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Hviid L, Jensen AR, Deitsch KW. PfEMP1 and var genes - Still of key importance in Plasmodium falciparum malaria pathogenesis and immunity. ADVANCES IN PARASITOLOGY 2024; 125:53-103. [PMID: 39095112 DOI: 10.1016/bs.apar.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The most severe form of malaria, caused by infection with Plasmodium falciparum parasites, continues to be an important cause of human suffering and poverty. The P. falciparum erythrocyte membrane protein 1 (PfEMP1) family of clonally variant antigens, which mediates the adhesion of infected erythrocytes to the vascular endothelium in various tissues and organs, is a central component of the pathogenesis of the disease and a key target of the acquired immune response to malaria. Much new knowledge has accumulated since we published a systematic overview of the PfEMP1 family almost ten years ago. In this chapter, we therefore aim to summarize research progress since 2015 on the structure, function, regulation etc. of this key protein family of arguably the most important human parasite. Recent insights regarding PfEMP1-specific immune responses and PfEMP1-specific vaccination against malaria, as well as an outlook for the coming years are also covered.
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Affiliation(s)
- Lars Hviid
- Centre for translational Medicine and Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.
| | - Anja R Jensen
- Centre for translational Medicine and Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States
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2
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Azizan S, Selvarajah SA, Tang J, Jeninga MD, Schulz D, Pareek K, Herr T, Day KP, De Koning-Ward TF, Petter M, Duffy MF. The P. falciparum alternative histones Pf H2A.Z and Pf H2B.Z are dynamically acetylated and antagonized by PfSir2 histone deacetylases at heterochromatin boundaries. mBio 2023; 14:e0201423. [PMID: 37882786 PMCID: PMC10746207 DOI: 10.1128/mbio.02014-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The malaria parasite Plasmodium falciparum relies on variant expression of members of multi-gene families as a strategy for environmental adaptation to promote parasite survival and pathogenesis. These genes are located in transcriptionally silenced DNA regions. A limited number of these genes escape gene silencing, and switching between them confers variant fitness on parasite progeny. Here, we show that PfSir2 histone deacetylases antagonize DNA-interacting acetylated alternative histones at the boundaries between active and silent DNA. This finding implicates acetylated alternative histones in the mechanism regulating P. falciparum variant gene silencing and thus malaria pathogenesis. This work also revealed that acetylation of alternative histones at promoters is dynamically associated with promoter activity across the genome, implicating acetylation of alternative histones in gene regulation genome wide. Understanding mechanisms of gene regulation in P. falciparum may aid in the development of new therapeutic strategies for malaria, which killed 619,000 people in 2021.
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Affiliation(s)
- Suffian Azizan
- School of BioSciences, The University of Melbourne, Melbourne, Australia
- Bio21 Institute, Parkville, Victoria, Australia
| | - Shamista A. Selvarajah
- School of BioSciences, The University of Melbourne, Melbourne, Australia
- Bio21 Institute, Parkville, Victoria, Australia
| | - Jingyi Tang
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, Australia
| | - Myriam D. Jeninga
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | | | - Kapil Pareek
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Tamara Herr
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Karen P. Day
- Bio21 Institute, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tania F. De Koning-Ward
- School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, Australia
| | - Michaela Petter
- Universitätsklinikum Erlangen, Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Michael F. Duffy
- Bio21 Institute, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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3
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Hristov BH, Noble WS, Bertero A. Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558852. [PMID: 37790381 PMCID: PMC10542540 DOI: 10.1101/2023.09.21.558852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Most studies of genome organization have focused on intra-chromosomal (cis) contacts because they harbor key features such as DNA loops and topologically associating domains. Inter-chromosomal (trans) contacts have received much less attention, and tools for interrogating potential biologically relevant trans structures are lacking. Here, we develop a computational framework to identify sets of loci that jointly interact in trans from Hi-C data. This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans-contacting loci. We validate trans-C in three increasingly complex models of established trans contacts: the Plasmodium falciparum var genes, the mouse olfactory receptor "Greek islands", and the human RBM20 cardiac splicing factory. We then apply trans-C to systematically test the hypothesis that genes co-regulated by the same trans-acting element (i.e., a transcription or splicing factor) co-localize in three dimensions to form "RNA factories" that maximize the efficiency and accuracy of RNA biogenesis. We find that many loci with multiple binding sites of the same transcription factor interact with one another in trans, especially those bound by transcription factors with intrinsically disordered domains. Similarly, clustered binding of a subset of RNA binding proteins correlates with trans interaction of the encoding loci. These findings support the existence of trans interacting chromatin domains (TIDs) driven by RNA biogenesis. Trans-C provides an efficient computational framework for studying these and other types of trans interactions, empowering studies of a poorly understood aspect of genome architecture.
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Affiliation(s)
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
| | - Alessandro Bertero
- Molecular Biotechnology Center “Guido Tarone”, Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy
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4
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Wichers-Misterek JS, Krumkamp R, Held J, von Thien H, Wittmann I, Höppner YD, Ruge JM, Moser K, Dara A, Strauss J, Esen M, Fendel R, Sulyok Z, Jeninga MD, Kremsner PG, Sim BKL, Hoffman SL, Duffy MF, Otto TD, Gilberger TW, Silva JC, Mordmüller B, Petter M, Bachmann A. The exception that proves the rule: Virulence gene expression at the onset of Plasmodium falciparum blood stage infections. PLoS Pathog 2023; 19:e1011468. [PMID: 37384799 DOI: 10.1371/journal.ppat.1011468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Controlled human malaria infections (CHMI) are a valuable tool to study parasite gene expression in vivo under defined conditions. In previous studies, virulence gene expression was analyzed in samples from volunteers infected with the Plasmodium falciparum (Pf) NF54 isolate, which is of African origin. Here, we provide an in-depth investigation of parasite virulence gene expression in malaria-naïve European volunteers undergoing CHMI with the genetically distinct Pf 7G8 clone, originating in Brazil. Differential expression of var genes, encoding major virulence factors of Pf, PfEMP1s, was assessed in ex vivo parasite samples as well as in parasites from the in vitro cell bank culture that was used to generate the sporozoites (SPZ) for CHMI (Sanaria PfSPZ Challenge (7G8)). We report broad activation of mainly B-type subtelomeric located var genes at the onset of a 7G8 blood stage infection in naïve volunteers, mirroring the NF54 expression study and suggesting that the expression of virulence-associated genes is generally reset during transmission from the mosquito to the human host. However, in 7G8 parasites, we additionally detected a continuously expressed single C-type variant, Pf7G8_040025600, that was most highly expressed in both pre-mosquito cell bank and volunteer samples, suggesting that 7G8, unlike NF54, maintains expression of some previously expressed var variants during transmission. This suggests that in a new host, the parasite may preferentially express the variants that previously allowed successful infection and transmission. Trial registration: ClinicalTrials.gov - NCT02704533; 2018-004523-36.
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Affiliation(s)
- Jan Stephan Wichers-Misterek
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Ralf Krumkamp
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Heidrun von Thien
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Irene Wittmann
- Institute of Microbiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Yannick Daniel Höppner
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
| | - Julia M Ruge
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
| | - Kara Moser
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Antoine Dara
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Jan Strauss
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Meral Esen
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Zita Sulyok
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Myriam D Jeninga
- Institute of Microbiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Peter G Kremsner
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - B Kim Lee Sim
- Sanaria Inc., Rockville, Maryland, United States of America
| | | | - Michael F Duffy
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas D Otto
- School of Infection & Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Tim-Wolf Gilberger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisboa, Portugal
| | - Benjamin Mordmüller
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Michaela Petter
- Institute of Microbiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anna Bachmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Hamburg/Borstel/Lübeck/Riems, Germany
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5
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Zhang X, Florini F, Visone JE, Lionardi I, Gross MR, Patel V, Deitsch KW. A coordinated transcriptional switching network mediates antigenic variation of human malaria parasites. eLife 2022; 11:e83840. [PMID: 36515978 PMCID: PMC9833823 DOI: 10.7554/elife.83840] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022] Open
Abstract
Malaria parasites avoid immune clearance through their ability to systematically alter antigens exposed on the surface of infected red blood cells. This is accomplished by tightly regulated transcriptional control of individual members of a large, multicopy gene family called var and is the key to both the virulence and chronic nature of malaria infections. Expression of var genes is mutually exclusive and controlled epigenetically, however how large populations of parasites coordinate var gene switching to avoid premature exposure of the antigenic repertoire is unknown. Here, we provide evidence for a transcriptional network anchored by a universally conserved gene called var2csa that coordinates the switching process. We describe a structured switching bias that shifts overtime and could shape the pattern of var expression over the course of a lengthy infection. Our results provide an explanation for a previously mysterious aspect of malaria infections and shed light on how parasites possessing a relatively small repertoire of variant antigen-encoding genes can coordinate switching events to limit antigen exposure, thereby maintaining chronic infections.
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Affiliation(s)
- Xu Zhang
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Francesca Florini
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Joseph E Visone
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Irina Lionardi
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical CollegeNew YorkUnited States
| | - Mackensie R Gross
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Valay Patel
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
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6
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Quinn JE, Jeninga MD, Limm K, Pareek K, Meißgeier T, Bachmann A, Duffy MF, Petter M. The Putative Bromodomain Protein PfBDP7 of the Human Malaria Parasite Plasmodium Falciparum Cooperates With PfBDP1 in the Silencing of Variant Surface Antigen Expression. Front Cell Dev Biol 2022; 10:816558. [PMID: 35493110 PMCID: PMC9039026 DOI: 10.3389/fcell.2022.816558] [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: 11/16/2021] [Accepted: 03/18/2022] [Indexed: 01/08/2023] Open
Abstract
Epigenetic regulation is a critical mechanism in controlling virulence, differentiation, and survival of the human malaria parasite Plasmodium (P.) falciparum. Bromodomain proteins contribute to this process by binding to acetylated lysine residues of histones and thereby targeting the gene regulatory machinery to gene promoters. A protein complex containing the P. falciparum bromodomain proteins (PfBDP) 1 and PfBDP2 (BDP1/BDP2 core complex) was previously shown to play an essential role for the correct transcription of invasion related genes. Here, we performed a functional characterization of a third component of this complex, which we dubbed PfBDP7, because structural modelling predicted a typical bromodomain fold. We confirmed that PfBDP7 is a nuclear protein that interacts with PfBDP1 at invasion gene promoters in mature schizont stage parasites and contributes to their transcription. Although partial depletion of PfBDP7 showed no significant effect on parasite viability, conditional knock down of either PfBDP7 or PfBDP1 resulted in the de-repression of variant surface antigens (VSA), which are important pathogenicity factors. This de-repression was evident both on mRNA and protein level. To understand the underlying mechanism, we mapped the genome wide binding sites of PfBDP7 by ChIPseq and showed that in early schizonts, PfBDP7 and PfBDP1 are commonly enriched in heterochromatic regions across the gene body of all VSA families, including genes coding for PfEMP1, RIFIN, STEVOR, and PfMC-2TM. This suggests that PfBDP7 and PfBDP1 contribute to the silencing of VSAs by associating with heterochromatin. In conclusion, we identified PfBDP7 as a chromatin binding protein that is a constitutive part of the P. falciparum BDP1/BDP2 core complex and established PfBDP1 and PfBDP7 as novel players in the silencing of heterochromatin regulated virulence gene families of the malaria parasite P. falciparum.
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Affiliation(s)
- Jennifer E. Quinn
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Myriam D. Jeninga
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Katharina Limm
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Kapil Pareek
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Tina Meißgeier
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Bachmann
- Department of Cellular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Michael F. Duffy
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute, Parkville, VIC, Australia
| | - Michaela Petter
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
- Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, Australia
- *Correspondence: Michaela Petter,
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7
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Tang J, Chisholm SA, Yeoh LM, Gilson PR, Papenfuss AT, Day KP, Petter M, Duffy MF. Histone modifications associated with gene expression and genome accessibility are dynamically enriched at Plasmodium falciparum regulatory sequences. Epigenetics Chromatin 2020; 13:50. [PMID: 33225957 PMCID: PMC7682024 DOI: 10.1186/s13072-020-00365-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
Background The malaria parasite Plasmodium falciparum has an unusually euchromatic genome with poorly conserved positioning of nucleosomes in intergenic sequences and poorly understood mechanisms of gene regulation. Variant histones and histone modifications determine nucleosome stability and recruit trans factors, but their combinatorial contribution to gene regulation is unclear. Results Here, we show that the histone H3 acetylations H3K18ac and H3K27ac and the variant histone Pf H2A.Z are enriched together at regulatory sites upstream of genes. H3K18ac and H3K27ac together dynamically mark regulatory regions of genes expressed during the asexual life cycle. In contrast, H3K4me1 is depleted in intergenic sequence and dynamically depleted upstream of expressed genes. The temporal pattern of H3K27ac and H3K18ac enrichment indicates that they accumulate during S phase and mitosis and are retained at regulatory sequences until at least G1 phase and after cessation of expression of the cognate genes. We integrated our ChIPseq data with existing datasets to show that in schizont stages H3K18ac, H3K27ac and Pf H2A.Z colocalise with the transcription factor PfAP2-I and the bromodomain protein PfBDP1 and are enriched at stably positioned nucleosomes within regions of exposed DNA at active transcriptional start sites. Using transient transfections we showed that sequences enriched with colocalised H3K18ac, H3K27ac and Pf H2A.Z possess promoter activity in schizont stages, but no enhancer-like activity. Conclusions The dynamic H3 acetylations define P. falciparum regulatory sequences and contribute to gene activation. These findings expand the knowledge of the chromatin landscape that regulates gene expression in P. falciparum.
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Affiliation(s)
- Jingyi Tang
- Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia.,School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, VIC, 3216, Australia
| | - Scott A Chisholm
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia.,Bio21 Institute, Parkville, VIC, 3052, Australia
| | - Lee M Yeoh
- Bio21 Institute, Parkville, VIC, 3052, Australia.,Peter Doherty Institute, Melbourne, VIC, 3000, Australia.,Department of Microbiology and Immunology, The University of Melbourne, Victoria, 3000, Australia
| | - Paul R Gilson
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, VIC, 3004, Australia.,Monash University, Melbourne, VIC, 3800, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Mathematics and Statistics, University of Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Sir Peter MacCallum, Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Karen P Day
- Bio21 Institute, Parkville, VIC, 3052, Australia.,Peter Doherty Institute, Melbourne, VIC, 3000, Australia.,Department of Microbiology and Immunology, The University of Melbourne, Victoria, 3000, Australia
| | - Michaela Petter
- Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia.,Erlangen University, 91054, Erlangen, Germany
| | - Michael F Duffy
- Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia. .,Bio21 Institute, Parkville, VIC, 3052, Australia. .,Peter Doherty Institute, Melbourne, VIC, 3000, Australia. .,Department of Microbiology and Immunology, The University of Melbourne, Victoria, 3000, Australia.
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