Tag) to profile RNA polymerase II during anthracycline treatment in Drosophila cells. We observed that treatment with the anthracycline aclarubicin leads to elevated levels of RNA polymerase II and changes in chromatin accessibility. We found that promoter proximity and orientation affect chromatin changes during aclarubicin treatment, as closely spaced divergent promoter pairs show greater chromatin changes when compared to codirectionally oriented tandem promoters. We also found that aclarubicin treatment changes the distribution of noncanonical DNA G-quadruplex structures both at promoters and at G-rich pericentromeric repeats. Our work suggests that the cancer-killing activity of aclarubicin is driven by the disruption of nucleosomes and RNA polymerase II.
Collapse
Affiliation(s)
| | | | - Kami Ahmad
- Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| |
Collapse
|
12
|
Wang YC, Kelso AA, Karamafrooz A, Chen YH, Chen WK, Cheng CT, Qi Y, Gu L, Malkas L, Taglialatela A, Kung HJ, Moldovan GL, Ciccia A, Stark JM, Ann DK. Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA ubiquitination. Cell Rep 2023; 42:112296. [PMID: 36961817 PMCID: PMC10517088 DOI: 10.1016/j.celrep.2023.112296] [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: 09/20/2021] [Revised: 01/12/2023] [Accepted: 03/06/2023] [Indexed: 03/25/2023] Open
Abstract
The arginine dependency of cancer cells creates metabolic vulnerability. In this study, we examine the impact of arginine availability on DNA replication and genotoxicity resistance. Using DNA combing assays, we find that limiting extracellular arginine results in the arrest of cancer cells at S phase and a slowing or stalling of DNA replication. The translation of new histone H4 is arginine dependent and influences DNA replication. Increased proliferating cell nuclear antigen (PCNA) occupancy and helicase-like transcription factor (HLTF)-catalyzed PCNA K63-linked polyubiquitination protect arginine-starved cells from DNA damage. Arginine-deprived cancer cells display tolerance to genotoxicity in a PCNA K63-linked polyubiquitination-dependent manner. Our findings highlight the crucial role of extracellular arginine in nutrient-regulated DNA replication and provide potential avenues for the development of cancer treatments.
Collapse
Affiliation(s)
- Yi-Chang Wang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Andrew A Kelso
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Adak Karamafrooz
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yi-Hsuan Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Wei-Kai Chen
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Chun-Ting Cheng
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Yue Qi
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Long Gu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Linda Malkas
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hsing-Jien Kung
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, ROC
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - David K Ann
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA.
| |
Collapse
|
13
|
Wang YC, Kelso AA, Karamafrooz A, Chen YH, Chen WK, Cheng CT, Qi Y, Gu L, Malkas L, Kung HJ, Moldovan GL, Ciccia A, Stark JM, Ann DK. Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA polyubiquitination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526362. [PMID: 36778247 PMCID: PMC9915598 DOI: 10.1101/2023.01.31.526362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The unique arginine dependencies of cancer cell proliferation and survival creates metabolic vulnerability. Here, we investigate the impact of extracellular arginine availability on DNA replication and genotoxic resistance. Using DNA combing assays, we find that when extracellular arginine is limited, cancer cells are arrested at S-phase and DNA replication forks slow or stall instantly until arginine is re-supplied. The translation of new histone H4 is arginine-dependent and impacts DNA replication and the expression of newly synthesized histone H4 is reduced in the avascular nutrient-poor breast cancer xenograft tumor cores. Furthermore, we demonstrate that increased PCNA occupancy and HLTF-catalyzed PCNA K63-linked polyubiquitination protects arginine-starved cells from hydroxyurea-induced, DNA2-catalyzed nascent strand degradation. Finally, arginine-deprived cancer cells are tolerant to genotoxic insults in a PCNA K63-linked polyubiquitination-dependent manner. Together, these findings reveal that extracellular arginine is the "linchpin" for nutrient-regulated DNA replication. Such information could be leveraged to expand current modalities or design new drug targets against cancer.
Collapse
Affiliation(s)
- Yi-Chang Wang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Andrew A. Kelso
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Adak Karamafrooz
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yi-Hsuan Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Wei-Kai Chen
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Chun-Ting Cheng
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Yue Qi
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - Long Gu
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Linda Malkas
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Hsing-Jien Kung
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, ROC
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Jeremy M. Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - David K Ann
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| |
Collapse
|
14
|
Mühlen D, Li X, Dovgusha O, Jäckle H, Günesdogan U. Recycling of parental histones preserves the epigenetic landscape during embryonic development. SCIENCE ADVANCES 2023; 9:eadd6440. [PMID: 36724233 PMCID: PMC9891698 DOI: 10.1126/sciadv.add6440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 12/27/2022] [Indexed: 06/16/2023]
Abstract
Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onward. Lack of new histone synthesis leads to more accessible chromatin and reduced nucleosome occupancy, since only parental histones are available. This leads to up-regulated and spurious transcription, whereas the control of the developmental transcriptional program is partially maintained. The genomic positions of modified parental histone H2A, H2B, and H3 are largely restored during DNA replication. However, parental histones with active marks become more dispersed within gene bodies, which is linked to transcription. Together, the results suggest that parental histones are recycled to preserve the epigenetic landscape during DNA replication in vivo.
Collapse
Affiliation(s)
- Dominik Mühlen
- University of Göttingen, Göttingen Center for Molecular Biosciences, Department of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Department for Molecular Developmental Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Xiaojuan Li
- University of Göttingen, Göttingen Center for Molecular Biosciences, Department of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Oleksandr Dovgusha
- University of Göttingen, Göttingen Center for Molecular Biosciences, Department of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Herbert Jäckle
- Max Planck Institute for Multidisciplinary Sciences, Department for Molecular Developmental Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ufuk Günesdogan
- University of Göttingen, Göttingen Center for Molecular Biosciences, Department of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Department for Molecular Developmental Biology, Am Fassberg 11, 37077 Göttingen, Germany
| |
Collapse
|
15
|
Crucianelli C, Jaiswal J, Vijayakumar Maya A, Nogay L, Cosolo A, Grass I, Classen AK. Distinct signaling signatures drive compensatory proliferation via S-phase acceleration. PLoS Genet 2022; 18:e1010516. [PMID: 36520882 PMCID: PMC9799308 DOI: 10.1371/journal.pgen.1010516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/29/2022] [Accepted: 11/08/2022] [Indexed: 12/23/2022] Open
Abstract
Regeneration relies on cell proliferation to restore damaged tissues. Multiple signaling pathways activated by local or paracrine cues have been identified to promote regenerative proliferation. How different types of tissue damage may activate distinct signaling pathways and how these differences converge on regenerative proliferation is less well defined. To better understand how tissue damage and proliferative signals are integrated during regeneration, we investigate models of compensatory proliferation in Drosophila imaginal discs. We find that compensatory proliferation is associated with a unique cell cycle profile, which is characterized by short G1 and G2 phases and, surprisingly, by acceleration of the S-phase. S-phase acceleration can be induced by two distinct signaling signatures, aligning with inflammatory and non-inflammatory tissue damage. Specifically, non-autonomous activation of JAK/STAT and Myc in response to inflammatory damage, or local activation of Ras/ERK and Hippo/Yki in response to elevated cell death, promote accelerated nucleotide incorporation during S-phase. This previously unappreciated convergence of different damaging insults on the same regenerative cell cycle program reconciles previous conflicting observations on proliferative signaling in different tissue regeneration and tumor models.
Collapse
Affiliation(s)
- Carlo Crucianelli
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Janhvi Jaiswal
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Ananthakrishnan Vijayakumar Maya
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics, and Metabolism, Freiburg, Germany
| | - Liyne Nogay
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- International Max Planck Research School for Immunobiology, Epigenetics, and Metabolism, Freiburg, Germany
| | - Andrea Cosolo
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Isabelle Grass
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Anne-Kathrin Classen
- Hilde-Mangold-Haus, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- * E-mail:
| |
Collapse
|
16
|
Arrieta A, Vondriska TM. Nucleosome proteostasis and histone turnover. Front Mol Biosci 2022; 9:990006. [PMID: 36250018 PMCID: PMC9563994 DOI: 10.3389/fmolb.2022.990006] [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: 07/11/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Maintenance of protein folding homeostasis, or proteostasis is critical for cell survival as well as for execution of cell type specific biological processes such as muscle cell contractility, neuronal synapse and memory formation, and cell transition from a mitotic to post-mitotic cell type. Cell type specification is driven largely by chromatin organization, which dictates which genes are turned off or on, depending on cell needs and function. Loss of chromatin organization can have catastrophic consequences either on cell survival or cell type specific function. Chromatin organization is highly dependent on organization of nucleosomes, spatiotemporal nucleosome assembly and disassembly, and histone turnover. In this review our goal is to highlight why nucleosome proteostasis is critical for chromatin organization, how this process is mediated by histone chaperones and ATP-dependent chromatin remodelers and outline potential and established mechanisms of disrupted nucleosome proteostasis during disease. Finally, we highlight how these mechanisms of histone turnover and nucleosome proteostasis may conspire with unfolded protein response programs to drive histone turnover in cell growth and development.
Collapse
Affiliation(s)
- Adrian Arrieta
- Departments of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- *Correspondence: Adrian Arrieta,
| | - Thomas M. Vondriska
- Departments of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Departments of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Departments of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
17
|
Wang Y, Lih TSM, Chen L, Xu Y, Kuczler MD, Cao L, Pienta KJ, Amend SR, Zhang H. Optimized data-independent acquisition approach for proteomic analysis at single-cell level. Clin Proteomics 2022; 19:24. [PMID: 35810282 PMCID: PMC9270744 DOI: 10.1186/s12014-022-09359-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/26/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Single-cell proteomic analysis provides valuable insights into cellular heterogeneity allowing the characterization of the cellular microenvironment which is difficult to accomplish in bulk proteomic analysis. Currently, single-cell proteomic studies utilize data-dependent acquisition (DDA) mass spectrometry (MS) coupled with a TMT labelled carrier channel. Due to the extremely imbalanced MS signals among the carrier channel and other TMT reporter ions, the quantification is compromised. Thus, data-independent acquisition (DIA)-MS should be considered as an alternative approach towards single-cell proteomic study since it generates reproducible quantitative data. However, there are limited reports on the optimal workflow for DIA-MS-based single-cell analysis. METHODS We report an optimized DIA workflow for single-cell proteomics using Orbitrap Lumos Tribrid instrument. We utilized a breast cancer cell line (MDA-MB-231) and induced drug resistant polyaneuploid cancer cells (PACCs) to evaluate our established workflow. RESULTS We found that a short LC gradient was preferable for peptides extracted from single cell level with less than 2 ng sample amount. The total number of co-searching peptide precursors was also critical for protein and peptide identifications at nano- and sub-nano-gram levels. Post-translationally modified peptides could be identified from a nano-gram level of peptides. Using the optimized workflow, up to 1500 protein groups were identified from a single PACC corresponding to 0.2 ng of peptides. Furthermore, about 200 peptides with phosphorylation, acetylation, and ubiquitination were identified from global DIA analysis of 100 cisplatin resistant PACCs (20 ng). Finally, we used this optimized DIA approach to compare the whole proteome of MDA-MB-231 parental cells and induced PACCs at a single-cell level. We found the single-cell level comparison could reflect real protein expression changes and identify the protein copy number. CONCLUSIONS Our results demonstrate that the optimized DIA pipeline can serve as a reliable quantitative tool for single-cell as well as sub-nano-gram proteomic analysis.
Collapse
Affiliation(s)
- Yuefan Wang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | | | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Yuanwei Xu
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Morgan D Kuczler
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Liwei Cao
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Kenneth J Pienta
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Sarah R Amend
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA.
| |
Collapse
|
18
|
Yaseen Y, Kubba A, Shihab W, Tahtamouni L. Synthesis, docking study, and structure-activity relationship of novel niflumic acid derivatives acting as anticancer agents by inhibiting VEGFR or EGFR tyrosine kinase activities. PHARMACIA 2022. [DOI: 10.3897/pharmacia.69.e86504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new series of niflumic acid (NF) derivatives were synthesized by esterification of (NF) to give ester compound 1, which was treated with hydrazine hydrate to produce (NF) hydrazide 2. Hydrazine-1-carboxamide compounds (3A–C), and hydrazine-1-carbothioamide derivatives (4A–D) were synthesized by treatment of (NF) hydrazide with phenyl isocyanate, and phenyl isothiocyanate derivatives, respectively. The cyclization of (4B–D) and (3B) was achieved using NaOH solution to produce 1,2,4-triazole derivatives (5A–C) and 6, respectively. The prepared compounds were characterized using IR, 1HNMR, 13CNMR, and MS (ESI) spectroscopy. A molecular docking study was performed to evaluate the binding affinity of the synthesized compounds against EGFR and VEGFR kinase domains which revealed that compounds 3B, and 4A had the best binding energy (-7.87, and -7.33 kcal/mol, respectively) against VEGFR, while compound 5A had the best binding energy (-7.95 kcal/mol) against EGFR. The biological investigation results indicated that all the tested compounds caused cell killing in the two cancer cell lines (Hep G2 and A549) studied, with compound 4C being the most cytotoxic, as well as being cancer selective. Additionally, compound 4C-treated Hep G2 cells were arrested at the S and G2/M cell cycle phases. Cytotoxicity of compound 4C was attributed to apoptosis as determined by flow cytometry and qRT-PCR results of the apoptosis markers p53, BAX, and caspase-3. Finally, compound 4C inhibited VEGFR kinase activity, while compound 5B inhibited EGFR kinase activity. In conclusion, the novel (NF) derivatives are potent anticancer agents, inhibiting cell proliferation by inhibiting EGFR and VEGFR tyrosine kinase enzymes.
Collapse
|
19
|
Ahmad K, Henikoff S, Ramachandran S. Managing the Steady State Chromatin Landscape by Nucleosome Dynamics. Annu Rev Biochem 2022; 91:183-195. [PMID: 35303789 DOI: 10.1146/annurev-biochem-032620-104508] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gene regulation arises out of dynamic competition between nucleosomes, transcription factors, and other chromatin proteins for the opportunity to bind genomic DNA. The timescales of nucleosome assembly and binding of factors to DNA determine the outcomes of this competition at any given locus. Here, we review how these properties of chromatin proteins and the interplay between the dynamics of different factors are critical for gene regulation. We discuss how molecular structures of large chromatin-associated complexes, kinetic measurements, and high resolution mapping of protein-DNA complexes in vivo set the boundary conditions for chromatin dynamics, leading to models of how the steady state behaviors of regulatory elements arise. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; .,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
| |
Collapse
|
20
|
Abstract
The current model of replication-dependent (RD) histone biosynthesis posits that RD histone gene expression is coupled to DNA replication, occurring only in S phase of the cell cycle once DNA synthesis has begun. However, several key factors in the RD histone biosynthesis pathway are up-regulated by E2F or phosphorylated by CDK2, suggesting these processes may instead begin much earlier, at the point of cell-cycle commitment. In this study, we use both fixed- and live-cell imaging of human cells to address this question, revealing a hybrid model in which RD histone biosynthesis is first initiated in G1, followed by a strong increase in histone production in S phase of the cell cycle. This suggests a mechanism by which cells that have committed to the cell cycle build up an initial small pool of RD histones to be available for the start of DNA replication, before producing most of the necessary histones required in S phase. Thus, a clear distinction exists at completion of mitosis between cells that are born with the intention of proceeding through the cell cycle and replicating their DNA and cells that have chosen to exit the cell cycle and have no immediate need for histone synthesis.
Collapse
|
21
|
Liu B, Zhao H, Wu K, Großhans J. Temporal Gradients Controlling Embryonic Cell Cycle. BIOLOGY 2021; 10:biology10060513. [PMID: 34207742 PMCID: PMC8228447 DOI: 10.3390/biology10060513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022]
Abstract
Simple Summary Embryonic cells sense temporal gradients of regulatory signals to determine whether and when to proceed or remodel the cell cycle. Such a control mechanism is allowed to accurately link the cell cycle with the developmental program, including cell differentiation, morphogenesis, and gene expression. The mid-blastula transition has been a paradigm for timing in early embryogenesis in frog, fish, and fly, among others. It has been argued for decades now if the events associated with the mid-blastula transition, i.e., the onset of zygotic gene expression, remodeling of the cell cycle, and morphological changes, are determined by a control mechanism or by absolute time. Recent studies indicate that multiple independent signals and mechanisms contribute to the timing of these different processes. Here, we focus on the mechanisms for cell cycle remodeling, specifically in Drosophila, which relies on gradual changes of the signal over time. We discuss pathways for checkpoint activation, decay of Cdc25 protein levels, as well as depletion of deoxyribonucleotide metabolites and histone proteins. The gradual changes of these signals are linked to Cdk1 activity by readout mechanisms involving thresholds. Abstract Cell proliferation in early embryos by rapid cell cycles and its abrupt pause after a stereotypic number of divisions present an attractive system to study the timing mechanism in general and its coordination with developmental progression. In animals with large eggs, such as Xenopus, zebrafish, or Drosophila, 11–13 very fast and synchronous cycles are followed by a pause or slowdown of the cell cycle. The stage when the cell cycle is remodeled falls together with changes in cell behavior and activation of the zygotic genome and is often referred to as mid-blastula transition. The number of fast embryonic cell cycles represents a clear and binary readout of timing. Several factors controlling the cell cycle undergo dynamics and gradual changes in activity or concentration and thus may serve as temporal gradients. Recent studies have revealed that the gradual loss of Cdc25 protein, gradual depletion of free deoxyribonucleotide metabolites, or gradual depletion of free histone proteins impinge on Cdk1 activity in a threshold-like manner. In this review, we will highlight with a focus on Drosophila studies our current understanding and recent findings on the generation and readout of these temporal gradients, as well as their position within the regulatory network of the embryonic cell cycle.
Collapse
Affiliation(s)
- Boyang Liu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; (B.L.); (H.Z.); (K.W.)
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan 250012, China
| | - Han Zhao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; (B.L.); (H.Z.); (K.W.)
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan 250012, China
| | - Keliang Wu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; (B.L.); (H.Z.); (K.W.)
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan 250012, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan 250012, China
| | - Jörg Großhans
- Department of Biology, Philipps University, 35043 Marburg, Germany
- Correspondence:
| |
Collapse
|
22
|
Flaus A, Downs JA, Owen-Hughes T. Histone isoforms and the oncohistone code. Curr Opin Genet Dev 2021; 67:61-66. [PMID: 33285512 DOI: 10.1016/j.gde.2020.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/07/2020] [Indexed: 12/18/2022]
Abstract
Recent studies have highlighted the potential for missense mutations in histones to act as oncogenic drivers, leading to the term 'oncohistones'. While histone proteins are highly conserved, they are encoded by multigene families. There is heterogeneity among these genes at the level of the underlying sequence, the amino acid composition of the encoded histone isoform, and the expression levels. One question that arises, therefore, is whether all histone-encoding genes function equally as oncohistones. In this review, we consider this question and explore what this means in terms of the mechanisms by which oncohistones can exert their effects in chromatin.
Collapse
Affiliation(s)
- Andrew Flaus
- Centre for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
| |
Collapse
|
23
|
The XPB Subunit of the TFIIH Complex Plays a Critical Role in HIV-1 Transcription and XPB Inhibition by Spironolactone Prevents HIV-1 Reactivation from Latency. J Virol 2021; 95:JVI.01247-20. [PMID: 33239456 PMCID: PMC7851559 DOI: 10.1128/jvi.01247-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
HIV transcription requires assembly of cellular transcription factors at the HIV-1promoter. The TFIIH general transcription factor facilitates transcription initiation by opening the DNA strands around the transcription start site and phosphorylating the C-terminal domain for RNA polymerase II (RNAPII) for activation. Spironolactone (SP), an FDA approved aldosterone antagonist, triggers the proteasomal degradation of the XPB subunit of TFIIH, and concurrently suppresses acute HIV infection in vitro Here we investigated SP as a possible block-and-lock agent for a functional cure aimed at the transcriptional silencing of the viral reservoir. The long-term activity of SP was investigated in primary and cell line models of HIV-1 latency and reactivation. We show that SP rapidly inhibits HIV-1 transcription by reducing RNAPII recruitment to the HIV-1 genome. shRNA knockdown of XPB confirmed XPB degradation as the mechanism of action. Unfortunately, long-term pre-treatment with SP does not result in epigenetic suppression of HIV upon SP treatment interruption, since virus rapidly rebounds when XPB reemerges; however, SP alone without ART maintains the transcriptional suppression. Importantly, SP inhibits HIV reactivation from latency in both cell line models and resting CD4+T cells isolated from aviremic infected individuals upon cell stimulation with latency reversing agents. Furthermore, long-term treatment with concentrations of SP that potently degrade XPB does not lead to global dysregulation of cellular mRNA expression. Overall, these results suggest that XPB plays a key role in HIV transcriptional regulation and XPB degradation by SP strengthens the potential of HIV transcriptional inhibitors in block-and-lock HIV cure approaches.IMPORTANCE Antiretroviral therapy (ART) effectively reduces an individual's HIV loads to below the detection limit, nevertheless rapid viral rebound immediately ensues upon treatment interruption. Furthermore, virally suppressed individuals experience chronic immune activation from ongoing low-level virus expression. Thus, the importance of identifying novel therapeutics to explore in block-and-lock HIV functional cure approaches, aimed at the transcriptional and epigenetic silencing of the viral reservoir to block reactivation from latency. We investigated the potential of repurposing the FDA-approved spironolactone (SP), as one such drug. SP treatment rapidly degrades a host transcription factor subunit, XPB, inhibiting HIV transcription and blocking reactivation from latency. Long-term SP treatment does not affect cellular viability, cell cycle progression or global cellular transcription. SP alone blocks HIV transcription in the absence of ART but does not delay rebound upon drug removal as XPB rapidly reemerges. This study highlights XPB as a novel drug target in block-and-lock therapeutic approaches.
Collapse
|
24
|
Laursen SP, Bowerman S, Luger K. Archaea: The Final Frontier of Chromatin. J Mol Biol 2020; 433:166791. [PMID: 33383035 PMCID: PMC7987875 DOI: 10.1016/j.jmb.2020.166791] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 12/26/2022]
Abstract
The three domains of life employ various strategies to organize their genomes. Archaea utilize features similar to those found in both eukaryotic and bacterial chromatin to organize their DNA. In this review, we discuss the current state of research regarding the structure-function relationships of several archaeal chromatin proteins (histones, Alba, Cren7, and Sul7d). We address individual structures as well as inferred models for higher-order chromatin formation. Each protein introduces a unique phenotype to chromatin organization, and these structures are put into the context of in vivo and in vitro data. We close by discussing the present gaps in knowledge that are preventing further studies of the organization of archaeal chromatin, on both the organismal and domain level.
Collapse
Affiliation(s)
- Shawn P Laursen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, United States
| | - Samuel Bowerman
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, United States; Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States.
| |
Collapse
|
25
|
Koreski KP, Rieder LE, McLain LM, Chaubal A, Marzluff WF, Duronio RJ. Drosophila histone locus body assembly and function involves multiple interactions. Mol Biol Cell 2020; 31:1525-1537. [PMID: 32401666 PMCID: PMC7359574 DOI: 10.1091/mbc.e20-03-0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The histone locus body (HLB) assembles at replication-dependent (RD) histone loci and concentrates factors required for RD histone mRNA biosynthesis. The Drosophila melanogaster genome has a single locus comprised of ∼100 copies of a tandemly arrayed 5-kB repeat unit containing one copy of each of the 5 RD histone genes. To determine sequence elements required for D. melanogaster HLB formation and histone gene expression, we used transgenic gene arrays containing 12 copies of the histone repeat unit that functionally complement loss of the ∼200 endogenous RD histone genes. A 12x histone gene array in which all H3-H4 promoters were replaced with H2a-H2b promoters (12xPR) does not form an HLB or express high levels of RD histone mRNA in the presence of the endogenous histone genes. In contrast, this same transgenic array is active in HLB assembly and RD histone gene expression in the absence of the endogenous RD histone genes and rescues the lethality caused by homozygous deletion of the RD histone locus. The HLB formed in the absence of endogenous RD histone genes on the mutant 12x array contains all known factors present in the wild-type HLB including CLAMP, which normally binds to GAGA repeats in the H3-H4 promoter. These data suggest that multiple protein–protein and/or protein–DNA interactions contribute to HLB formation, and that the large number of endogenous RD histone gene copies sequester available factor(s) from attenuated transgenic arrays, thereby preventing HLB formation and gene expression on these arrays.
Collapse
Affiliation(s)
- Kaitlin P Koreski
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Leila E Rieder
- Department of Biology, Emory University, Atlanta, GA 30322
| | - Lyndsey M McLain
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Ashlesha Chaubal
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599.,Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| |
Collapse
|
26
|
Comparative Analysis of the Minimum Number of Replication Origins in Trypanosomatids and Yeasts. Genes (Basel) 2020; 11:genes11050523. [PMID: 32397111 PMCID: PMC7288466 DOI: 10.3390/genes11050523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Single-celled eukaryote genomes predominantly replicate through multiple origins. Although origin usage during the S-phase has been elucidated in some of these organisms, few studies have comparatively approached this dynamic. Here, we developed a user-friendly website able to calculate the length of the cell cycle phases for any organism. Next, using a formula developed by our group, we showed a comparative analysis among the minimum number of replication origins (MO) required to duplicate an entire chromosome within the S-phase duration in trypanosomatids (Trypanosoma cruzi, Leishmania major, and Trypanosoma brucei) and yeasts (Saccharomyces cerevisiae and Schizosaccharomyces pombe). Using the data obtained by our analysis, it was possible to predict the MO required in a situation of replication stress. Also, our findings allow establishing a threshold for the number of origins, which serves as a parameter for genome approaches that map origins. Moreover, our data suggest that when compared to yeasts, trypanosomatids use much more origins than the minimum needed. This is the first time a comparative analysis of the minimum number of origins has been successfully applied. These data may provide new insight into the understanding of the replication mechanism and a new methodological framework for studying single-celled eukaryote genomes.
Collapse
|
27
|
Lowe DJ, Herzog M, Mosler T, Cohen H, Felton S, Beli P, Raj K, Galanty Y, Jackson SP. Chronic irradiation of human cells reduces histone levels and deregulates gene expression. Sci Rep 2020; 10:2200. [PMID: 32042076 PMCID: PMC7010678 DOI: 10.1038/s41598-020-59163-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/24/2020] [Indexed: 01/10/2023] Open
Abstract
Over the past decades, there have been huge advances in understanding cellular responses to ionising radiation (IR) and DNA damage. These studies, however, were mostly executed with cell lines and mice using single or multiple acute doses of radiation. Hence, relatively little is known about how continuous exposure to low dose ionising radiation affects normal cells and organisms, even though our cells are constantly exposed to low levels of radiation. We addressed this issue by examining the consequences of exposing human primary cells to continuous ionising γ-radiation delivered at 6-20 mGy/h. Although these dose rates are estimated to inflict fewer than a single DNA double-strand break (DSB) per hour per cell, they still caused dose-dependent reductions in cell proliferation and increased cellular senescence. We concomitantly observed histone protein levels to reduce by up to 40%, which in contrast to previous observations, was not mainly due to protein degradation but instead correlated with reduced histone gene expression. Histone reductions were accompanied by enlarged nuclear size paralleled by an increase in global transcription, including that of pro-inflammatory genes. Thus, chronic irradiation, even at low dose-rates, can induce cell senescence and alter gene expression via a hitherto uncharacterised epigenetic route. These features of chronic radiation represent a new aspect of radiation biology.
Collapse
Affiliation(s)
- Donna J Lowe
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire, OX11 0RQ, UK.
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Mareike Herzog
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | | | - Howard Cohen
- Elizabeth House Surgery, Warlingham, Surrey, CR6 9LF, UK
| | - Sarah Felton
- Department of Dermatology, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire, OX11 0RQ, UK
| | - Yaron Galanty
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| |
Collapse
|
28
|
da Silva MS, Cayres-Silva GR, Vitarelli MO, Marin PA, Hiraiwa PM, Araújo CB, Scholl BB, Ávila AR, McCulloch R, Reis MS, Elias MC. Transcription activity contributes to the firing of non-constitutive origins in African trypanosomes helping to maintain robustness in S-phase duration. Sci Rep 2019; 9:18512. [PMID: 31811174 PMCID: PMC6898680 DOI: 10.1038/s41598-019-54366-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022] Open
Abstract
The co-synthesis of DNA and RNA potentially generates conflicts between replication and transcription, which can lead to genomic instability. In trypanosomatids, eukaryotic parasites that perform polycistronic transcription, this phenomenon and its consequences are still little studied. Here, we showed that the number of constitutive origins mapped in the Trypanosoma brucei genome is less than the minimum required to complete replication within S-phase duration. By the development of a mechanistic model of DNA replication considering replication-transcription conflicts and using immunofluorescence assays and DNA combing approaches, we demonstrated that the activation of non-constitutive (backup) origins are indispensable for replication to be completed within S-phase period. Together, our findings suggest that transcription activity during S phase generates R-loops, which contributes to the emergence of DNA lesions, leading to the firing of backup origins that help maintain robustness in S-phase duration. The usage of this increased pool of origins, contributing to the maintenance of DNA replication, seems to be of paramount importance for the survival of this parasite that affects million people around the world.
Collapse
Affiliation(s)
- Marcelo S da Silva
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Gustavo R Cayres-Silva
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Marcela O Vitarelli
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Paula A Marin
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Priscila M Hiraiwa
- Plataforma de citometria de fluxo, Instituto Carlos Chagas, FIOCRUZ, Paraná, Brazil
| | - Christiane B Araújo
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Bruno B Scholl
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Andrea R Ávila
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, FIOCRUZ, Paraná, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Marcelo S Reis
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
| | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
| |
Collapse
|
29
|
Ju F, Liu S, Zhang S, Ma H, Chen J, Ge C, Shen Q, Zhang X, Zhao X, Zhang Y, Pang C. Transcriptome analysis and identification of genes associated with fruiting branch internode elongation in upland cotton. BMC PLANT BIOLOGY 2019; 19:415. [PMID: 31590649 PMCID: PMC6781417 DOI: 10.1186/s12870-019-2011-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Appropriate plant architecture can improve the amount of cotton boll opening and allow increased planting density, thus increasing the level of cotton mechanical harvesting and cotton yields. The internodes of cotton fruiting branches are an important part of cotton plant architecture. Thus, studying the molecular mechanism of internode elongation in cotton fruiting branches is highly important. RESULTS In this study, we selected internodes of cotton fruiting branches at three different stages from two cultivars whose internode lengths differed significantly. A total of 76,331 genes were detected by transcriptome sequencing. By KEGG pathway analysis, we found that DEGs were significantly enriched in the plant hormone signal transduction pathway. The transcriptional data and qRT-PCR results showed that members of the GH3 gene family, which are involved in auxin signal transduction, and CKX enzymes, which can reduce the level of CKs, were highly expressed in the cultivar XLZ77, which has relatively short internodes. Genes related to ethylene synthase (ACS), EIN2/3 and ERF in the ethylene signal transduction pathway and genes related to JAR1, COI1 and MYC2 in the JA signal transduction pathway were also highly expressed in XLZ77. Plant hormone determination results showed that the IAA and CK contents significantly decreased in cultivar XLZ77 compared with those in cultivar L28, while the ACC (the precursor of ethylene) and JA contents significantly increased. GO enrichment analysis revealed that the GO categories associated with promoting cell elongation, such as cell division, the cell cycle process and cell wall organization, were significantly enriched, and related genes were highly expressed in L28. However, genes related to the sphingolipid metabolic process and lignin biosynthetic process, whose expression can affect cell elongation, were highly expressed in XLZ77. In addition, 2067 TFs were differentially expressed. The WRKY, ERF and bHLH TF families were the top three largest families whose members were active in the two varieties, and the expression levels of most of the genes encoding these TFs were upregulated in XLZ77. CONCLUSIONS Auxin and CK are positive regulators of internode elongation in cotton branches. In contrast, ethylene and JA may act as negative regulators of internode elongation in cotton branches. Furthermore, the WRKY, ERF and bHLH TFs were identified as important inhibitors of internode elongation in cotton. In XLZ77(a short-internode variety), the mass synthesis of ethylene and amino acid conjugation of auxin led to the inhibition of plant cell elongation, while an increase in JA content and degradation of CKs led to a slow rate of cell division, which eventually resulted in a phenotype that presented relatively short internodes on the fruiting branches. The results of this study not only provide gene resources for the genetic improvement of cotton plant architecture but also lay a foundation for improved understanding of the molecular mechanism of the internode elongation of cotton branches.
Collapse
Affiliation(s)
- Feiyan Ju
- State Key Laboratory of Cotton Biology (Hebei Base)/College of Agronomy, Hebei Agricultural University, Baoding, 071001 Hebei China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Shaodong Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Siping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Huijuan Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Jing Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Changwei Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Qian Shen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Xiaomeng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Xinhua Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| | - Yongjiang Zhang
- State Key Laboratory of Cotton Biology (Hebei Base)/College of Agronomy, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455112 Henan China
| |
Collapse
|
30
|
Chari S, Wilky H, Govindan J, Amodeo AA. Histone concentration regulates the cell cycle and transcription in early development. Development 2019; 146:dev.177402. [PMID: 31511251 DOI: 10.1242/dev.177402] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022]
Abstract
The early embryos of many animals, including flies, fish and frogs, have unusually rapid cell cycles and delayed onset of transcription. These divisions are dependent on maternally supplied RNAs and proteins including histones. Previous work suggests that the pool size of maternally provided histones can alter the timing of zygotic genome activation (ZGA) in frogs and fish. Here, we examine the effects of under- and overexpression of maternal histones in Drosophila embryogenesis. Decreasing histone concentration advances zygotic transcription, cell cycle elongation, Chk1 activation and gastrulation. Conversely, increasing histone concentration delays transcription and results in an additional nuclear cycle before gastrulation. Numerous zygotic transcripts are sensitive to histone concentration, and the promoters of histone-sensitive genes are associated with specific chromatin features linked to increased histone turnover. These include enrichment of the pioneer transcription factor Zelda, and lack of SIN3A and associated histone deacetylases. Our findings uncover a crucial regulatory role for histone concentrations in ZGA of Drosophila.
Collapse
Affiliation(s)
- Sudarshan Chari
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Henry Wilky
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jayalakshmi Govindan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Amanda A Amodeo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
31
|
Histone stress: an unexplored source of chromosomal instability in cancer? Curr Genet 2019; 65:1081-1088. [DOI: 10.1007/s00294-019-00967-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 01/24/2023]
|
32
|
Dorafshan E, Kahn TG, Glotov A, Savitsky M, Walther M, Reuter G, Schwartz YB. Ash1 counteracts Polycomb repression independent of histone H3 lysine 36 methylation. EMBO Rep 2019; 20:embr.201846762. [PMID: 30833342 DOI: 10.15252/embr.201846762] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/11/2022] Open
Abstract
Polycomb repression is critical for metazoan development. Equally important but less studied is the Trithorax system, which safeguards Polycomb target genes from the repression in cells where they have to remain active. It was proposed that the Trithorax system acts via methylation of histone H3 at lysine 4 and lysine 36 (H3K36), thereby inhibiting histone methyltransferase activity of the Polycomb complexes. Here we test this hypothesis by asking whether the Trithorax group protein Ash1 requires H3K36 methylation to counteract Polycomb repression. We show that Ash1 is the only Drosophila H3K36-specific methyltransferase necessary to prevent excessive Polycomb repression of homeotic genes. Unexpectedly, our experiments reveal no correlation between the extent of H3K36 methylation and the resistance to Polycomb repression. Furthermore, we find that complete substitution of the zygotic histone H3 with a variant in which lysine 36 is replaced by arginine does not cause excessive repression of homeotic genes. Our results suggest that the model, where the Trithorax group proteins methylate histone H3 to inhibit the histone methyltransferase activity of the Polycomb complexes, needs revision.
Collapse
Affiliation(s)
| | - Tatyana G Kahn
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | | | | | - Matthias Walther
- Institute of Developmental Genetics, Martin-Luther University of Halle-Wittenberg, Halle, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gunter Reuter
- Institute of Developmental Genetics, Martin-Luther University of Halle-Wittenberg, Halle, Germany
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| |
Collapse
|
33
|
Shindo Y, Amodeo AA. Dynamics of Free and Chromatin-Bound Histone H3 during Early Embryogenesis. Curr Biol 2019; 29:359-366.e4. [DOI: 10.1016/j.cub.2018.12.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/29/2018] [Accepted: 12/13/2018] [Indexed: 11/27/2022]
|
34
|
Probing the Function of Metazoan Histones with a Systematic Library of H3 and H4 Mutants. Dev Cell 2018; 48:406-419.e5. [PMID: 30595536 DOI: 10.1016/j.devcel.2018.11.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/15/2018] [Accepted: 11/28/2018] [Indexed: 11/21/2022]
Abstract
Replication-dependent histone genes often reside in tandemly arrayed gene clusters, hindering systematic loss-of-function analyses. Here, we used CRISPR/Cas9 and the attP/attB double-integration system to alter numbers and sequences of histone genes in their original genomic context in Drosophila melanogaster. As few as 8 copies of the histone gene unit supported embryo development and adult viability, whereas flies with 20 copies were indistinguishable from wild-types. By hierarchical assembly, 40 alanine-substitution mutations (covering all known modified residues in histones H3 and H4) were introduced and characterized. Mutations at multiple residues compromised viability, fertility, and DNA-damage responses. In particular, H4K16 was necessary for expression of male X-linked genes, male viability, and maintenance of ovarian germline stem cells, whereas H3K27 was essential for late embryogenesis. Simplified mosaic analysis showed that H3R26 is required for H3K27 trimethylation. We have developed a powerful strategy and valuable reagents to systematically probe histone functions in D. melanogaster.
Collapse
|
35
|
Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
Collapse
Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| |
Collapse
|
36
|
Barfield SJ, Aglyamova GV, Bay LK, Matz MV. Contrasting effects of
Symbiodinium
identity on coral host transcriptional profiles across latitudes. Mol Ecol 2018; 27:3103-3115. [DOI: 10.1111/mec.14774] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/29/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Sarah J. Barfield
- Department of Integrative Biology University of Texas at Austin Austin Texas
| | - Galina V. Aglyamova
- Department of Integrative Biology University of Texas at Austin Austin Texas
| | - Line K. Bay
- Australian Institute of Marine Science Townsville QLD Australia
| | - Mikhail V. Matz
- Department of Integrative Biology University of Texas at Austin Austin Texas
| |
Collapse
|
37
|
Cruz-Becerra G, Valerio-Cabrera S, Juárez M, Bucio-Mendez A, Zurita M. TFIIH localization is highly dynamic during zygotic genome activation in Drosophila, and its depletion causes catastrophic mitosis. J Cell Sci 2018; 131:jcs.211631. [PMID: 29643118 DOI: 10.1242/jcs.211631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
In Drosophila, zygotic genome activation occurs in pre-blastoderm embryos during rapid mitotic divisions. How the transcription machinery is coordinated to achieve this goal in a very brief time span is still poorly understood. Transcription factor II H (TFIIH) is fundamental for transcription initiation by RNA polymerase II (RNAPII). Herein, we show the in vivo dynamics of TFIIH at the onset of transcription in Drosophila embryos. TFIIH shows an oscillatory behaviour between the nucleus and cytoplasm. TFIIH foci are observed from interphase to metaphase, and colocalize with those for RNAPII phosphorylated at serine 5 (RNAPIIS5P) at prophase, suggesting that transcription occurs during the first mitotic phases. Furthermore, embryos with defects in subunits of either the CAK or the core subcomplexes of TFIIH show catastrophic mitosis. Although, transcriptome analyses show altered expression of several maternal genes that participate in mitosis, the global level of RNAPIIS5P in TFIIH mutant embryos is similar to that in the wild type, therefore, a direct role for TFIIH in mitosis cannot be ruled out. These results provide important insights regarding the role of a basal transcription machinery component when the zygotic genome is activated.
Collapse
Affiliation(s)
- Grisel Cruz-Becerra
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| | - Sarai Valerio-Cabrera
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| | - Mandy Juárez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| | - Alyeri Bucio-Mendez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología. Universidad Nacional Autónoma de México, Av Universidad 2001, Cuernavaca Morelos 62250, México
| |
Collapse
|
38
|
Maya Miles D, Peñate X, Sanmartín Olmo T, Jourquin F, Muñoz Centeno MC, Mendoza M, Simon MN, Chavez S, Geli V. High levels of histones promote whole-genome-duplications and trigger a Swe1 WEE1-dependent phosphorylation of Cdc28 CDK1. eLife 2018; 7:35337. [PMID: 29580382 PMCID: PMC5871333 DOI: 10.7554/elife.35337] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/05/2018] [Indexed: 12/13/2022] Open
Abstract
Whole-genome duplications (WGDs) have played a central role in the evolution of genomes and constitute an important source of genome instability in cancer. Here, we show in Saccharomyces cerevisiae that abnormal accumulations of histones are sufficient to induce WGDs. Our results link these WGDs to a reduced incorporation of the histone variant H2A.Z to chromatin. Moreover, we show that high levels of histones promote Swe1WEE1 stabilisation thereby triggering the phosphorylation and inhibition of Cdc28CDK1 through a mechanism different of the canonical DNA damage response. Our results link high levels of histones to a specific type of genome instability that is quite frequently observed in cancer and uncovers a new mechanism that might be able to respond to high levels of histones.
Collapse
Affiliation(s)
- Douglas Maya Miles
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| | - Xenia Peñate
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Trinidad Sanmartín Olmo
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Frederic Jourquin
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| | - Maria Cruz Muñoz Centeno
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Manuel Mendoza
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Marie-Noelle Simon
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| | - Sebastian Chavez
- Instituto de Biomedicina de Sevilla, Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Vincent Geli
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Equipe Labellisée Ligue, Marseille, France
| |
Collapse
|
39
|
Andley UP, Tycksen E, McGlasson-Naumann BN, Hamilton PD. Probing the changes in gene expression due to α-crystallin mutations in mouse models of hereditary human cataract. PLoS One 2018; 13:e0190817. [PMID: 29338044 PMCID: PMC5770019 DOI: 10.1371/journal.pone.0190817] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022] Open
Abstract
The mammalian eye lens expresses a high concentration of crystallins (α, β and γ-crystallins) to maintain the refractive index essential for lens transparency. Crystallins are long-lived proteins that do not turnover throughout life. The structural destabilization of crystallins by UV exposure, glycation, oxidative stress and mutations in crystallin genes leads to protein aggregation and development of cataracts. Several destabilizing mutations in crystallin genes are linked with human autosomal dominant hereditary cataracts. To investigate the mechanism by which the α-crystallin mutations Cryaa-R49C and Cryab-R120G lead to cataract formation, we determined whether these mutations cause an altered expression of specific transcripts in the lens at an early postnatal age by RNA-seq analysis. Using knock-in mouse models previously generated in our laboratory, in the present work, we identified genes that exhibited altered abundance in the mutant lenses, including decreased transcripts for Clic5, an intracellular water channel in Cryaa-R49C heterozygous mutant lenses, and increased transcripts for Eno1b in Cryab-R120G heterozygous mutant lenses. In addition, RNA-seq analysis revealed increased histones H2B, H2A, and H4 gene expression in Cryaa-R49C mutant lenses, suggesting that the αA-crystallin mutation regulates histone expression via a transcriptional mechanism. Additionally, these studies confirmed the increased expression of histones H2B, H2A, and H4 by proteomic analysis of Cryaa-R49C knock-in and Cryaa;Cryab gene knockout lenses reported previously. Taken together, these findings offer additional insight into the early transcriptional changes caused by Cryaa and Cryab mutations associated with autosomal dominant human cataracts, and indicate that the transcript levels of certain genes are affected by the expression of mutant α-crystallin in vivo.
Collapse
Affiliation(s)
- Usha P. Andley
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
| | - Eric Tycksen
- Genome Technology Access Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brittney N. McGlasson-Naumann
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Paul D. Hamilton
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
| |
Collapse
|
40
|
Amulic B, Knackstedt SL, Abu Abed U, Deigendesch N, Harbort CJ, Caffrey BE, Brinkmann V, Heppner FL, Hinds PW, Zychlinsky A. Cell-Cycle Proteins Control Production of Neutrophil Extracellular Traps. Dev Cell 2017; 43:449-462.e5. [DOI: 10.1016/j.devcel.2017.10.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 07/12/2017] [Accepted: 10/09/2017] [Indexed: 01/09/2023]
|
41
|
Alexiadis A, Delidakis C, Kalantidis K. Snipper, an Eri1 homologue, affects histone mRNA abundance and is crucial for normal Drosophila melanogaster development. FEBS Lett 2017. [PMID: 28626879 DOI: 10.1002/1873-3468.12719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The conserved 3'-5' RNA exonuclease ERI1 is implicated in RNA interference inhibition, 5.8S rRNA maturation and histone mRNA maturation and turnover. The single ERI1 homologue in Drosophila melanogaster Snipper (Snp) is a 3'-5' exonuclease, but its in vivo function remains elusive. Here, we report Snp requirement for normal Drosophila development, since its perturbation leads to larval arrest and tissue-specific downregulation results in abnormal tissue development. Additionally, Snp directly interacts with histone mRNA, and its depletion results in drastic reduction in histone transcript levels. We propose that Snp protects the 3'-ends of histone mRNAs and upon its absence, histone transcripts are readily degraded. This in turn may lead to cell cycle delay or arrest, causing growth arrest and developmental perturbations.
Collapse
Affiliation(s)
- Anastasios Alexiadis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| | - Christos Delidakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| |
Collapse
|
42
|
Onderak AM, Anderson JT. Loss of the RNA helicase SKIV2L2 impairs mitotic progression and replication-dependent histone mRNA turnover in murine cell lines. RNA (NEW YORK, N.Y.) 2017; 23:910-926. [PMID: 28351885 PMCID: PMC5435864 DOI: 10.1261/rna.060640.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/02/2017] [Indexed: 06/06/2023]
Abstract
RNA surveillance via the nuclear exosome requires cofactors such as the helicase SKIV2L2 to process and degrade certain noncoding RNAs. This research aimed to characterize the phenotype associated with RNAi knockdown of Skiv2l2 in two murine cancer cell lines: Neuro2A and P19. SKIV2L2 depletion in Neuro2A and P19 cells induced changes in gene expression indicative of cell differentiation and reduced cellular proliferation by 30%. Propidium iodide-based cell-cycle analysis of Skiv2l2 knockdown cells revealed defective progression through the G2/M phase and an accumulation of mitotic cells, suggesting SKIV2L2 contributes to mitotic progression. Since SKIV2L2 targets RNAs to the nuclear exosome for processing and degradation, we identified RNA targets elevated in cells depleted of SKIV2L2 that could account for the observed twofold increase in mitotic cells. Skiv2l2 knockdown cells accumulated replication-dependent histone mRNAs, among other RNAs, that could impede mitotic progression and indirectly trigger differentiation.
Collapse
Affiliation(s)
- Alexis M Onderak
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, USA
| | - James T Anderson
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, USA
| |
Collapse
|
43
|
Prado F, Maya D. Regulation of Replication Fork Advance and Stability by Nucleosome Assembly. Genes (Basel) 2017; 8:genes8020049. [PMID: 28125036 PMCID: PMC5333038 DOI: 10.3390/genes8020049] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/04/2017] [Accepted: 01/16/2017] [Indexed: 12/13/2022] Open
Abstract
The advance of replication forks to duplicate chromosomes in dividing cells requires the disassembly of nucleosomes ahead of the fork and the rapid assembly of parental and de novo histones at the newly synthesized strands behind the fork. Replication-coupled chromatin assembly provides a unique opportunity to regulate fork advance and stability. Through post-translational histone modifications and tightly regulated physical and genetic interactions between chromatin assembly factors and replisome components, chromatin assembly: (1) controls the rate of DNA synthesis and adjusts it to histone availability; (2) provides a mechanism to protect the integrity of the advancing fork; and (3) regulates the mechanisms of DNA damage tolerance in response to replication-blocking lesions. Uncoupling DNA synthesis from nucleosome assembly has deleterious effects on genome integrity and cell cycle progression and is linked to genetic diseases, cancer, and aging.
Collapse
Affiliation(s)
- Felix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), Spanish National Research Council (CSIC), Seville 41092, Spain.
| | - Douglas Maya
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), Spanish National Research Council (CSIC), Seville 41092, Spain.
| |
Collapse
|
44
|
El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J. MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones. Epigenetics Chromatin 2017; 10:2. [PMID: 28096900 PMCID: PMC5223428 DOI: 10.1186/s13072-016-0109-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants. RESULTS We propose two proteomics-oriented manually curated databases for mouse and human histone variants. We manually curated >1700 gene, transcript and protein entries to produce a non-redundant list of 83 mouse and 85 human histones. These entries were annotated in accordance with the current nomenclature and unified with the "HistoneDB2.0 with Variants" database. This resource is provided in a format that can be directly read by programs used for mass spectrometry data interpretation. In addition, it was used to interpret mass spectrometry data acquired on histones extracted from mouse testis. Several histone variants, which had so far only been inferred by homology or detected at the RNA level, were detected by mass spectrometry, confirming the existence of their protein form. CONCLUSIONS Mouse and human histone entries were collected from different databases and subsequently curated to produce a non-redundant protein-centric resource, MS_HistoneDB. It is dedicated to the proteomic study of histones in mouse and human and will hopefully facilitate the identification and functional study of histone variants.
Collapse
Affiliation(s)
- Sara El Kennani
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Annie Adrait
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Saadi Khochbin
- CNRS UMR 5309 INSERM U1209, Institute of Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - Christophe Bruley
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Delphine Pflieger
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| | - Jérôme Govin
- INSERM, U1038, CEA, BIG FR CNRS 3425-BGE, Université Grenoble Alpes, Grenoble, France
| |
Collapse
|
45
|
Sokolova M, Turunen M, Mortusewicz O, Kivioja T, Herr P, Vähärautio A, Björklund M, Taipale M, Helleday T, Taipale J. Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion. Cell Cycle 2016; 16:189-199. [PMID: 27929715 PMCID: PMC5283814 DOI: 10.1080/15384101.2016.1261765] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
To identify cell cycle regulators that enable cancer cells to replicate DNA and divide in an unrestricted manner, we performed a parallel genome-wide RNAi screen in normal and cancer cell lines. In addition to many shared regulators, we found that tumor and normal cells are differentially sensitive to loss of the histone genes transcriptional regulator CASP8AP2. In cancer cells, loss of CASP8AP2 leads to a failure to synthesize sufficient amount of histones in the S-phase of the cell cycle, resulting in slowing of individual replication forks. Despite this, DNA replication fails to arrest, and tumor cells progress in an elongated S-phase that lasts several days, finally resulting in death of most of the affected cells. In contrast, depletion of CASP8AP2 in normal cells triggers a response that arrests viable cells in S-phase. The arrest is dependent on p53, and preceded by accumulation of markers of DNA damage, indicating that nucleosome depletion is sensed in normal cells via a DNA-damage -like response that is defective in tumor cells.
Collapse
Affiliation(s)
- Maria Sokolova
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Mikko Turunen
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Oliver Mortusewicz
- b Science for Life laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Teemu Kivioja
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Patrick Herr
- b Science for Life laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Anna Vähärautio
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Mikael Björklund
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Minna Taipale
- c Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Thomas Helleday
- b Science for Life laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Jussi Taipale
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland.,c Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| |
Collapse
|
46
|
Yuan K, Seller CA, Shermoen AW, O'Farrell PH. Timing the Drosophila Mid-Blastula Transition: A Cell Cycle-Centered View. Trends Genet 2016; 32:496-507. [PMID: 27339317 DOI: 10.1016/j.tig.2016.05.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/19/2016] [Accepted: 05/23/2016] [Indexed: 11/18/2022]
Abstract
At the mid-blastula transition (MBT), externally developing embryos refocus from increasing cell number to elaboration of the body plan. Studies in Drosophila reveal a sequence of changes in regulators of Cyclin:Cdk1 that increasingly restricts the activity of this cell cycle kinase to slow cell cycles during early embryogenesis. By reviewing these events, we provide an outline of the mechanisms slowing the cell cycle at and around the time of MBT. The perspectives developed should provide a guiding paradigm for the study of other MBT changes as the embryo transits from maternal control to a regulatory program centered on the expression of zygotic genes.
Collapse
Affiliation(s)
- Kai Yuan
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Charles A Seller
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Antony W Shermoen
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA 94158, USA
| | - Patrick H O'Farrell
- Department of Biophysics and Biochemistry, University of California San Francisco (UCSF), San Francisco, CA 94158, USA.
| |
Collapse
|
47
|
Ramachandran S, Henikoff S. Transcriptional Regulators Compete with Nucleosomes Post-replication. Cell 2016; 165:580-92. [PMID: 27062929 PMCID: PMC4855302 DOI: 10.1016/j.cell.2016.02.062] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 12/08/2015] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
Every nucleosome across the genome must be disrupted and reformed when the replication fork passes, but how chromatin organization is re-established following replication is unknown. To address this problem, we have developed Mapping In vivo Nascent Chromatin with EdU and sequencing (MINCE-seq) to characterize the genome-wide location of nucleosomes and other chromatin proteins behind replication forks at high temporal and spatial resolution. We find that the characteristic chromatin landscape at Drosophila promoters and enhancers is lost upon replication. The most conspicuous changes are at promoters that have high levels of RNA polymerase II (RNAPII) stalling and DNA accessibility and show specific enrichment for the BRM remodeler. Enhancer chromatin is also disrupted during replication, suggesting a role for transcription factor (TF) competition in nucleosome re-establishment. Thus, the characteristic nucleosome landscape emerges from a uniformly packaged genome by the action of TFs, RNAPII, and remodelers minutes after replication fork passage.
Collapse
Affiliation(s)
- Srinivas Ramachandran
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
| |
Collapse
|
48
|
Toompuu M, Kärblane K, Pata P, Truve E, Sarmiento C. ABCE1 is essential for S phase progression in human cells. Cell Cycle 2016; 15:1234-47. [PMID: 26985706 DOI: 10.1080/15384101.2016.1160972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
ABCE1 is a highly conserved protein universally present in eukaryotes and archaea, which is crucial for the viability of different organisms. First identified as RNase L inhibitor, ABCE1 is currently recognized as an essential translation factor involved in several stages of eukaryotic translation and ribosome biogenesis. The nature of vital functions of ABCE1, however, remains unexplained. Here, we study the role of ABCE1 in human cell proliferation and its possible connection to translation. We show that ABCE1 depletion by siRNA results in a decreased rate of cell growth due to accumulation of cells in S phase, which is accompanied by inefficient DNA synthesis and reduced histone mRNA and protein levels. We infer that in addition to the role in general translation, ABCE1 is involved in histone biosynthesis and DNA replication and therefore is essential for normal S phase progression. In addition, we analyze whether ABCE1 is implicated in transcript-specific translation via its association with the eIF3 complex subunits known to control the synthesis of cell proliferation-related proteins. The expression levels of a few such targets regulated by eIF3A, however, were not consistently affected by ABCE1 depletion.
Collapse
Affiliation(s)
- Marina Toompuu
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Kairi Kärblane
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Pille Pata
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Erkki Truve
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Cecilia Sarmiento
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| |
Collapse
|
49
|
Cheaib M, Dehghani Amirabad A, Nordström KJV, Schulz MH, Simon M. Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia. DNA Res 2015; 22:293-305. [PMID: 26231545 PMCID: PMC4535620 DOI: 10.1093/dnares/dsv014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/28/2015] [Indexed: 12/31/2022] Open
Abstract
Phenotypic variation of a single genotype is achieved by alterations in gene expression patterns. Regulation of such alterations depends on their time scale, where short-time adaptations differ from permanently established gene expression patterns maintained by epigenetic mechanisms. In the ciliate Paramecium, serotypes were described for an epigenetically controlled gene expression pattern of an individual multigene family. Paradoxically, individual serotypes can be triggered in Paramecium by alternating environments but are then stabilized by epigenetic mechanisms, thus raising the question to which extend their expression follows environmental stimuli. To characterize environmental adaptation in the context of epigenetically controlled serotype expression, we used RNA-seq to characterize transcriptomes of serotype pure cultures. The resulting vegetative transcriptome resource is first analysed for genes involved in the adaptive response to the altered environment. Secondly, we identified groups of genes that do not follow the adaptive response but show co-regulation with the epigenetically controlled serotype system, suggesting that their gene expression pattern becomes manifested by similar mechanisms. In our experimental set-up, serotype expression and the entire group of co-regulated genes were stable among environmental changes and only heat-shock genes altered expression of these gene groups. The data suggest that the maintenance of these gene expression patterns in a lineage represents epigenetically controlled robustness counteracting short-time adaptation processes.
Collapse
Affiliation(s)
- Miriam Cheaib
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany
| | - Azim Dehghani Amirabad
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany Cluster of Excellence for Multimodal Computing and Interaction, Saarland University and Max Planck Institute for Informatics, Saarbrücken 66123, Germany
| | - Karl J V Nordström
- Epigenetics Department, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany
| | - Marcel H Schulz
- Cluster of Excellence for Multimodal Computing and Interaction, Saarland University and Max Planck Institute for Informatics, Saarbrücken 66123, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany
| |
Collapse
|
50
|
McKay DJ, Klusza S, Penke TJR, Meers MP, Curry KP, McDaniel SL, Malek PY, Cooper SW, Tatomer DC, Lieb JD, Strahl BD, Duronio RJ, Matera AG. Interrogating the function of metazoan histones using engineered gene clusters. Dev Cell 2015; 32:373-86. [PMID: 25669886 DOI: 10.1016/j.devcel.2014.12.025] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/07/2014] [Accepted: 12/30/2014] [Indexed: 01/11/2023]
Abstract
Histones and their posttranslational modifications influence the regulation of many DNA-dependent processes. Although an essential role for histone-modifying enzymes in these processes is well established, defining the specific contribution of individual histone residues remains a challenge because many histone-modifying enzymes have nonhistone targets. This challenge is exacerbated by the paucity of suitable approaches to genetically engineer histone genes in metazoans. Here, we describe a platform in Drosophila for generating and analyzing any desired histone genotype, and we use it to test the in vivo function of three histone residues. We demonstrate that H4K20 is neither essential for DNA replication nor for completion of development, unlike inferences drawn from analyses of H4K20 methyltransferases. We also show that H3K36 is required for viability and H3K27 is essential for maintenance of cellular identity but not for gene activation. These findings highlight the power of engineering histones to interrogate genome structure and function in animals.
Collapse
Affiliation(s)
- Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephen Klusza
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Taylor J R Penke
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael P Meers
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kaitlin P Curry
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephen L McDaniel
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pamela Y Malek
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephen W Cooper
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Deirdre C Tatomer
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason D Lieb
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian D Strahl
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - A Gregory Matera
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|