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Yukawa M, Jagannathan S, Vallabh S, Kartashov AV, Chen X, Weirauch MT, Barski A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. J Exp Med 2020; 217:jem.20182009. [PMID: 31653690 PMCID: PMC7037242 DOI: 10.1084/jem.20182009] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/06/2019] [Accepted: 09/23/2019] [Indexed: 12/24/2022] Open
Abstract
Activation of T cells is dependent on the organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naive T cells within 5 h of activation. These newly opened regions were strongly enriched for the AP-1 motif, and indeed, ChIP-seq demonstrated AP-1 binding at >70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced the expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1-dependent elements with risk loci for multiple immune diseases, including multiple sclerosis, inflammatory bowel disease, and allergic disease. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.
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Affiliation(s)
- Masashi Yukawa
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sajjeev Jagannathan
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sushmitha Vallabh
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Andrey V Kartashov
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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2
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Kotliar M, Kartashov AV, Barski A. CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language. Gigascience 2019; 8:giz084. [PMID: 31321430 PMCID: PMC6639121 DOI: 10.1093/gigascience/giz084] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/21/2019] [Accepted: 06/21/2019] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Massive growth in the amount of research data and computational analysis has led to increased use of pipeline managers in biomedical computational research. However, each of the >100 such managers uses its own way to describe pipelines, leading to difficulty porting workflows to different environments and therefore poor reproducibility of computational studies. For this reason, the Common Workflow Language (CWL) was recently introduced as a specification for platform-independent workflow description, and work began to transition existing pipelines and workflow managers to CWL. FINDINGS Herein, we present CWL-Airflow, a package that adds support for CWL to the Apache Airflow pipeline manager. CWL-Airflow uses CWL version 1.0 specification and can run workflows on stand-alone MacOS/Linux servers, on clusters, or on a variety of cloud platforms. A sample CWL pipeline for processing of chromatin immunoprecipitation sequencing data is provided. CONCLUSIONS CWL-Airflow will provide users with the features of a fully fledged pipeline manager and the ability to execute CWL workflows anywhere Airflow can run-from a laptop to a cluster or cloud environment. CWL-Airflow is available under Apache License, version 2.0 (Apache-2.0), and can be downloaded from https://barski-lab.github.io/cwl-airflow, https://scicrunch.org/resolver/RRID:SCR_017196.
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Affiliation(s)
- Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
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3
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Barski A, Yukawa M, Jagannathan S, Kartashov AV, Chen X, Weirauch MT. Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.125.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Activation of T cells is dependent on organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naïve T cells within 5 hours of activation. These newly open regions were strongly enriched for the AP-1 motif, and indeed, ChIP-seq demonstrated AP-1 binding at more than 70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation, was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1–dependent elements with risk loci for multiple immune diseases, most notably multiple sclerosis. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.
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4
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Pashkovskiy PP, Soshinkova TN, Korolkova DV, Kartashov AV, Zlobin IE, Lyubimov VY, Kreslavski VD, Kuznetsov VV. The effect of light quality on the pro-/antioxidant balance, activity of photosystem II, and expression of light-dependent genes in Eutrema salsugineum callus cells. Photosynth Res 2018; 136:199-214. [PMID: 29071562 DOI: 10.1007/s11120-017-0459-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
The antioxidant balance, photochemical activity of photosystem II (PSII), and photosynthetic pigment content, as well as the expression of genes involved in the light signalling of callus lines of Eutrema salsugineum plants (earlier Thellungiella salsuginea) under different spectral light compositions were studied. Growth of callus in red light (RL, maximum 660 nm), in contrast to blue light (BL, maximum 450 nm), resulted in a lower H2O2 content and thiobarbituric acid reactive substances (TBARS). The BL increased the activities of key antioxidant enzymes in comparison with the white light (WL) and RL and demonstrated the minimum level of PSII photochemical activity. The activities of catalase (CAT) and peroxidase (POD) had the highest values in BL, which, along with the increased H2O2 and TBARS content, indicate a higher level of oxidative stress in the cells. The expression levels of the main chloroplast protein genes of PSII (PSBA and PSBD), the NADPH-dependent oxidase gene of the plasma membrane (RbohD), the protochlorophyllide oxidoreductase genes (POR B, C) involved in the biosynthesis of chlorophyll, and the key photoreceptor signalling genes (CIB1, CRY2, PhyB, PhyA, and PIF3) were determined. Possible mechanisms of light quality effects on the physiological parameters of callus cells are discussed.
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Affiliation(s)
- P P Pashkovskiy
- Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia.
| | - T N Soshinkova
- Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
| | - D V Korolkova
- Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
| | - A V Kartashov
- Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
| | - I E Zlobin
- Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
| | - V Yu Lyubimov
- Institute of Basic Biological Problems Russian Academy of Sciences, Pushchino, Russia
| | - V D Kreslavski
- Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
- Institute of Basic Biological Problems Russian Academy of Sciences, Pushchino, Russia
| | - Vl V Kuznetsov
- Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
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5
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Rochman Y, Dienger-Stambaugh K, Richgels PK, Lewkowich IP, Kartashov AV, Barski A, Khurana Hershey GK, Leonard WJ, Singh H. TSLP signaling in CD4 + T cells programs a pathogenic T helper 2 cell state. Sci Signal 2018. [PMID: 29535264 DOI: 10.1126/scisignal.aam8858] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pathogenic T helper 2 (TH2) cells, which produce increased amounts of the cytokines interleukin-5 (IL-5) and IL-13, promote allergic disorders, including asthma. Thymic stromal lymphopoietin (TSLP), a cytokine secreted by epithelial and innate immune cells, stimulates such pathogenic TH2 cell responses. We found that TSLP signaling in mouse CD4+ T cells initiated transcriptional changes associated with TH2 cell programming. IL-4 signaling amplified and stabilized the genomic response of T cells to TSLP, which increased the frequency of T cells producing IL-4, IL-5, and IL-13. Furthermore, the TSLP- and IL-4-programmed TH2 cells had a pathogenic phenotype, producing greater amounts of IL-5 and IL-13 and other proinflammatory cytokines than did TH2 cells stimulated with IL-4 alone. TSLP-mediated TH2 cell induction involved distinct molecular pathways, including activation of the transcription factor STAT5 through the kinase JAK2 and repression of the transcription factor BCL6. Mice that received wild-type CD4+ T cells had exacerbated pathogenic TH2 cell responses upon exposure to house dust mites compared to mice that received TSLP receptor-deficient CD4+ T cells. Transient TSLP signaling stably programmed pathogenic potential in memory TH2 cells. In human CD4+ T cells, TSLP and IL-4 promoted the generation of TH2 cells that produced greater amounts of IL-5 and IL-13. Compared to healthy controls, asthmatic children showed enhancement of such T cell responses in peripheral blood. Our data support a sequential cytokine model for pathogenic TH2 cell differentiation and provide a mechanistic basis for the therapeutic targeting of TSLP signaling in human allergic diseases.
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Affiliation(s)
- Yrina Rochman
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA. .,Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Krista Dienger-Stambaugh
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Phoebe K Richgels
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ian P Lewkowich
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Harinder Singh
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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6
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Barski A, Cuddapah S, Kartashov AV, Liu C, Imamichi H, Yang W, Peng W, Lane HC, Zhao K. Rapid Recall Ability of Memory T cells is Encoded in their Epigenome. Sci Rep 2017; 7:39785. [PMID: 28054639 PMCID: PMC5215294 DOI: 10.1038/srep39785] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022] Open
Abstract
Even though T-cell receptor (TCR) stimulation together with co-stimulation is sufficient for the activation of both naïve and memory T cells, the memory cells are capable of producing lineage specific cytokines much more rapidly than the naïve cells. The mechanisms behind this rapid recall response of the memory cells are still not completely understood. Here, we performed epigenetic profiling of human resting naïve, central and effector memory T cells using ChIP-Seq and found that unlike the naïve cells, the regulatory elements of the cytokine genes in the memory T cells are marked by activating histone modifications even in the resting state. Therefore, the ability to induce expression of rapid recall genes upon activation is associated with the deposition of positive histone modifications during memory T cell differentiation. We propose a model of T cell memory, in which immunological memory state is encoded epigenetically, through poising and transcriptional memory.
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Affiliation(s)
- Artem Barski
- Divisions of Allergy &Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Suresh Cuddapah
- Department of Environmental Medicine, New York University School of Medicine, NY, 10987, USA
| | - Andrey V Kartashov
- Divisions of Allergy &Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Chong Liu
- Divisions of Allergy &Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Hiromi Imamichi
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wenjing Yang
- Department of Physics, The George Washington University, D.C., 20052, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, D.C., 20052, USA
| | - H Clifford Lane
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Bian F, Gao F, Kartashov AV, Jegga AG, Barski A, Das SK. Polycomb repressive complex 1 controls uterine decidualization. Sci Rep 2016; 6:26061. [PMID: 27181215 PMCID: PMC4867636 DOI: 10.1038/srep26061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/27/2016] [Indexed: 01/21/2023] Open
Abstract
Uterine stromal cell decidualization is an essential part of the reproductive process. Decidual tissue development requires a highly regulated control of the extracellular tissue remodeling; however the mechanism of this regulation remains unknown. Through systematic expression studies, we detected that Cbx4/2, Rybp, and Ring1B [components of polycomb repressive complex 1 (PRC1)] are predominantly utilized in antimesometrial decidualization with polyploidy. Immunofluorescence analyses revealed that PRC1 members are co-localized with its functional histone modifier H2AK119ub1 (mono ubiquitination of histone-H2A at lysine-119) in polyploid cell. A potent small-molecule inhibitor of Ring1A/B E3-ubiquitin ligase or siRNA-mediated suppression of Cbx4 caused inhibition of H2AK119ub1, in conjunction with perturbation of decidualization and polyploidy development, suggesting a role for Cbx4/Ring1B-containing PRC1 in these processes. Analyses of genetic signatures by RNA-seq studies showed that the inhibition of PRC1 function affects 238 genes (154 up and 84 down) during decidualization. Functional enrichment analyses identified that about 38% genes primarily involved in extracellular processes are specifically targeted by PRC1. Furthermore, ~15% of upregulated genes exhibited a significant overlap with the upregulated Bmp2 null-induced genes in mice. Overall, Cbx4/Ring1B-containing PRC1 controls decidualization via regulation of extracellular gene remodeling functions and sheds new insights into underlying molecular mechanism(s) through transcriptional repression regulation.
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Affiliation(s)
- Fenghua Bian
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Fei Gao
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrey V Kartashov
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Anil G Jegga
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sanjoy K Das
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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8
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Jagannathan L, Jose CC, Arita A, Kluz T, Sun H, Zhang X, Yao Y, Kartashov AV, Barski A, Costa M, Cuddapah S. Nuclear Factor κB1/RelA Mediates Inflammation in Human Lung Epithelial Cells at Atmospheric Oxygen Levels. J Cell Physiol 2015; 231:1611-20. [PMID: 26588041 DOI: 10.1002/jcp.25262] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 01/04/2023]
Abstract
Oxygen levels range from 2% to 9% in vivo. Atmospheric O2 levels (21%) are known to induce cell proliferation defects and cellular senescence in primary cell cultures. However, the mechanistic basis of the deleterious effects of higher O2 levels is not fully understood. On the other hand, immortalized cells including cancer cell lines, which evade cellular senescence are normally cultured at 21% O2 and the effects of higher O2 on these cells are understudied. Here, we addressed this problem by culturing immortalized human bronchial epithelial (BEAS-2B) cells at ambient atmospheric, 21% O2 and lower, 10% O2. Our results show increased inflammatory response at 21% O2 but not at 10% O2. We found higher RelA binding at the NF-κB1/RelA target gene promoters as well as upregulation of several pro-inflammatory cytokines in cells cultured at 21% O2. RelA knockdown prevented the upregulation of the pro-inflammatory cytokines at 21% O2, suggesting NF-κB1/RelA as a major mediator of inflammatory response in cells cultured at 21% O2. Interestingly, unlike the 21% O2 cultured cells, exposure of 10% O2 cultured cells to H2O2 did not elicit inflammatory response, suggesting increased ability to tolerate oxidative stress in cells cultured at lower O2 levels.
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Affiliation(s)
- Lakshmanan Jagannathan
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Cynthia C Jose
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Adriana Arita
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Thomas Kluz
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Xiaoru Zhang
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Yixin Yao
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Andrey V Kartashov
- Division of Allergy and Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Artem Barski
- Division of Allergy and Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Suresh Cuddapah
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
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9
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Bouffi C, Kartashov AV, Schollaert KL, Chen X, Bacon WC, Weirauch MT, Barski A, Fulkerson PC. Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis. J Immunol 2015; 195:2683-95. [PMID: 26268651 DOI: 10.4049/jimmunol.1500510] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/14/2015] [Indexed: 12/13/2022]
Abstract
The production of mature eosinophils (Eos) is a tightly orchestrated process with the aim to sustain normal Eos levels in tissues while also maintaining low numbers of these complex and sensitive cells in the blood. To identify regulators of homeostatic eosinophilopoiesis in mice, we took a global approach to identify genome-wide transcriptome and epigenome changes that occur during homeostasis at critical developmental stages, including Eos-lineage commitment and lineage maturation. Our analyses revealed a markedly greater number of transcriptome alterations associated with Eos maturation (1199 genes) than with Eos-lineage commitment (490 genes), highlighting the greater transcriptional investment necessary for differentiation. Eos-lineage-committed progenitors (EoPs) were noted to express high levels of granule proteins and contain granules with an ultrastructure distinct from that of mature resting Eos. Our analyses also delineated a 976-gene Eos-lineage transcriptome that included a repertoire of 56 transcription factors, many of which have never previously been associated with Eos. EoPs and Eos, but not granulocyte-monocyte progenitors or neutrophils, expressed Helios and Aiolos, members of the Ikaros family of transcription factors, which regulate gene expression via modulation of chromatin structure and DNA accessibility. Epigenetic studies revealed a distinct distribution of active chromatin marks between genes induced with lineage commitment and genes induced with cell maturation during Eos development. In addition, Aiolos and Helios binding sites were significantly enriched in genes expressed by EoPs and Eos with active chromatin, highlighting a potential novel role for Helios and Aiolos in regulating gene expression during Eos development.
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Affiliation(s)
- Carine Bouffi
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Kaila L Schollaert
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Xiaoting Chen
- School of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH 45221
| | - W Clark Bacon
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229; and
| | - Artem Barski
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229; Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Patricia C Fulkerson
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229;
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10
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Kartashov AV, Barski A. BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. Genome Biol 2015; 16:158. [PMID: 26248465 PMCID: PMC4531538 DOI: 10.1186/s13059-015-0720-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/07/2015] [Indexed: 01/24/2023] Open
Abstract
High-throughput sequencing has revolutionized biology by enhancing our ability to perform genome-wide studies. However, due to lack of bioinformatics expertise, modern technologies are still beyond the capabilities of many laboratories. Herein, we present the BioWardrobe platform, which allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly web interface, without the need for programming expertise. Predefined pipelines allow users to download data, visualize results on a genome browser, calculate RPKMs (reads per kilobase per million) and identify peaks. Advanced capabilities include differential gene expression and binding analysis, and creation of average tag -density profiles and heatmaps. BioWardrobe can be found at http://biowardrobe.com.
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Affiliation(s)
- Andrey V Kartashov
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA. .,Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
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11
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Abstract
Background The male germline transcriptome changes dramatically during the mitosis-to-meiosis transition to activate late spermatogenesis genes and to transiently suppress genes commonly expressed in somatic lineages and spermatogenesis progenitor cells, termed somatic/progenitor genes. Results These changes reflect epigenetic regulation. Induction of late spermatogenesis genes during spermatogenesis is facilitated by poised chromatin established in the stem cell phases of spermatogonia, whereas silencing of somatic/progenitor genes during meiosis and postmeiosis is associated with formation of bivalent domains which also allows the recovery of the somatic/progenitor program after fertilization. Importantly, during spermatogenesis mechanisms of epigenetic regulation on sex chromosomes are different from autosomes: X-linked somatic/progenitor genes are suppressed by meiotic sex chromosome inactivation without deposition of H3K27me3. Conclusions Our results suggest that bivalent H3K27me3 and H3K4me2/3 domains are not limited to developmental promoters (which maintain bivalent domains that are silent throughout the reproductive cycle), but also underlie reversible silencing of somatic/progenitor genes during the mitosis-to-meiosis transition in late spermatogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0159-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ho-Su Sin
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.,Present address: Department of Developmental Biology, Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA
| | - Kazuteru Hasegawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.,Present address: Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Artem Barski
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.
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Rochman Y, Yukawa M, Kartashov AV, Barski A. Functional characterization of human T cell hyporesponsiveness induced by CTLA4-Ig. PLoS One 2015; 10:e0122198. [PMID: 25860138 PMCID: PMC4393265 DOI: 10.1371/journal.pone.0122198] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/08/2015] [Indexed: 01/08/2023] Open
Abstract
During activation, T cells integrate multiple signals from APCs and cytokine milieu. The blockade of these signals can have clinical benefits as exemplified by CTLA4-Ig, which blocks interaction of B7 co-stimulatory molecules on APCs with CD28 on T cells. Variants of CTLA4-Ig, abatacept and belatacept are FDA approved as immunosuppressive agents in arthritis and transplantation, yet murine studies suggested that CTLA4-Ig could be beneficial in a number of other diseases. However, detailed analysis of human CD4 cell hyporesponsivness induced by CTLA4-Ig has not been performed. Herein, we established a model to study the effect of CTLA4-Ig on the activation of human naïve T cells in a human mixed lymphocytes system. Comparison of human CD4 cells activated in the presence or absence of CTLA4-Ig showed that co-stimulation blockade during TCR activation does not affect NFAT signaling but results in decreased activation of NF-κB and AP-1 transcription factors followed by a profound decrease in proliferation and cytokine production. The resulting T cells become hyporesponsive to secondary activation and, although capable of receiving TCR signals, fail to proliferate or produce cytokines, demonstrating properties of anergic cells. However, unlike some models of T cell anergy, these cells did not possess increased levels of the TCR signaling inhibitor CBLB. Rather, the CTLA4-Ig-induced hyporesponsiveness was associated with an elevated level of p27kip1 cyclin-dependent kinase inhibitor.
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Affiliation(s)
- Yrina Rochman
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Masashi Yukawa
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Andrey V. Kartashov
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
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Hasegawa K, Sin HS, Maezawa S, Broering TJ, Kartashov AV, Alavattam KG, Ichijima Y, Zhang F, Bacon WC, Greis KD, Andreassen PR, Barski A, Namekawa SH. SCML2 establishes the male germline epigenome through regulation of histone H2A ubiquitination. Dev Cell 2015; 32:574-88. [PMID: 25703348 PMCID: PMC4391279 DOI: 10.1016/j.devcel.2015.01.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 12/23/2014] [Accepted: 01/16/2015] [Indexed: 01/03/2023]
Abstract
Gametogenesis is dependent on the expression of germline-specific genes. However, it remains unknown how the germline epigenome is distinctly established from that of somatic lineages. Here we show that genes commonly expressed in somatic lineages and spermatogenesis-progenitor cells undergo repression in a genome-wide manner in late stages of the male germline and identify underlying mechanisms. SCML2, a germline-specific subunit of a Polycomb repressive complex 1 (PRC1), establishes the unique epigenome of the male germline through two distinct antithetical mechanisms. SCML2 works with PRC1 and promotes RNF2-dependent ubiquitination of H2A, thereby marking somatic/progenitor genes on autosomes for repression. Paradoxically, SCML2 also prevents RNF2-dependent ubiquitination of H2A on sex chromosomes during meiosis, thereby enabling unique epigenetic programming of sex chromosomes for male reproduction. Our results reveal divergent mechanisms involving a shared regulator by which the male germline epigenome is distinguished from that of the soma and progenitor cells.
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Affiliation(s)
- Kazuteru Hasegawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Ho-Su Sin
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Tyler J Broering
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Yosuke Ichijima
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - W Clark Bacon
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Kenneth D Greis
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Artem Barski
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.
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Sin HS, Barski A, Zhang F, Kartashov AV, Nussenzweig A, Chen J, Andreassen PR, Namekawa SH. RNF8 regulates active epigenetic modifications and escape gene activation from inactive sex chromosomes in post-meiotic spermatids. Genes Dev 2013; 26:2737-48. [PMID: 23249736 DOI: 10.1101/gad.202713.112] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sex chromosomes are uniquely subject to chromosome-wide silencing during male meiosis, and silencing persists into post-meiotic spermatids. Against this background, a select set of sex chromosome-linked genes escapes silencing and is activated in post-meiotic spermatids. Here, we identify a novel mechanism that regulates escape gene activation in an environment of chromosome-wide silencing in murine germ cells. We show that RNF8-dependent ubiquitination of histone H2A during meiosis establishes active epigenetic modifications, including dimethylation of H3K4 on the sex chromosomes. RNF8-dependent active epigenetic memory, defined by dimethylation of H3K4, persists throughout meiotic division. Various active epigenetic modifications are subsequently established on the sex chromosomes in post-meiotic spermatids. These RNF8-dependent modifications include trimethylation of H3K4, histone lysine crotonylation (Kcr), and incorporation of the histone variant H2AFZ. RNF8-dependent epigenetic programming regulates escape gene activation from inactive sex chromosomes in post-meiotic spermatids. Kcr accumulates at transcriptional start sites of sex-linked genes activated in an RNF8-dependent manner, and a chromatin conformational change is associated with RNF8-dependent epigenetic programming. Furthermore, we demonstrate that this RNF8-dependent pathway is distinct from that which recognizes DNA double-strand breaks. Our results establish a novel connection between a DNA damage response factor (RNF8) and epigenetic programming, specifically in establishing active epigenetic modifications and gene activation.
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Affiliation(s)
- Ho-Su Sin
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
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Kartashov AV, Serafini G, Dong M, Shipovskov S, Gazaryan I, Besenbacher F, Ferapontova EE. Long-range electron transfer in recombinant peroxidases anisotropically orientated on gold electrodes. Phys Chem Chem Phys 2010; 12:10098-107. [DOI: 10.1039/c0cp00605j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Boguslavskaya LS, Panteleeva IY, Morozova TV, Kartashov AV, Chuvatkin NN. α-Fluoroacrylates: synthesis, properties and use. Russ Chem Rev 2007. [DOI: 10.1070/rc1990v059n09abeh003563] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Boguslavskaya LS, Kartashov AV, Chuvatkin NN. Selective replacement of hydrogen at a saturated carbon atom under the action of oxidising agents. Russ Chem Rev 2007. [DOI: 10.1070/rc1990v059n06abeh003539] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Boguslavskaya LS, Chuvatkin NN, Kartashov AV. Oxidative Substitution of Halogen Atoms in Organic Halogeno-derivatives — a New Type of Nucleophilic Substitution Reactions at a Saturated Carbon Atom. Russ Chem Rev 2007. [DOI: 10.1070/rc1988v057n08abeh003388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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