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von Grüning H, Coradin M, Mendoza MR, Reader J, Sidoli S, Garcia BA, Birkholtz LM. A dynamic and combinatorial histone code drives malaria parasite asexual and sexual development. Mol Cell Proteomics 2022; 21:100199. [PMID: 35051657 PMCID: PMC8941266 DOI: 10.1016/j.mcpro.2022.100199] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/07/2023] Open
Abstract
Histone posttranslational modifications (PTMs) frequently co-occur on the same chromatin domains or even in the same molecule. It is now established that these “histone codes” are the result of cross talk between enzymes that catalyze multiple PTMs with univocal readout as compared with these PTMs in isolation. Here, we performed a comprehensive identification and quantification of histone codes of the malaria parasite, Plasmodium falciparum. We used advanced quantitative middle-down proteomics to identify combinations of PTMs in both the proliferative, asexual stages and transmissible, sexual gametocyte stages of P. falciparum. We provide an updated, high-resolution compendium of 77 PTMs on H3 and H3.3, of which 34 are newly identified in P. falciparum. Coexisting PTMs with unique stage distinctions were identified, indicating that many of these combinatorial PTMs are associated with specific stages of the parasite life cycle. We focused on the code H3R17me2K18acK23ac for its unique presence in mature gametocytes; chromatin proteomics identified a gametocyte-specific SAGA-like effector complex including the transcription factor AP2-G2, which we tied to this specific histone code, as involved in regulating gene expression in mature gametocytes. Ultimately, this study unveils previously undiscovered histone PTMs and their functional relationship with coexisting partners. These results highlight that investigating chromatin regulation in the parasite using single histone PTM assays might overlook higher-order gene regulation for distinct proliferation and differentiation processes. First middle-down chromatin proteomics compendium of the malaria parasite, Plasmodium falciparum. Novel histone PTMs (including arginine methylation) in both asexual parasites and transmissible gametocytes. Histone PTM cross talk is dynamic life cycle stage stratified. Gametocytes rely on histone PTM connectivity to allow onward transmission. AP2-G2 is an important effector of H3K18acK23ac in mature gametocytes.
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Affiliation(s)
- Hilde von Grüning
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa; Institute for Sustainable Malaria Control, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa
| | - Mariel Coradin
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariel R Mendoza
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa; Institute for Sustainable Malaria Control, University of Pretoria, Private bag X20, Hatfield, Pretoria, South Africa.
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Function of cofactor Akirin2 in the regulation of gene expression in model human Caucasian neutrophil-like HL60 cells. Biosci Rep 2021; 41:229302. [PMID: 34291801 PMCID: PMC8298264 DOI: 10.1042/bsr20211120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/22/2022] Open
Abstract
The Akirin family of transcription cofactors are involved throughout the metazoan in the regulation of different biological processes (BPs) such as immunity, interdigital regression, muscle and neural development. Akirin do not have catalytic or DNA-binding capability and exert its regulatory function primarily through interacting proteins such as transcription factors, chromatin remodelers, and RNA-associated proteins. In the present study, we focused on the human Akirin2 regulome and interactome in neutrophil-like model human Caucasian promyelocytic leukemia HL60 cells. Our hypothesis is that metazoan evolved to have Akirin2 functional complements and different Akirin2-mediated mechanisms for the regulation of gene expression. To address this hypothesis, experiments were conducted using transcriptomics, proteomics and systems biology approaches in akirin2 knockdown and wildtype (WT) HL60 cells to characterize Akirin2 gene/protein targets, functional complements and to provide evidence of different mechanisms that may be involved in Akirin2-mediated regulation of gene expression. The results revealed Akirin2 gene/protein targets in multiple BPs with higher representation of immunity and identified immune response genes as candidate Akirin2 functional complements. In addition to linking chromatin remodelers with transcriptional activation, Akirin2 also interacts with histone H3.1 for regulation of gene expression.
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Tun N, Shibata Y, Soe MT, Htun MW, Koji T. Histone deacetylase inhibitors suppress transdifferentiation of gonadotrophs to prolactin cells and proliferation of prolactin cells induced by diethylstilbestrol in male mouse pituitary. Histochem Cell Biol 2018; 151:291-303. [DOI: 10.1007/s00418-018-1760-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2018] [Indexed: 01/11/2023]
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Dean A, van den Driesche S, Wang Y, McKinnell C, Macpherson S, Eddie SL, Kinnell H, Hurtado-Gonzalez P, Chambers TJ, Stevenson K, Wolfinger E, Hrabalkova L, Calarrao A, Bayne RA, Hagen CP, Mitchell RT, Anderson RA, Sharpe RM. Analgesic exposure in pregnant rats affects fetal germ cell development with inter-generational reproductive consequences. Sci Rep 2016; 6:19789. [PMID: 26813099 PMCID: PMC4728385 DOI: 10.1038/srep19789] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/18/2015] [Indexed: 02/06/2023] Open
Abstract
Analgesics which affect prostaglandin (PG) pathways are used by most pregnant women. As germ cells (GC) undergo developmental and epigenetic changes in fetal life and are PG targets, we investigated if exposure of pregnant rats to analgesics (indomethacin or acetaminophen) affected GC development and reproductive function in resulting offspring (F1) or in the F2 generation. Exposure to either analgesic reduced F1 fetal GC number in both sexes and altered the tempo of fetal GC development sex-dependently, with delayed meiotic entry in oogonia but accelerated GC differentiation in males. These effects persisted in adult F1 females as reduced ovarian and litter size, whereas F1 males recovered normal GC numbers and fertility by adulthood. F2 offspring deriving from an analgesic-exposed F1 parent also exhibited sex-specific changes. F2 males exhibited normal reproductive development whereas F2 females had smaller ovaries and reduced follicle numbers during puberty/adulthood; as similar changes were found for F2 offspring of analgesic-exposed F1 fathers or mothers, we interpret this as potentially indicating an analgesic-induced change to GC in F1. Assuming our results are translatable to humans, they raise concerns that analgesic use in pregnancy could potentially affect fertility of resulting daughters and grand-daughters.
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Affiliation(s)
- Afshan Dean
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Sander van den Driesche
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Yili Wang
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Chris McKinnell
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Sheila Macpherson
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Sharon L Eddie
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Hazel Kinnell
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Pablo Hurtado-Gonzalez
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Tom J Chambers
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Kerrie Stevenson
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Elke Wolfinger
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Lenka Hrabalkova
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Ana Calarrao
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Rosey Al Bayne
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Casper P Hagen
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Rod T Mitchell
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Richard A Anderson
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Richard M Sharpe
- MRC Centre for Reproductive Health, The Queen's Medical Research Institute University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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