1
|
Kioko M, Pance A, Mwangi S, Goulding D, Kemp A, Rono M, Ochola-Oyier LI, Bull PC, Bejon P, Rayner JC, Abdi AI. Extracellular vesicles could be a putative posttranscriptional regulatory mechanism that shapes intracellular RNA levels in Plasmodium falciparum. Nat Commun 2023; 14:6447. [PMID: 37833314 PMCID: PMC10575976 DOI: 10.1038/s41467-023-42103-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Plasmodium falciparum secretes extracellular vesicles (PfEVs) that contain parasite-derived RNA. However, the significance of the secreted RNA remains unexplored. Here, we compare secreted and intracellular RNA from asexual cultures of six P. falciparum lines. We find that secretion of RNA via extracellular vesicles is not only periodic throughout the asexual intraerythrocytic developmental cycle but is also highly conserved across P. falciparum isolates. We further demonstrate that the phases of RNA secreted via extracellular vesicles are discernibly shifted compared to those of the intracellular RNA within the secreting whole parasite. Finally, transcripts of genes with no known function during the asexual intraerythrocytic developmental cycle are enriched in PfEVs compared to the whole parasite. We conclude that the secretion of extracellular vesicles could be a putative posttranscriptional RNA regulation mechanism that is part of or synergise the classic RNA decay processes to maintain intracellular RNA levels in P. falciparum.
Collapse
Affiliation(s)
- Mwikali Kioko
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Open University, Milton Keynes, UK
| | - Alena Pance
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
- School of Life and Medical Science, University of Hertfordshire, Hatfield, UK
| | - Shaban Mwangi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - David Goulding
- Pathogens and Microbes Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Alison Kemp
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Martin Rono
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya
| | | | - Pete C Bull
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philip Bejon
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C Rayner
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Abdirahman I Abdi
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Pwani University Biosciences Research Centre, Pwani University, Kilifi, Kenya.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
2
|
Ruperao P, Rangan P, Shah T, Thakur V, Kalia S, Mayes S, Rathore A. The Progression in Developing Genomic Resources for Crop Improvement. Life (Basel) 2023; 13:1668. [PMID: 37629524 PMCID: PMC10455509 DOI: 10.3390/life13081668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Sequencing technologies have rapidly evolved over the past two decades, and new technologies are being continually developed and commercialized. The emerging sequencing technologies target generating more data with fewer inputs and at lower costs. This has also translated to an increase in the number and type of corresponding applications in genomics besides enhanced computational capacities (both hardware and software). Alongside the evolving DNA sequencing landscape, bioinformatics research teams have also evolved to accommodate the increasingly demanding techniques used to combine and interpret data, leading to many researchers moving from the lab to the computer. The rich history of DNA sequencing has paved the way for new insights and the development of new analysis methods. Understanding and learning from past technologies can help with the progress of future applications. This review focuses on the evolution of sequencing technologies, their significant enabling role in generating plant genome assemblies and downstream applications, and the parallel development of bioinformatics tools and skills, filling the gap in data analysis techniques.
Collapse
Affiliation(s)
- Pradeep Ruperao
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi 110012, India;
| | - Trushar Shah
- International Institute of Tropical Agriculture (IITA), Nairobi 30709-00100, Kenya;
| | - Vivek Thakur
- Department of Systems & Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India;
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi 110003, India;
| | - Sean Mayes
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Abhishek Rathore
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad 502324, India
| |
Collapse
|
3
|
Jeninga MD, Tang J, Selvarajah SA, Maier AG, Duffy MF, Petter M. Plasmodium falciparum gametocytes display global chromatin remodelling during sexual differentiation. BMC Biol 2023; 21:65. [PMID: 37013531 PMCID: PMC10071754 DOI: 10.1186/s12915-023-01568-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The protozoan malaria parasite Plasmodium falciparum has a complex life cycle during which it needs to differentiate into multiple morphologically distinct life forms. A key process for transmission of the disease is the development of male and female gametocytes in the human blood, yet the mechanisms determining sexual dimorphism in these haploid, genetically identical sexual precursor cells remain largely unknown. To understand the epigenetic program underlying the differentiation of male and female gametocytes, we separated the two sexual forms by flow cytometry and performed RNAseq as well as comprehensive ChIPseq profiling of several histone variants and modifications. RESULTS We show that in female gametocytes the chromatin landscape is globally remodelled with respect to genome-wide patterns and combinatorial usage of histone variants and histone modifications. We identified sex specific differences in heterochromatin distribution, implicating exported proteins and ncRNAs in sex determination. Specifically in female gametocytes, the histone variants H2A.Z/H2B.Z were highly enriched in H3K9me3-associated heterochromatin. H3K27ac occupancy correlated with stage-specific gene expression, but in contrast to asexual parasites this was unlinked to H3K4me3 co-occupancy at promoters in female gametocytes. CONCLUSIONS Collectively, we defined novel combinatorial chromatin states differentially organising the genome in gametocytes and asexual parasites and unravelled fundamental, sex-specific differences in the epigenetic code. Our chromatin maps represent an important resource for future understanding of the mechanisms driving sexual differentiation in P. falciparum.
Collapse
Affiliation(s)
- Myriam D Jeninga
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Jingyi Tang
- Department of Medicine, University of Melbourne, Bio21 Institute, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Shamista A Selvarajah
- Department of Medicine, University of Melbourne, Bio21 Institute, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Alexander G Maier
- The Australian National University, Research School of Biology, 134 Linnaeus Way, Canberra, ACT, 2601, Australia
| | - Michael F Duffy
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute, 792 Elizabeth Street, Melbourne, VIC, 3000, Australia
- Bio21 Institute, 30 Flemington Road, Parkville, VIC, 3052, Australia
| | - Michaela Petter
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany.
- Department of Medicine, University of Melbourne, Bio21 Institute, 30 Flemington Road, Parkville, VIC, 3052, Australia.
| |
Collapse
|
4
|
Epigenetic and Epitranscriptomic Gene Regulation in Plasmodium falciparum and How We Can Use It against Malaria. Genes (Basel) 2022; 13:genes13101734. [PMID: 36292619 PMCID: PMC9601349 DOI: 10.3390/genes13101734] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Malaria, caused by Plasmodium parasites, is still one of the biggest global health challenges. P. falciparum is the deadliest species to humans. In this review, we discuss how this parasite develops and adapts to the complex and heterogenous environments of its two hosts thanks to varied chromatin-associated and epigenetic mechanisms. First, one small family of transcription factors, the ApiAP2 proteins, functions as master regulators of spatio-temporal patterns of gene expression through the parasite life cycle. In addition, chromatin plasticity determines variable parasite cell phenotypes that link to parasite growth, virulence and transmission, enabling parasite adaptation within host conditions. In recent years, epitranscriptomics is emerging as a new regulatory layer of gene expression. We present evidence of the variety of tRNA and mRNA modifications that are being characterized in Plasmodium spp., and the dynamic changes in their abundance during parasite development and cell fate. We end up outlining that new biological systems, like the mosquito model, to decipher the unknowns about epigenetic mechanisms in vivo; and novel methodologies, to study the function of RNA modifications; are needed to discover the Achilles heel of the parasite. With this new knowledge, future strategies manipulating the epigenetics and epitranscriptomic machinery of the parasite have the potential of providing new weapons against malaria.
Collapse
|
5
|
Li Z, Zhao B, Qin C, Wang Y, Li T, Wang W. Chromatin Dynamics in Digestive System Cancer: Commander and Regulator. Front Oncol 2022; 12:935877. [PMID: 35965507 PMCID: PMC9372441 DOI: 10.3389/fonc.2022.935877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Digestive system tumors have a poor prognosis due to complex anatomy, insidious onset, challenges in early diagnosis, and chemoresistance. Epidemiological statistics has verified that digestive system tumors rank first in tumor-related death. Although a great number of studies are devoted to the molecular biological mechanism, early diagnostic markers, and application of new targeted drugs in digestive system tumors, the therapeutic effect is still not satisfactory. Epigenomic alterations including histone modification and chromatin remodeling are present in human cancers and are now known to cooperate with genetic changes to drive the cancer phenotype. Chromatin is the carrier of genetic information and consists of DNA, histones, non-histone proteins, and a small amount of RNA. Chromatin and nucleosomes control the stability of the eukaryotic genome and regulate DNA processes such as transcription, replication, and repair. The dynamic structure of chromatin plays a key role in this regulatory function. Structural fluctuations expose internal DNA and thus provide access to the nuclear machinery. The dynamic changes are affected by various complexes and epigenetic modifications. Variation of chromatin dynamics produces early and superior regulation of the expression of related genes and downstream pathways, thereby controlling tumor development. Intervention at the chromatin level can change the process of cancer earlier and is a feasible option for future tumor diagnosis and treatment. In this review, we introduced chromatin dynamics including chromatin remodeling, histone modifications, and chromatin accessibility, and current research on chromatin regulation in digestive system tumors was also summarized.
Collapse
|
6
|
Saxena H, Gupta A. P. falciparum PfRUVBL proteins binds at TARE region and var gene promoter located in subtelomeric region. Pathog Dis 2022; 80:6595874. [PMID: 35640888 DOI: 10.1093/femspd/ftac018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/14/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
In order to survive and establish infection, Plasmodium parasite employ various strategies to evade host immune response. Var genes family, a repertoire of 60 genes, express parasite-specific protein PfEMP1, a variable surface antigen, on the membrane of infected erythrocyte, and by continuously switching the variants of PfEMP1, helps the parasite to avoid detection and destruction by host immune system during intra-erythrocytic developmental cycle. Although chromatin modifications are recognized to be a prominent phenomenon in regulation of mono-allelic expression of these var genes, however the precise histone codes and molecular players & mechanisms guiding these modifications are yet to be unravelled in depth. In this study, we have functionally characterized RUVBL proteins of P. falciparum and shown that PfMYST (an essential lysine acetyl transferase) and PfRUVBL protein complex occupy the TARE region and var gene promoter in ring stage of the parasite. Further we have demonstrated that PfMYST/PfRUVBL complex interact with core histone, H3 & H4. Overall the findings of this study adds a layer by identifying the potential role of epigenetic regulators, PfMYST & PfRUVBL in regulation of monoallelic expression of var genes in malaria parasite.
Collapse
Affiliation(s)
- Himani Saxena
- Epigenetics and Human disease laboratory, Department of Life Sciences, Shiv Nadar University, Delhi-NCR, India
| | - Ashish Gupta
- Epigenetics and Human disease laboratory, Department of Life Sciences, Shiv Nadar University, Delhi-NCR, India
| |
Collapse
|
7
|
Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
Collapse
|
8
|
Impact of Sickle Cell Trait Hemoglobin on the Intraerythrocytic Transcriptional Program of Plasmodium falciparum. mSphere 2021; 6:e0075521. [PMID: 34668757 PMCID: PMC8527989 DOI: 10.1128/msphere.00755-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sickle-trait hemoglobin (HbAS) confers nearly complete protection from severe, life-threatening falciparum malaria in African children. Despite this clear protection, the molecular mechanisms by which HbAS confers these protective phenotypes remain incompletely understood. As a forward genetic screen for aberrant parasite transcriptional responses associated with parasite neutralization in HbAS red blood cells (RBCs), we performed comparative transcriptomic analyses of Plasmodium falciparum in normal (HbAA) and HbAS erythrocytes during both in vitro cultivation of reference parasite strains and naturally occurring P. falciparum infections in Malian children with HbAA or HbAS. During in vitro cultivation, parasites matured normally in HbAS RBCs, and the temporal expression was largely unperturbed of the highly ordered transcriptional program that underlies the parasite’s maturation throughout the intraerythrocytic development cycle (IDC). However, differential expression analysis identified hundreds of transcripts aberrantly expressed in HbAS, largely occurring late in the IDC. Surprisingly, transcripts encoding members of the Maurer’s clefts were overexpressed in HbAS despite impaired parasite protein export in these RBCs, while parasites in HbAS RBCs underexpressed transcripts associated with the endoplasmic reticulum and those encoding serine repeat antigen proteases that promote parasite egress. Analyses of P. falciparum transcriptomes from 32 children with uncomplicated malaria identified stage-specific differential expression: among infections composed of ring-stage parasites, only cyclophilin 19B was underexpressed in children with HbAS, while trophozoite-stage infections identified a range of differentially expressed transcripts, including downregulation in HbAS of several transcripts associated with severe malaria in collateral studies. Collectively, our comparative transcriptomic screen in vitro and in vivo indicates that P. falciparum adapts to HbAS by altering its protein chaperone and folding machinery, oxidative stress response, and protein export machinery. Because HbAS consistently protects from severe P. falciparum, modulation of these responses may offer avenues by which to neutralize P. falciparum parasites. IMPORTANCE Sickle-trait hemoglobin (HbAS) confers nearly complete protection from severe, life-threatening malaria, yet the molecular mechanisms that underlie HbAS protection from severe malaria remain incompletely understood. Here, we used transcriptome sequencing (RNA-seq) to measure the impact of HbAS on the blood-stage transcriptome of Plasmodium falciparum in in vitro time series experiments and in vivo samples from natural infections. Our in vitro time series data reveal that, during its blood stage, P. falciparum’s gene expression in HbAS is impacted primarily through alterations in the abundance of gene products as opposed to variations in the timing of gene expression. Collectively, our in vitro and in vivo data indicate that P. falciparum adapts to HbAS by altering its protein chaperone and folding machinery, oxidative stress response, and protein export machinery. Due to the persistent association of HbAS and protection from severe disease, these processes that are modified in HbAS may offer strategies to neutralize P. falciparum.
Collapse
|
9
|
Miao J, Wang C, Lucky AB, Liang X, Min H, Adapa SR, Jiang R, Kim K, Cui L. A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum. PLoS Pathog 2021; 17:e1009351. [PMID: 34403450 PMCID: PMC8396726 DOI: 10.1371/journal.ppat.1009351] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/27/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
The histone acetyltransferase GCN5-associated SAGA complex is evolutionarily conserved from yeast to human and functions as a general transcription co-activator in global gene regulation. In this study, we identified a divergent GCN5 complex in Plasmodium falciparum, which contains two plant homeodomain (PHD) proteins (PfPHD1 and PfPHD2) and a plant apetela2 (AP2)-domain transcription factor (PfAP2-LT). To dissect the functions of the PfGCN5 complex, we generated parasite lines with either the bromodomain in PfGCN5 or the PHD domain in PfPHD1 deleted. The two deletion mutants closely phenocopied each other, exhibiting significantly reduced merozoite invasion of erythrocytes and elevated sexual conversion. These domain deletions caused dramatic decreases not only in histone H3K9 acetylation but also in H3K4 trimethylation, indicating synergistic crosstalk between the two euchromatin marks. Domain deletion in either PfGCN5 or PfPHD1 profoundly disturbed the global transcription pattern, causing altered expression of more than 60% of the genes. At the schizont stage, these domain deletions were linked to specific down-regulation of merozoite genes involved in erythrocyte invasion, many of which contain the AP2-LT binding motif and are also regulated by AP2-I and BDP1, suggesting targeted recruitment of the PfGCN5 complex to the invasion genes by these specific factors. Conversely, at the ring stage, PfGCN5 or PfPHD1 domain deletions disrupted the mutually exclusive expression pattern of the entire var gene family, which encodes the virulent factor PfEMP1. Correlation analysis between the chromatin state and alteration of gene expression demonstrated that up- and down-regulated genes in these mutants are highly correlated with the silent and active chromatin states in the wild-type parasite, respectively. Collectively, the PfGCN5 complex represents a novel HAT complex with a unique subunit composition including an AP2 transcription factor, which signifies a new paradigm for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist. Epigenetic regulation of gene expression plays essential roles in orchestrating the general and parasite-specific cellular pathways in the malaria parasite Plasmodium falciparum. To better understand the epigenetic mechanisms in this parasite, we characterized the histone acetyltransferase GCN5-mediated transcription regulation during intraerythrocytic development of the parasite. Using tandem affinity purification and proteomic characterization, we identified that the PfGCN5-associated complex contains nine core components, including two PHD domain proteins (PfPHD1 and PfPHD2) and an AP2-domain transcription factor, which is divergent from the canonical GCN5 complexes evolutionarily conserved from yeast to human. To understand the functions of the PfGCN5 complex, we performed domain deletions in two subunits of this complex, PfGCN5 and PfPHD1. We found that the two deletion mutants displayed very similar growth phenotypes, including significantly reduced merozoite invasion rates and elevated sexual conversion. These two mutants were associated with dramatic decreases in histone H3K9 acetylation and H3K4 trimethylation, which led to global changes in chromatin states and gene expression. Consistent with the phenotypes, genes significantly affected by the PfGCN5 and PfPHD1 gene disruption include those participating in parasite-specific pathways such as invasion, virulence, and sexual development. In conclusion, this study presents a new model of the PfGCN5 complex for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist.
Collapse
Affiliation(s)
- Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- * E-mail: (JM); (LC)
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Amuza Byaruhanga Lucky
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Xiaoying Liang
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Hui Min
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Swamy Rakesh Adapa
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Rays Jiang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- * E-mail: (JM); (LC)
| |
Collapse
|
10
|
Peculiarities of Plasmodium falciparum Gene Regulation and Chromatin Structure. Int J Mol Sci 2021; 22:ijms22105168. [PMID: 34068393 PMCID: PMC8153576 DOI: 10.3390/ijms22105168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/14/2022] Open
Abstract
The highly complex life cycle of the human malaria parasite, Plasmodium falciparum, is based on an orchestrated and tightly regulated gene expression program. In general, eukaryotic transcription regulation is determined by a combination of sequence-specific transcription factors binding to regulatory DNA elements and the packaging of DNA into chromatin as an additional layer. The accessibility of regulatory DNA elements is controlled by the nucleosome occupancy and changes of their positions by an active process called nucleosome remodeling. These epigenetic mechanisms are poorly explored in P. falciparum. The parasite genome is characterized by an extraordinarily high AT-content and the distinct architecture of functional elements, and chromatin-related proteins also exhibit high sequence divergence compared to other eukaryotes. Together with the distinct biochemical properties of nucleosomes, these features suggest substantial differences in chromatin-dependent regulation. Here, we highlight the peculiarities of epigenetic mechanisms in P. falciparum, addressing chromatin structure and dynamics with respect to their impact on transcriptional control. We focus on the specialized chromatin remodeling enzymes and discuss their essential function in P. falciparum gene regulation.
Collapse
|
11
|
Machado M, Steinke S, Ganter M. Plasmodium Reproduction, Cell Size, and Transcription: How to Cope With Increasing DNA Content? Front Cell Infect Microbiol 2021; 11:660679. [PMID: 33898332 PMCID: PMC8062723 DOI: 10.3389/fcimb.2021.660679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmodium, the unicellular parasite that causes malaria, evolved a highly unusual mode of reproduction. During its complex life cycle, invasive or transmissive stages alternate with proliferating stages, where a single parasite can produce tens of thousands of progeny. In the clinically relevant blood stage of infection, the parasite replicates its genome up to thirty times and forms a multinucleated cell before daughter cells are assembled. Thus, within a single cell cycle, Plasmodium develops from a haploid to a polypoid cell, harboring multiple copies of its genome. Polyploidy creates several biological challenges, such as imbalances in genome output, and cells can respond to this by changing their size and/or alter the production of RNA species and protein to achieve expression homeostasis. However, the effects and possible adaptations of Plasmodium to the massively increasing DNA content are unknown. Here, we revisit and embed current Plasmodium literature in the context of polyploidy and propose potential mechanisms of the parasite to cope with the increasing gene dosage.
Collapse
Affiliation(s)
- Marta Machado
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany.,Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Salome Steinke
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus Ganter
- Centre for Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
12
|
Tabassum W, Bhattacharyya S, Varunan SM, Bhattacharyya MK. Febrile temperature causes transcriptional downregulation of Plasmodium falciparum Sirtuins through Hsp90-dependent epigenetic modification. Mol Microbiol 2021; 115:1025-1038. [PMID: 33538363 DOI: 10.1111/mmi.14692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/30/2021] [Accepted: 01/30/2021] [Indexed: 11/28/2022]
Abstract
Sirtuins (PfSIR2A and PfSIR2B) are implicated to play pivotal roles in the silencing of sub-telomeric genes and the maintenance of telomere length in P. falciparum 3D7 strain. Here, we identify the key factors that regulate the cellular abundance and activity of these two histone deacetylases. Our results demonstrate that PfSIR2A and PfSIR2B are transcriptionally downregulated at the mid-ring stage in response to febrile temperature. We found that the molecular chaperone PfHsp90 acts as a repressor of PfSIR2A & B transcription. By virtue of its presence in the PfSIR2A & B promoter proximal regions PfHsp90 helps recruiting H3K9me3, conferring heterochromatic state, and thereby leading to the downregulation of PfSIR2A & B transcription. Such transcriptional downregulation can be reversed by the addition of 17-(allylamino)-17-demethoxygeldanamycin or Radicicol, two potent inhibitors of PfHsp90. The reduced occupancy of PfSir2 at sub-telomeric var promoters leads to the de-repression of var genes. Thus, here we uncover how exposure to febrile temperature, a hallmark of malaria, enables the parasites to manipulate the expression of the two prominent epigenetic modifiers PfSir2A and PfSir2B.
Collapse
Affiliation(s)
- Wahida Tabassum
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sunanda Bhattacharyya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Shalu M Varunan
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | |
Collapse
|
13
|
Hollin T, Le Roch KG. From Genes to Transcripts, a Tightly Regulated Journey in Plasmodium. Front Cell Infect Microbiol 2020; 10:618454. [PMID: 33425787 PMCID: PMC7793691 DOI: 10.3389/fcimb.2020.618454] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022] Open
Abstract
Over the past decade, we have witnessed significant progresses in understanding gene regulation in Apicomplexa including the human malaria parasite, Plasmodium falciparum. This parasite possesses the ability to convert in multiple stages in various hosts, cell types, and environments. Recent findings indicate that P. falciparum is talented at using efficient and complementary molecular mechanisms to ensure a tight control of gene expression at each stage of its life cycle. Here, we review the current understanding on the contribution of the epigenome, atypical transcription factors, and chromatin organization to regulate stage conversion in P. falciparum. The adjustment of these regulatory mechanisms occurring during the progression of the life cycle will be extensively discussed.
Collapse
Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
| |
Collapse
|
14
|
Conboy K, Henshall DC, Brennan GP. Epigenetic principles underlying epileptogenesis and epilepsy syndromes. Neurobiol Dis 2020; 148:105179. [PMID: 33181318 DOI: 10.1016/j.nbd.2020.105179] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/21/2022] Open
Abstract
Epilepsy is a network disorder driven by fundamental changes in the function of the cells which compose these networks. Driving this aberrant cellular function are large scale changes in gene expression and gene expression regulation. Recent studies have revealed rapid and persistent changes in epigenetic control of gene expression as a critical regulator of the epileptic transcriptome. Epigenetic-mediated gene output regulates many aspects of cellular physiology including neuronal structure, neurotransmitter assembly and abundance, protein abundance of ion channels and other critical neuronal processes. Thus, understanding the contribution of epigenetic-mediated gene regulation could illuminate novel regulatory mechanisms which may form the basis of novel therapeutic approaches to treat epilepsy. In this review we discuss the effects of epileptogenic brain insults on epigenetic regulation of gene expression, recent efforts to target epigenetic processes to block epileptogenesis and the prospects of an epigenetic-based therapy for epilepsy, and finally we discuss technological advancements which have facilitated the interrogation of the epigenome.
Collapse
Affiliation(s)
- Karen Conboy
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland; FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland; FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
| | - Gary P Brennan
- FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland; School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| |
Collapse
|
15
|
Wang C, Gibbons J, Adapa SR, Oberstaller J, Liao X, Zhang M, Adams JH, Jiang RHY. The human malaria parasite genome is configured into thousands of coexpressed linear regulatory units. J Genet Genomics 2020; 47:513-521. [PMID: 33272860 DOI: 10.1016/j.jgg.2020.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/07/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022]
Abstract
The human malaria parasite Plasmodium falciparum thrives in radically different host environments in mosquitoes and humans, with only a limited set of transcription factors. The nature of regulatory elements or their target genes in the P. falciparum genome remains elusive. Here, we found that this eukaryotic parasite uses an efficient way to maximally use genetic and epigenetic regulation to form regulatory units (RUs) during blood infections. Genes located in the same RU tend to have the same pattern of expression over time and are associated with open chromatin along regulatory elements. To precisely define and quantify these RUs, a novel hidden Markov model was developed to capture the regulatory structure in a genome-wide fashion by integrating expression and epigenetic evidence. We successfully identified thousands of RUs and cross-validated with previous findings. We found more genes involved in red blood cell (RBC) invasion located in the same RU as the PfAP2-I (AP2-I) transcription factor, demonstrating that AP2-I is responsible for regulating RBC invasion. Our study has provided a regulatory mechanism for a compact eukaryotic genome and offers new insights into the in vivo transcriptional regulation of the P. falciparum intraerythrocytic stage.
Collapse
Affiliation(s)
- Chengqi Wang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Justin Gibbons
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Swamy R Adapa
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Jenna Oberstaller
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Xiangyun Liao
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Min Zhang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - John H Adams
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Rays H Y Jiang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA.
| |
Collapse
|
16
|
Dynamic Chromatin Structure and Epigenetics Control the Fate of Malaria Parasites. Trends Genet 2020; 37:73-85. [PMID: 32988634 DOI: 10.1016/j.tig.2020.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022]
Abstract
Multiple hosts and various life cycle stages prompt the human malaria parasite, Plasmodium falciparum, to acquire sophisticated molecular mechanisms to ensure its survival, spread, and transmission to its next host. To face these environmental challenges, increasing evidence suggests that the parasite has developed complex and complementary layers of regulatory mechanisms controlling gene expression. Here, we discuss the recent developments in the discovery of molecular components that contribute to cell replication and differentiation and highlight the major contributions of epigenetics, transcription factors, and nuclear architecture in controlling gene regulation and life cycle progression in Plasmodium spp.
Collapse
|
17
|
Ruiz JL, Gómez-Díaz E. The second life of Plasmodium in the mosquito host: gene regulation on the move. Brief Funct Genomics 2020; 18:313-357. [PMID: 31058281 DOI: 10.1093/bfgp/elz007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/08/2019] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
Malaria parasites face dynamically changing environments and strong selective constraints within human and mosquito hosts. To survive such hostile and shifting conditions, Plasmodium switches transcriptional programs during development and has evolved mechanisms to adjust its phenotype through heterogeneous patterns of gene expression. In vitro studies on culture-adapted isolates have served to set the link between chromatin structure and functional gene expression. Yet, experimental evidence is limited to certain stages of the parasite in the vertebrate, i.e. blood, while the precise mechanisms underlying the dynamic regulatory landscapes during development and in the adaptation to within-host conditions remain poorly understood. In this review, we discuss available data on transcriptional and epigenetic regulation in Plasmodium mosquito stages in the context of sporogonic development and phenotypic variation, including both bet-hedging and environmentally triggered direct transcriptional responses. With this, we advocate the mosquito offers an in vivo biological model to investigate the regulatory networks, transcription factors and chromatin-modifying enzymes and their modes of interaction with regulatory sequences, which might be responsible for the plasticity of the Plasmodium genome that dictates stage- and cell type-specific blueprints of gene expression.
Collapse
Affiliation(s)
- José L Ruiz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
| |
Collapse
|
18
|
Formaldehyde-assisted isolation of regulatory DNA elements from Arabidopsis leaves. Nat Protoc 2020; 15:713-733. [PMID: 32042178 DOI: 10.1038/s41596-019-0277-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 12/03/2019] [Indexed: 12/14/2022]
Abstract
Eukaryotic gene transcription is associated with the eviction of nucleosomes and the formation of open chromatin, which enables the recruitment of transcriptional coactivators and other regulatory factors. Open chromatin is thus a hallmark of functional regulatory DNA elements in genomes. In recent years, formaldehyde-assisted isolation of regulatory elements (FAIRE) has proven powerful in identifying open chromatin in the genome of various eukaryotes, particularly yeast, human, and mouse. However, it has proven challenging to adapt the FAIRE protocol for use on plant material, and the few available protocols all have their drawbacks (e.g., applicability only to specific developmental stages). In this Protocol Extension, we describe a reliable FAIRE protocol for mature Arabidopsis (Arabidopsis thaliana) leaves that adapts the original protocol for use on plants. The main differences between this protocol extension and the earlier FAIRE protocol are an increased formaldehyde concentration in the chromatin crosslinking buffer, application of a repeated vacuum to increase crosslinking efficiency, and altered composition of the DNA extraction buffer. The protocol is applicable to leaf chromatin of unstressed and stressed plants and can be completed within 1 week. Here, we also describe downstream analysis using qPCR and next-generation sequencing. However, this Protocol Extension should also be compatible with downstream hybridization to a DNA microarray. In addition, it is likely that only minor adaptations will be necessary to apply this protocol to other Arabidopsis organs or plant species.
Collapse
|
19
|
Batugedara G, Lu XM, Saraf A, Sardiu ME, Cort A, Abel S, Prudhomme J, Washburn MP, Florens L, Bunnik EM, Le Roch KG. The chromatin bound proteome of the human malaria parasite. Microb Genom 2020; 6:e000327. [PMID: 32017676 PMCID: PMC7067212 DOI: 10.1099/mgen.0.000327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
Proteins interacting with DNA are fundamental for mediating processes such as gene expression, DNA replication and maintenance of genome integrity. Accumulating evidence suggests that the chromatin of apicomplexan parasites, such as Plasmodium falciparum, is highly organized, and this structure provides an epigenetic mechanism for transcriptional regulation. To investigate how parasite chromatin structure is being regulated, we undertook comparative genomics analysis using 12 distinct eukaryotic genomes. We identified conserved and parasite-specific chromatin-associated domains (CADs) and proteins (CAPs). We then used the chromatin enrichment for proteomics (ChEP) approach to experimentally capture CAPs in P. falciparum. A topological scoring analysis of the proteomics dataset revealed stage-specific enrichments of CADs and CAPs. Finally, we characterized, two candidate CAPs: a conserved homologue of the structural maintenance of chromosome 3 protein and a homologue of the crowded-like nuclei protein, a plant-like protein functionally analogous to animal nuclear lamina proteins. Collectively, our results provide a comprehensive overview of CAPs in apicomplexans, and contribute to our understanding of the complex molecular components regulating chromatin structure and genome architecture in these deadly parasites.
Collapse
Affiliation(s)
- Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Xueqing M. Lu
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Anthony Cort
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Michael P. Washburn
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| |
Collapse
|
20
|
Calarco L, Barratt J, Ellis J. Detecting sequence variants in clinically important protozoan parasites. Int J Parasitol 2019; 50:1-18. [PMID: 31857072 DOI: 10.1016/j.ijpara.2019.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/29/2019] [Accepted: 10/01/2019] [Indexed: 02/06/2023]
Abstract
Second and third generation sequencing methods are crucial for population genetic studies, and variant detection is a popular approach for exploiting this sequence data. While mini- and microsatellites are historically useful markers for studying important Protozoa such as Toxoplasma and Plasmodium spp., detecting non-repetitive variants such as those found in genes can be fundamental to investigating a pathogen's biology. These variants, namely single nucleotide polymorphisms and insertions and deletions, can help elucidate the genetic basis of an organism's pathogenicity, identify selective pressures, and resolve phylogenetic relationships. They also have the added benefit of possessing a comparatively low mutation rate, which contributes to their stability. However, there is a plethora of variant analysis tools with nuanced pipelines and conflicting recommendations for best practise, which can be confounding. This lack of standardisation means that variant analysis requires careful parameter optimisation, an understanding of its limitations, and the availability of high quality data. This review explores the value of variant detection when applied to non-model organisms such as clinically important protozoan pathogens. The limitations of current methods are discussed, including special considerations that require the end-users' attention to ensure that the results generated are reproducible, and the biological conclusions drawn are valid.
Collapse
Affiliation(s)
- Larissa Calarco
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia.
| | - Joel Barratt
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - John Ellis
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| |
Collapse
|
21
|
Toenhake CG, Bártfai R. What functional genomics has taught us about transcriptional regulation in malaria parasites. Brief Funct Genomics 2019; 18:290-301. [PMID: 31220867 PMCID: PMC6859821 DOI: 10.1093/bfgp/elz004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/08/2019] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Malaria parasites are characterized by a complex life cycle that is accompanied by dynamic gene expression patterns. The factors and mechanisms that regulate gene expression in these parasites have been searched for even before the advent of next generation sequencing technologies. Functional genomics approaches have substantially boosted this area of research and have yielded significant insights into the interplay between epigenetic, transcriptional and post-transcriptional mechanisms. Recently, considerable progress has been made in identifying sequence-specific transcription factors and DNA-encoded regulatory elements. Here, we review the insights obtained from these efforts including the characterization of core promoters, the involvement of sequence-specific transcription factors in life cycle progression and the mapping of gene regulatory elements. Furthermore, we discuss recent developments in the field of functional genomics and how they might contribute to further characterization of this complex gene regulatory network.
Collapse
Affiliation(s)
- Christa G Toenhake
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Richárd Bártfai
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, the Netherlands
| |
Collapse
|
22
|
Abel S, Le Roch KG. The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites. Brief Funct Genomics 2019; 18:302-313. [PMID: 31220857 PMCID: PMC6859822 DOI: 10.1093/bfgp/elz005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/25/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022] Open
Abstract
Due to the unique selective pressures and extreme changes faced by the human malaria parasite Plasmodium falciparum throughout its life cycle, the parasite has evolved distinct features to alter its gene expression patterns. Along with classical gene regulation by transcription factors (TFs), of which only one family, the AP2 TFs, has been described in the parasite genome, a large body of evidence points toward chromatin structure and epigenetic factors mediating the changes in gene expression associated with parasite life cycle stages. These attributes may be critically important for immune evasion, host cell invasion and development of the parasite in its two hosts, the human and the Anopheles vector. Thus, the factors involved in the maintenance and regulation of chromatin and epigenetic features represent potential targets for antimalarial drugs. In this review, we discuss the mechanisms in P. falciparum that regulate chromatin structure, nucleosome landscape, the 3-dimensional structure of the genome and additional distinctive features created by parasite-specific genes and gene families. We review conserved traits of chromatin in eukaryotes in order to highlight what is unique in the parasite.
Collapse
Affiliation(s)
- Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| |
Collapse
|
23
|
Sadiyah MF, Roychoudhuri R. Genome-Wide Measurement and Computational Analysis of Transcription Factor Binding and Chromatin Accessibility in Lymphocytes. CURRENT PROTOCOLS IN IMMUNOLOGY 2019; 126:e84. [PMID: 31483104 DOI: 10.1002/cpim.84] [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] [Indexed: 11/07/2022]
Abstract
Cells of the adaptive immune system, including CD4+ and CD8+ T cells, as well as B cells, possess the ability to undergo dynamic changes in population size, differentiation state, and function to counteract diverse and temporally stochastic threats from the external environment. To achieve this, lymphocytes must be able to rapidly control their gene-expression programs in a cell-type-specific manner and in response to extrinsic signals. Such capacity is provided by transcription factors (TFs), which bind to the available repertoire of regulatory DNA elements in distinct lymphocyte subsets to program cell-type-specific gene expression. Here we provide a set of protocols that utilize massively parallel sequencing-based approaches to map genome-wide TF-binding sites and accessible chromatin, with consideration of the unique aspects and technical issues facing their application to lymphocytes. We show how to computationally validate and analyze aligned data to map differentially enriched/accessible sites, identify enriched DNA sequence motifs, and detect the position of nucleosomes adjacent to accessible DNA elements. These techniques, when applied to immune cells, can enhance our understanding of how gene-expression programs are controlled within lymphocytes to coordinate immune function in homeostasis and disease. © 2019 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- M Firas Sadiyah
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, United Kingdom
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, United Kingdom
| |
Collapse
|
24
|
Read DF, Cook K, Lu YY, Le Roch KG, Noble WS. Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features. PLoS Comput Biol 2019; 15:e1007329. [PMID: 31509524 PMCID: PMC6756558 DOI: 10.1371/journal.pcbi.1007329] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 09/23/2019] [Accepted: 08/12/2019] [Indexed: 12/02/2022] Open
Abstract
Empirical evidence suggests that the malaria parasite Plasmodium falciparum employs a broad range of mechanisms to regulate gene transcription throughout the organism's complex life cycle. To better understand this regulatory machinery, we assembled a rich collection of genomic and epigenomic data sets, including information about transcription factor (TF) binding motifs, patterns of covalent histone modifications, nucleosome occupancy, GC content, and global 3D genome architecture. We used these data to train machine learning models to discriminate between high-expression and low-expression genes, focusing on three distinct stages of the red blood cell phase of the Plasmodium life cycle. Our results highlight the importance of histone modifications and 3D chromatin architecture in Plasmodium transcriptional regulation and suggest that AP2 transcription factors may play a limited regulatory role, perhaps operating in conjunction with epigenetic factors.
Collapse
Affiliation(s)
- David F. Read
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kate Cook
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Yang Y. Lu
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, United States of America
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| |
Collapse
|
25
|
Ruiz JL, Tena JJ, Bancells C, Cortés A, Gómez-Skarmeta JL, Gómez-Díaz E. Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2019; 46:9414-9431. [PMID: 30016465 PMCID: PMC6182165 DOI: 10.1093/nar/gky643] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/10/2018] [Indexed: 12/27/2022] Open
Abstract
Human malaria is a devastating disease and a major cause of poverty in resource-limited countries. To develop and adapt within hosts Plasmodium falciparum undergoes drastic switches in gene expression. To identify regulatory regions in the parasite genome, we performed genome-wide profiling of chromatin accessibility in two culture-adapted isogenic subclones at four developmental stages during the intraerythrocytic cycle by using the Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq). Tn5 transposase hypersensitivity sites (THSSs) localize preferentially at transcriptional start sites (TSSs). Chromatin accessibility by ATAC-seq is predictive of active transcription and of the levels of histone marks H3K9ac and H3K4me3. Our assay allows the identification of novel regulatory regions including TSS and enhancer-like elements. We show that the dynamics in the accessible chromatin profile matches temporal transcription during development. Motif analysis of stage-specific ATAC-seq sites predicts the in vivo binding sites and function of multiple ApiAP2 transcription factors. At last, the alternative expression states of some clonally variant genes (CVGs), including eba, phist, var and clag genes, associate with a differential ATAC-seq signal at their promoters. Altogether, this study identifies genome-wide regulatory regions likely to play an essential function in the developmental transitions and in CVG expression in P. falciparum.
Collapse
Affiliation(s)
- José Luis Ruiz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, Seville 41092, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville 41013, Spain
| | - Cristina Bancells
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain
| | - Alfred Cortés
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain.,ICREA, Barcelona, Catalonia 08010, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville 41013, Spain
| | - Elena Gómez-Díaz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, Seville 41092, Spain.,Instituto de Parasitología y Biomedicina 'López-Neyra' (IPBLN), Consejo Superior de Investigaciones Científicas, Granada 18016, Spain
| |
Collapse
|
26
|
Transcriptome-wide dynamics of extensive m 6A mRNA methylation during Plasmodium falciparum blood-stage development. Nat Microbiol 2019; 4:2246-2259. [PMID: 31384004 DOI: 10.1038/s41564-019-0521-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/20/2019] [Indexed: 01/17/2023]
Abstract
Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-h life cycle. Although substantial post-transcriptional regulation of this hardwired program has been observed, it remains unclear how these processes are mediated on a transcriptome-wide level. To this end, we identified mRNA modifications in the P. falciparum transcriptome and performed a comprehensive characterization of N6-methyladenosine (m6A) over the course of blood-stage development. Using mass spectrometry and m6A RNA sequencing, we demonstrate that m6A is highly developmentally regulated, exceeding m6A levels known in any other eukaryote. We characterize a distinct m6A writer complex and show that knockdown of the putative m6A methyltransferase, PfMT-A70, by CRISPR interference leads to increased levels of transcripts that normally contain m6A. In accordance, we find an inverse correlation between m6A methylation and mRNA stability or translational efficiency. We further identify two putative m6A-binding YTH proteins that are likely to be involved in the regulation of these processes across the parasite's life cycle. Our data demonstrate unique features of an extensive m6A mRNA methylation programme in malaria parasites and reveal its crucial role in dynamically fine-tuning the transcriptional cascade of a unicellular eukaryote.
Collapse
|
27
|
Gohl DM, Magli A, Garbe J, Becker A, Johnson DM, Anderson S, Auch B, Billstein B, Froehling E, McDevitt SL, Beckman KB. Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification. Genome Biol 2019; 20:85. [PMID: 31036053 PMCID: PMC6489363 DOI: 10.1186/s13059-019-1691-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/09/2019] [Indexed: 01/15/2023] Open
Abstract
Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next-generation sequencing. However, PCR amplification can introduce significant quantitative error. We describe REcount, a novel PCR-free direct counting method. Comparing measurements of defined plasmid pools to droplet digital PCR data demonstrates that REcount is highly accurate and reproducible. We use REcount to provide new insights into clustering biases due to molecule length across different Illumina sequencers and illustrate the impacts on interpretation of next-generation sequencing data and the economics of data generation.
Collapse
Affiliation(s)
- Daryl M. Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 USA
| | - Alessandro Magli
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455 USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455 USA
| | - John Garbe
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Aaron Becker
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | | | - Shea Anderson
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Benjamin Auch
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Bradley Billstein
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
- Present Address: Illumina, Inc, San Diego, CA 92122 USA
| | - Elyse Froehling
- University of Minnesota Genomics Center, Minneapolis, MN 55455 USA
| | - Shana L. McDevitt
- Vincent J. Coates Genomics Sequencing Laboratory, University of California, Berkeley, CA 94720 USA
| | | |
Collapse
|
28
|
Fang Y, Wu D, Birukov KG. Mechanosensing and Mechanoregulation of Endothelial Cell Functions. Compr Physiol 2019; 9:873-904. [PMID: 30873580 PMCID: PMC6697421 DOI: 10.1002/cphy.c180020] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Vascular endothelial cells (ECs) form a semiselective barrier for macromolecules and cell elements regulated by dynamic interactions between cytoskeletal elements and cell adhesion complexes. ECs also participate in many other vital processes including innate immune reactions, vascular repair, secretion, and metabolism of bioactive molecules. Moreover, vascular ECs represent a unique cell type exposed to continuous, time-dependent mechanical forces: different patterns of shear stress imposed by blood flow in macrovasculature and by rolling blood cells in the microvasculature; circumferential cyclic stretch experienced by the arterial vascular bed caused by heart propulsions; mechanical stretch of lung microvascular endothelium at different magnitudes due to spontaneous respiration or mechanical ventilation in critically ill patients. Accumulating evidence suggests that vascular ECs contain mechanosensory complexes, which rapidly react to changes in mechanical loading, process the signal, and develop context-specific adaptive responses to rebalance the cell homeostatic state. The significance of the interactions between specific mechanical forces in the EC microenvironment together with circulating bioactive molecules in the progression and resolution of vascular pathologies including vascular injury, atherosclerosis, pulmonary edema, and acute respiratory distress syndrome has been only recently recognized. This review will summarize the current understanding of EC mechanosensory mechanisms, modulation of EC responses to humoral factors by surrounding mechanical forces (particularly the cyclic stretch), and discuss recent findings of magnitude-specific regulation of EC functions by transcriptional, posttranscriptional and epigenetic mechanisms using -omics approaches. We also discuss ongoing challenges and future opportunities in developing new therapies targeting dysregulated mechanosensing mechanisms to treat vascular diseases. © 2019 American Physiological Society. Compr Physiol 9:873-904, 2019.
Collapse
Affiliation(s)
- Yun Fang
- Department of Medicine, University of Chicago, Chicago, Illinois, USA,Correspondence to
| | - David Wu
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Konstantin G. Birukov
- Department of Anesthesiology, University of Maryland Baltimore School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
29
|
Jabeena CA, Rajavelu A. Epigenetic Players of Chromatin Structure Regulation in Plasmodium falciparum. Chembiochem 2019; 20:1225-1230. [PMID: 30632244 DOI: 10.1002/cbic.201800718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Indexed: 12/16/2022]
Abstract
The protozoan parasite Plasmodium has evolved to survive in different hosts and environments. The diverse strategies of adaptation to different niches involve differential gene expression mechanisms mediated by chromatin plasticity that are poorly characterized in Plasmodium. The parasite employs a wide variety of regulatory mechanisms to complete their life cycle and survive inside hosts. Among them, epigenetic-mediated mechanisms have been implicated for controlling chromatin organization, gene regulation, morphological differentiation, and antigenic variation. The differential gene expression in parasite is largely dependent on the nature of the chromatin structure. The histone core methylation marks and methyl mark readers contribute to chromatin dynamics. Here, we review the recent developments on various epigenetic marks and its enzymes in the Plasmodium falciparum, how these marks play a key role in the regulation of transcriptional activity of variable genes and coordinate the differential gene expression. We also discuss the possible roles of these epigenetic marks in chromatin structure regulation and plasticity at various stages of its development.
Collapse
Affiliation(s)
- C A Jabeena
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala, 695014, India.,Manipal Academy of Higher Education, Tiger Circle Road, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - Arumugam Rajavelu
- Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, Kerala, 695014, India
| |
Collapse
|
30
|
Ng CS, Sinha A, Aniweh Y, Nah Q, Babu IR, Gu C, Chionh YH, Dedon PC, Preiser PR. tRNA epitranscriptomics and biased codon are linked to proteome expression in Plasmodium falciparum. Mol Syst Biol 2018; 14:e8009. [PMID: 30287681 PMCID: PMC6171970 DOI: 10.15252/msb.20178009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 12/24/2022] Open
Abstract
Among components of the translational machinery, ribonucleoside modifications on tRNAs are emerging as critical regulators of cell physiology and stress response. Here, we demonstrate highly coordinated behavior of the repertoire of tRNA modifications of Plasmodium falciparum throughout the intra-erythrocytic developmental cycle (IDC). We observed both a synchronized increase in 22 of 28 modifications from ring to trophozoite stage, consistent with tRNA maturation during translational up-regulation, and asynchronous changes in six modifications. Quantitative analysis of ~2,100 proteins across the IDC revealed that up- and down-regulated proteins in late but not early stages have a marked codon bias that directly correlates with parallel changes in tRNA modifications and enhanced translational efficiency. We thus propose a model in which tRNA modifications modulate the abundance of stage-specific proteins by enhancing translation efficiency of codon-biased transcripts for critical genes. These findings reveal novel epitranscriptomic and translational control mechanisms in the development and pathogenesis of Plasmodium parasites.
Collapse
Affiliation(s)
- Chee Sheng Ng
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ameya Sinha
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yaw Aniweh
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Qianhui Nah
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
| | - Indrakanti Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yok Hian Chionh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- Department of Microbiology and Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter R Preiser
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| |
Collapse
|
31
|
Blighe K, DeDionisio L, Christie KA, Chawes B, Shareef S, Kakouli-Duarte T, Chao-Shern C, Harding V, Kelly RS, Castellano L, Stebbing J, Lasky-Su JA, Nesbit MA, Moore CBT. Gene editing in the context of an increasingly complex genome. BMC Genomics 2018; 19:595. [PMID: 30086710 PMCID: PMC6081867 DOI: 10.1186/s12864-018-4963-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/26/2018] [Indexed: 12/15/2022] Open
Abstract
The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majority of variation across human populations with landmark projects such as 1000 Genomes; in cancer, we have catalogued mutations across the primary carcinomas; whilst, for other diseases, we have identified the genetic variants with strongest association. Despite this, we are still awaiting the genetic revolution in healthcare to materialise and translate itself into the health benefits for which we had hoped. A major problem we face relates to our underestimation of the complexity of the genome, and that of biological mechanisms, generally. Fixation on DNA sequence alone and a 'rigid' mode of thinking about the genome has meant that the folding and structure of the DNA molecule -and how these relate to regulation- have been underappreciated. Projects like ENCODE have additionally taught us that regulation at the level of RNA is just as important as that at the spatiotemporal level of chromatin.In this review, we chart the course of the major advances in the biomedical sciences in the era pre- and post the release of the first draft sequence of the human genome, taking a focus on technology and how its development has influenced these. We additionally focus on gene editing via CRISPR/Cas9 as a key technique, in particular its use in the context of complex biological mechanisms. Our aim is to shift the mode of thinking about the genome to that which encompasses a greater appreciation of the folding of the DNA molecule, DNA- RNA/protein interactions, and how these regulate expression and elaborate disease mechanisms.Through the composition of our work, we recognise that technological improvement is conducive to a greater understanding of biological processes and life within the cell. We believe we now have the technology at our disposal that permits a better understanding of disease mechanisms, achievable through integrative data analyses. Finally, only with greater understanding of disease mechanisms can techniques such as gene editing be faithfully conducted.
Collapse
Affiliation(s)
- K Blighe
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA.
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK.
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, WC1E 6DD, London, UK.
| | - L DeDionisio
- Avellino Laboratories, Menlo Park, CA, 94025, USA
| | - K A Christie
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
| | - B Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - S Shareef
- University of Raparin, Ranya, Kurdistan Region, Iraq
| | - T Kakouli-Duarte
- Institute of Technology Carlow, Department of Science and Health, Kilkenny Road, Carlow, Ireland
| | - C Chao-Shern
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
- Avellino Laboratories, Menlo Park, CA, 94025, USA
| | - V Harding
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - R S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA
| | - L Castellano
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- JMS Building, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - J Stebbing
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - J A Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA
| | - M A Nesbit
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
| | - C B T Moore
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK.
- Avellino Laboratories, Menlo Park, CA, 94025, USA.
| |
Collapse
|
32
|
Batugedara G, Le Roch KG. Unraveling the 3D genome of human malaria parasites. Semin Cell Dev Biol 2018; 90:144-153. [PMID: 30009946 DOI: 10.1016/j.semcdb.2018.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/03/2018] [Indexed: 01/31/2023]
Abstract
The chromosomes within the eukaryotic cell nucleus are highly dynamic and adopt complex hierarchical structures. Understanding how this three-dimensional (3D) nuclear architectureaffects gene regulation, cell cycle progression and disease pathogenesis are important biological questions in development and disease. Recently, many genome-wide technologies including chromosome conformation capture (3C) and 3C-based methodologies (4C, 5C, and Hi-C) have been developed to investigate 3D chromatin structure. In this review, we introduce 3D genome methodologies, with a focus on their application for understanding the nuclear architecture of the human malaria parasite, Plasmodium falciparum. An increasing amount of evidence now suggests that gene regulation in the parasite is largely regulated by epigenetic mechanisms and nuclear reorganization. Here, we explore the 3D genome architecture of P. falciparum, including local and global chromatin structure. In addition, molecular components important for maintaining 3D chromatin organization including architectural proteins and long non-coding RNAs are discussed. Collectively, these studies contribute to our understanding of how the plasticity of 3D genome architecture regulates gene expression and cell cycle progression in this deadly parasite.
Collapse
Affiliation(s)
- Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA.
| |
Collapse
|
33
|
Zhang M, Wang C, Otto TD, Oberstaller J, Liao X, Adapa SR, Udenze K, Bronner IF, Casandra D, Mayho M, Brown J, Li S, Swanson J, Rayner JC, Jiang RHY, Adams JH. Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science 2018; 360:360/6388/eaap7847. [PMID: 29724925 DOI: 10.1126/science.aap7847] [Citation(s) in RCA: 537] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022]
Abstract
Severe malaria is caused by the apicomplexan parasite Plasmodium falciparum. Despite decades of research, the distinct biology of these parasites has made it challenging to establish high-throughput genetic approaches to identify and prioritize therapeutic targets. Using transposon mutagenesis of P. falciparum in an approach that exploited its AT-rich genome, we generated more than 38,000 mutants, saturating the genome and defining mutability and fitness costs for over 87% of genes. Of 5399 genes, our study defined 2680 genes as essential for optimal growth of asexual blood stages in vitro. These essential genes are associated with drug resistance, represent leading vaccine candidates, and include approximately 1000 Plasmodium-conserved genes of unknown function. We validated this approach by testing proteasome pathways for individual mutants associated with artemisinin sensitivity.
Collapse
Affiliation(s)
- Min Zhang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Jenna Oberstaller
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Xiangyun Liao
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Kenneth Udenze
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Iraad F Bronner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Deborah Casandra
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Matthew Mayho
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Jacqueline Brown
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Suzanne Li
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Justin Swanson
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK.
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
| | - John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
| |
Collapse
|
34
|
Sen U, Saxena H, Khurana J, Nayak A, Gupta A. Plasmodium falciparum RUVBL3 protein: a novel DNA modifying enzyme and an interacting partner of essential HAT protein MYST. Sci Rep 2018; 8:10917. [PMID: 30026605 PMCID: PMC6053374 DOI: 10.1038/s41598-018-29137-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/26/2018] [Indexed: 11/09/2022] Open
Abstract
RUVBLs constitute a conserved group of ATPase proteins that play significant role in a variety of cellular processes including transcriptional regulation, cell cycle and DNA damage repair. Three RUVBL homologues, namely, PfRUVBL1, PfRUVBL2 and PfRUVBL3 have been identified in P. falciparum, unlike its eukaryotic counterparts, which have two RUVBL proteins (RUVBL1 & RUVBL2). The present study expands our understanding of PfRUVBL3 protein and thereby basic biology of Plasmodium in general. Here, we have shown that parasite PfRUVBL3 is a true homolog of human/yeast RUVBL2 protein. Our result show that PfRUVBL3 constitutively expresses throughout the stages of intra-erythrocytic cycle (IDC) with varied localization. In addition to ATPase and oligomerization activity, we have for the first time shown that PfRUVBL3 possess DNA cleavage activity which interestingly is dependent on its insertion domain. Furthermore, we have also identified RUVBL3 to be an interacting partner of an essential chromatin remodeling protein PfMYST and together they colocalize with H3K9me1 histone in parasitophorous vacuole during the ring stage of IDC suggesting their potential involvement in chromatin remodeling and gene transcription.
Collapse
Affiliation(s)
- Utsav Sen
- Department of Life Sciences, Shiv Nadar University, Greater Noida, 201314, India
| | - Himani Saxena
- Department of Life Sciences, Shiv Nadar University, Greater Noida, 201314, India
| | - Juhi Khurana
- Department of Life Sciences, Shiv Nadar University, Greater Noida, 201314, India
| | - Akshaykumar Nayak
- Department of Life Sciences, Shiv Nadar University, Greater Noida, 201314, India
| | - Ashish Gupta
- Department of Life Sciences, Shiv Nadar University, Greater Noida, 201314, India.
| |
Collapse
|
35
|
Abstract
Eukaryotic pathogens must survive in different hosts, respond to changing environments, and exploit specialized niches to propagate. Plasmodium parasites cause human malaria during bloodstream infections, where they must persist long enough to be transmitted. Parasites have evolved diverse strategies of variant gene expression that control critical biological processes of blood-stage infections, including antigenic variation, erythrocyte invasion, innate immune evasion, and nutrient acquisition, as well as life-cycle transitions. Epigenetic mechanisms within the parasite are being elucidated, with discovery of epigenomic marks associated with gene silencing and activation, and the identification of epigenetic regulators and chromatin proteins that are required for the switching and maintenance of gene expression. Here, we review the key epigenetic processes that facilitate transition through the parasite life cycle and epigenetic regulatory mechanisms utilized by Plasmodium parasites to survive changing environments and consider epigenetic switching in the context of the outcome of human infections.
Collapse
Affiliation(s)
- Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA; ,
| | - Kristen M Skillman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA; ,
| |
Collapse
|
36
|
Toenhake CG, Fraschka SAK, Vijayabaskar MS, Westhead DR, van Heeringen SJ, Bártfai R. Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development. Cell Host Microbe 2018; 23:557-569.e9. [PMID: 29649445 PMCID: PMC5899830 DOI: 10.1016/j.chom.2018.03.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/05/2018] [Accepted: 03/05/2018] [Indexed: 02/07/2023]
Abstract
Underlying the development of malaria parasites within erythrocytes and the resulting pathogenicity is a hardwired program that secures proper timing of gene transcription and production of functionally relevant proteins. How stage-specific gene expression is orchestrated in vivo remains unclear. Here, using the assay for transposase accessible chromatin sequencing (ATAC-seq), we identified ∼4,000 regulatory regions in P. falciparum intraerythrocytic stages. The vast majority of these sites are located within 2 kb upstream of transcribed genes and their chromatin accessibility pattern correlates positively with abundance of the respective mRNA transcript. Importantly, these regions are sufficient to drive stage-specific reporter gene expression and DNA motifs enriched in stage-specific sets of regulatory regions interact with members of the P. falciparum AP2 transcription factor family. Collectively, this study provides initial insights into the in vivo gene regulatory network of P. falciparum intraerythrocytic stages and should serve as a valuable resource for future studies.
Collapse
Affiliation(s)
- Christa Geeke Toenhake
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, 6525 GA, the Netherlands
| | | | | | - David Robert Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Simon Jan van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, Nijmegen, 6525 GA, the Netherlands
| | - Richárd Bártfai
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, 6525 GA, the Netherlands.
| |
Collapse
|
37
|
Abstract
Transcription is regulated by transcription factor (TF) binding at promoters and distal regulatory elements and histone modifications that control the accessibility of these elements. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard assay for identifying genome-wide protein-DNA interactions in vitro and in vivo. As large-scale ChIP-seq data sets have been collected for different TFs and histone modifications, their potential to predict gene expression can be used to test hypotheses about the mechanisms of gene regulation. In addition, complementary functional genomics assays provide a global view of chromatin accessibility and long-range cis-regulatory interactions that are being combined with TF binding and histone remodeling to study the regulation of gene expression. Thus, ChIP-seq analysis is now widely integrated with other functional genomics assays to better understand gene regulatory mechanisms. In this review, we discuss advances and challenges in integrating ChIP-seq data to identify context-specific chromatin states associated with gene activity. We describe the overall computational design of integrating ChIP-seq data with other functional genomics assays. We also discuss the challenges of extending these methods to low-input ChIP-seq assays and related single-cell assays.
Collapse
Affiliation(s)
| | - Ali Mortazavi
- Corresponding author: Ali Mortazavi, Department of Developmental and Cell Biology, 2300 Biological Sciences 3, University of California, Irvine, CA 92697, USA. Tel: (949)824-6762; E-mail:
| |
Collapse
|
38
|
Schang AL, Sabéran-Djoneidi D, Mezger V. The impact of epigenomic next-generation sequencing approaches on our understanding of neuropsychiatric disorders. Clin Genet 2017; 93:467-480. [DOI: 10.1111/cge.13097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/31/2022]
Affiliation(s)
- A.-L. Schang
- CNRS; UMR7216 Épigénétique et Destin Cellulaire; F-75205 Paris Cedex 13 France
- Univ Paris Diderot; Sorbonne Paris Cité, F-75205 Paris Cedex 13 France
- Département Hospitalo-Universitaire PROTECT; Paris France
| | - D. Sabéran-Djoneidi
- CNRS; UMR7216 Épigénétique et Destin Cellulaire; F-75205 Paris Cedex 13 France
- Univ Paris Diderot; Sorbonne Paris Cité, F-75205 Paris Cedex 13 France
| | - V. Mezger
- CNRS; UMR7216 Épigénétique et Destin Cellulaire; F-75205 Paris Cedex 13 France
- Univ Paris Diderot; Sorbonne Paris Cité, F-75205 Paris Cedex 13 France
| |
Collapse
|
39
|
Ubhe S, Rawat M, Verma S, Anamika K, Karmodiya K. Genome-wide identification of novel intergenic enhancer-like elements: implications in the regulation of transcription in Plasmodium falciparum. BMC Genomics 2017; 18:656. [PMID: 28836940 PMCID: PMC5569477 DOI: 10.1186/s12864-017-4052-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 08/11/2017] [Indexed: 01/28/2023] Open
Abstract
Background The molecular mechanisms of transcriptional regulation are poorly understood in Plasmodium falciparum. In addition, most of the genes in Plasmodium falciparum are transcriptionally poised and only a handful of cis-regulatory elements are known to operate in transcriptional regulation. Here, we employed an epigenetic signature based approach to identify significance of previously uncharacterised intergenic regions enriched with histone modification marks leading to discovery of enhancer-like elements. Results We found that enhancer-like elements are significantly enriched with H3K4me1, generate unique non-coding bi-directional RNAs and majority of them can function as cis-regulators. Furthermore, functional enhancer reporter assay demonstrates that the enhancer-like elements regulate transcription of target genes in Plasmodium falciparum. Our study also suggests that the Plasmodium genome segregates functionally related genes into discrete housekeeping and pathogenicity/virulence clusters, presumably for robust transcriptional control of virulence/pathogenicity genes. Conclusions This report contributes to the understanding of parasite regulatory genomics by identification of enhancer-like elements, defining their epigenetic and transcriptional features and provides a resource of functional cis-regulatory elements that may give insights into the virulence/pathogenicity of Plasmodium falciparum. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4052-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Suyog Ubhe
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, 411008, India
| | - Mukul Rawat
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, 411008, India
| | - Srikant Verma
- Labs, Persistent Systems Limited, Pingala - Aryabhata, Erandwane, Pune, 411004, India
| | - Krishanpal Anamika
- Labs, Persistent Systems Limited, Pingala - Aryabhata, Erandwane, Pune, 411004, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, 411008, India.
| |
Collapse
|
40
|
Gupta AP, Zhu L, Tripathi J, Kucharski M, Patra A, Bozdech Z. Histone 4 lysine 8 acetylation regulates proliferation and host-pathogen interaction in Plasmodium falciparum. Epigenetics Chromatin 2017; 10:40. [PMID: 28830512 PMCID: PMC5568195 DOI: 10.1186/s13072-017-0147-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/07/2017] [Indexed: 01/09/2023] Open
Abstract
Background The dynamics of histone modifications in Plasmodium falciparum indicates the existence of unique mechanisms that link epigenetic factors with transcription. Here, we studied the impact of acetylated histone code on transcriptional regulation during the intraerythrocytic developmental cycle (IDC) of P. falciparum. Results Using a dominant-negative transgenic approach, we showed that acetylations of histone H4 play a direct role in transcription. Specifically, these histone modifications mediate an inverse transcriptional relationship between the factors of cell proliferation and host–parasite interaction. Out of the four H4 acetylations, H4K8ac is likely the rate-limiting, regulatory step, which modulates the overall dynamics of H4 posttranslational modifications. H4K8ac exhibits maximum responsiveness to HDAC inhibitors and has a highly dynamic distribution pattern along the genome of P. falciparum during the IDC. Moreover, H4K8ac functions mainly in the euchromatin where its occupancy shifts from intergenic regions located upstream of 5′ end of open reading frame into the protein coding regions. This shift is directly or indirectly associated with transcriptional activities at the corresponding genes. H4K8ac is also active in the heterochromatin where it stimulates expression of the main antigenic gene family (var) by its presence in the promoter region. Conclusions Overall, we demonstrate that H4K8ac is a potential major regulator of chromatin-linked transcriptional changes during P. falciparum life cycle which is associated not only with euchromatin but also with heterochromatin environment. This is potentially a highly significant finding that suggests a regulatory connection between growth and parasite–host interaction both of which play a major role in malaria parasite virulence. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0147-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Archana P Gupta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jaishree Tripathi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Michal Kucharski
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Alok Patra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| |
Collapse
|
41
|
Lu X, Batugedara G, Lee M, Prudhomme J, Bunnik EM, Le Roch K. Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2017; 45:7825-7840. [PMID: 28531310 PMCID: PMC5737683 DOI: 10.1093/nar/gkx464] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/18/2022] Open
Abstract
Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular players that regulate stage-specific gene expression and Pol II pausing will contribute to our continuous search for novel antimalarial drug targets.
Collapse
MESH Headings
- Animals
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Genes, Protozoan
- Humans
- Malaria, Falciparum/blood
- Malaria, Falciparum/parasitology
- Plasmodium falciparum/genetics
- Plasmodium falciparum/growth & development
- Plasmodium falciparum/pathogenicity
- Promoter Regions, Genetic
- RNA Polymerase II/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- Sequence Analysis, RNA
- Transcription, Genetic
Collapse
Affiliation(s)
- Xueqing Maggie Lu
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Michael Lee
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Evelien M. Bunnik
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Karine G. Le Roch
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| |
Collapse
|
42
|
Single-molecule analysis reveals that DNA replication dynamics vary across the course of schizogony in the malaria parasite Plasmodium falciparum. Sci Rep 2017. [PMID: 28638076 PMCID: PMC5479783 DOI: 10.1038/s41598-017-04407-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The mechanics of DNA replication and cell cycling are well-characterized in model organisms, but less is known about these basic aspects of cell biology in early-diverging Apicomplexan parasites, which do not divide by canonical binary fission but undergo unconventional cycles. Schizogony in the malaria parasite, Plasmodium, generates ~16–24 new nuclei via independent, asynchronous rounds of genome replication prior to cytokinesis and little is known about the control of DNA replication that facilitates this. We have characterised replication dynamics in P. falciparum throughout schizogony, using DNA fibre labelling and combing to visualise replication forks at a single-molecule level. We show that origins are very closely spaced in Plasmodium compared to most model systems, and that replication dynamics vary across the course of schizogony, from faster synthesis rates and more widely-spaced origins through to slower synthesis rates and closer-spaced origins. This is the opposite of the pattern usually seen across S-phase in human cells, when a single genome is replicated. Replication forks also appear to stall at an unusually high rate throughout schizogony. Our work explores Plasmodium DNA replication in unprecedented detail and opens up tremendous scope for analysing cell cycle dynamics and developing interventions targetting this unique aspect of malaria biology.
Collapse
|
43
|
Batugedara G, Lu XM, Bunnik EM, Le Roch KG. The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite. Trends Parasitol 2017; 33:364-377. [PMID: 28065669 PMCID: PMC5410391 DOI: 10.1016/j.pt.2016.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/28/2016] [Accepted: 12/07/2016] [Indexed: 12/11/2022]
Abstract
The human malaria parasite, Plasmodium falciparum, depends on a coordinated regulation of gene expression for development and propagation within the human host. Recent developments suggest that gene regulation in the parasite is largely controlled by epigenetic mechanisms. Here, we discuss recent advancements contributing to our understanding of the mechanisms controlling gene regulation in the parasite, including nucleosome landscape, histone modifications, and nuclear architecture. In addition, various processes involved in regulation of parasite-specific genes and gene families are examined. Finally, we address the use of epigenetic processes as targets for novel antimalarial therapies. Collectively, these topics highlight the unique biology of P. falciparum, and contribute to our understanding of mechanisms regulating gene expression in this deadly parasite.
Collapse
Affiliation(s)
- Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Xueqing M Lu
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
| | - Evelien M Bunnik
- Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA.
| |
Collapse
|
44
|
Gupta AP, Bozdech Z. Epigenetic landscapes underlining global patterns of gene expression in the human malaria parasite, Plasmodium falciparum. Int J Parasitol 2017; 47:399-407. [PMID: 28414071 DOI: 10.1016/j.ijpara.2016.10.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/15/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022]
Abstract
The dynamic chromatin landscape displaying combinatorial complexity of the epigenome impacts gene expression that underlies many events of differentiation and cell cycle progression. In the past few years, epigenetic mechanisms have emerged as important processes involved in the tight gene regulation in malaria parasites, Plasmodium spp. Focusing predominantly on Plasmodium falciparum, the species associated with the most severe form of the disease, many advances have been made in our understanding of the interaction between transcriptional regulation and epigenetic mechanisms as the pivotal processes in regulating life cycle progression, host parasite interactions and parasite adaptation to the host environment. This review focuses on the epigenome and its effect on transcriptional regulation in P. falciparum, highlighting its unique, evolutionary diverse features.
Collapse
Affiliation(s)
- Archana P Gupta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| |
Collapse
|
45
|
Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites. Sci Rep 2017; 7:607. [PMID: 28377601 PMCID: PMC5428830 DOI: 10.1038/s41598-017-00687-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/08/2017] [Indexed: 01/24/2023] Open
Abstract
Gene expression in Plasmodia integrates post-transcriptional regulation with epigenetic marking of active genomic regions through histone post-translational modifications (PTMs). To generate insights into the importance of histone PTMs to the entire asexual and sexual developmental cycles of the parasite, we used complementary and comparative quantitative chromatin proteomics to identify and functionally characterise histone PTMs in 8 distinct life cycle stages of P. falciparum parasites. ~500 individual histone PTMs were identified of which 106 could be stringently validated. 46 individual histone PTMs and 30 co-existing PTMs were fully quantified with high confidence. Importantly, 15 of these histone PTMs are novel for Plasmodia (e.g. H3K122ac, H3K27me3, H3K56me3). The comparative nature of the data revealed a highly dynamic histone PTM landscape during life cycle development, with a set of histone PTMs (H3K4ac, H3K9me1 and H3K36me2) displaying a unique and conserved abundance profile exclusively during gametocytogenesis (P < 0.001). Euchromatic histone PTMs are abundant during schizogony and late gametocytes; heterochromatic PTMs mark early gametocytes. Collectively, this data provides the most accurate, complete and comparative chromatin proteomic analyses of the entire life cycle development of malaria parasites. A substantial association between histone PTMs and stage-specific transition provides insights into the intricacies characterising Plasmodial developmental biology.
Collapse
|
46
|
Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning. PLoS Pathog 2016; 12:e1006080. [PMID: 28033404 PMCID: PMC5198986 DOI: 10.1371/journal.ppat.1006080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/19/2016] [Indexed: 11/19/2022] Open
Abstract
The packaging and organization of genomic DNA into chromatin represents an additional regulatory layer of gene expression, with specific nucleosome positions that restrict the accessibility of regulatory DNA elements. The mechanisms that position nucleosomes in vivo are thought to depend on the biophysical properties of the histones, sequence patterns, like phased di-nucleotide repeats and the architecture of the histone octamer that folds DNA in 1.65 tight turns. Comparative studies of human and P. falciparum histones reveal that the latter have a strongly reduced ability to recognize internal sequence dependent nucleosome positioning signals. In contrast, the nucleosomes are positioned by AT-repeat sequences flanking nucleosomes in vivo and in vitro. Further, the strong sequence variations in the plasmodium histones, compared to other mammalian histones, do not present adaptations to its AT-rich genome. Human and parasite histones bind with higher affinity to GC-rich DNA and with lower affinity to AT-rich DNA. However, the plasmodium nucleosomes are overall less stable, with increased temperature induced mobility, decreased salt stability of the histones H2A and H2B and considerable reduced binding affinity to GC-rich DNA, as compared with the human nucleosomes. In addition, we show that plasmodium histone octamers form the shortest known nucleosome repeat length (155bp) in vitro and in vivo. Our data suggest that the biochemical properties of the parasite histones are distinct from the typical characteristics of other eukaryotic histones and these properties reflect the increased accessibility of the P. falciparum genome. Nucleosomes are not positioned randomly on DNA but on preferential sites with respect to the underlying DNA sequence. Histones belong to the most conserved eukaryotic proteins, as sequence dependent nucleosome positioning is an essential regulatory feature of nucleosomes, determining the accessibility of regulatory factors to DNA. We determined the biochemical properties of plasmodium histones and show that they are distinct from human forms, explaining the accessible chromatin structure of P. falciparum. Amino acid exchanges in the histones do not present an adaption to the AT-rich genome, but rather reduce the binding affinity to GC-rich DNA sequences, resulting in rather unstable nucleosomes with labile H2A and H2B, requiring extra-nucleosomal positioning signals to keep them on place. Plasmodium chromatin exhibits the shortest nucleosome spacing known to date potentially inhibiting the formation of higher order structures and maintaining chromatin accessible.
Collapse
|
47
|
Abstract
Malaria continues to impose a significant disease burden on low- and middle-income countries in the tropics. However, revolutionary progress over the last 3 years in nucleic acid sequencing, reverse genetics, and post-genome analyses has generated step changes in our understanding of malaria parasite (Plasmodium spp.) biology and its interactions with its host and vector. Driven by the availability of vast amounts of genome sequence data from Plasmodium species strains, relevant human populations of different ethnicities, and mosquito vectors, researchers can consider any biological component of the malarial process in isolation or in the interactive setting that is infection. In particular, considerable progress has been made in the area of population genomics, with Plasmodium falciparum serving as a highly relevant model. Such studies have demonstrated that genome evolution under strong selective pressure can be detected. These data, combined with reverse genetics, have enabled the identification of the region of the P. falciparum genome that is under selective pressure and the confirmation of the functionality of the mutations in the kelch13 gene that accompany resistance to the major frontline antimalarial, artemisinin. Furthermore, the central role of epigenetic regulation of gene expression and antigenic variation and developmental fate in P. falciparum is becoming ever clearer. This review summarizes recent exciting discoveries that genome technologies have enabled in malaria research and highlights some of their applications to healthcare. The knowledge gained will help to develop surveillance approaches for the emergence or spread of drug resistance and to identify new targets for the development of antimalarial drugs and perhaps vaccines.
Collapse
Affiliation(s)
- Sebastian Kirchner
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - B Joanne Power
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Andrew P Waters
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
| |
Collapse
|
48
|
Wang C, Adapa SR, Gibbons J, Sutton S, Jiang RHY. Punctuated chromatin states regulate Plasmodium falciparum antigenic variation at the intron and 2 kb upstream regions. BMC Genomics 2016; 17:652. [PMID: 27538502 PMCID: PMC4990864 DOI: 10.1186/s12864-016-3005-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/10/2016] [Indexed: 11/27/2022] Open
Abstract
Background Understanding the regulation mechanism of var gene expression is crucial for explaining antigenic variation in Plasmodium falciparum. Recent work observed that while all var genes produce transcripts, only a few var genes exhibit high expression levels. However, the global regulation of var expression and the relationship between epigenetic and genetic control remains to be established. Result We have systematically reanalyzed the existing genomic data including chromatin configurations and gene expressions; and for the first time used robust statistical methods to show that the intron and 2 kb upstream regions of each endogenous var gene always maintain high chromatin accessibility, with high potential to bind transcription factors (TFs). The levels of transcripts for different var gene family members are associated with this chromatin accessibility. Any given var gene thus shows punctuated chromatin states throughout the asexual life cycle. This is demonstrated by three independent transcript datasets. Chromatin accessibility in the var intron and 2 kb upstream regions are also positively correlated with their GC content, suggesting the level of var genes silencing might be encoded in their intron sequences. Interestingly, both var intron and 2 kb upstream regions exhibit higher chromatin accessibility when the genes have relatively lower transcription levels, suggesting a punctuated repressive function for these regulatory elements. Conclusion By integrating and analyzing epigenomic, genomic and transcriptomic data, our work reveals a novel distal element in var control. We found dynamic modulations of specific epigenetic marks around the var intron and distal upstream regions are involved in the general var gene expression patterns in malarial antigenic variation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3005-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Chengqi Wang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Swamy R Adapa
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Justin Gibbons
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA.,Department of Molecular Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Stephen Sutton
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Rays H Y Jiang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA.
| |
Collapse
|
49
|
The nuclear envelope and gene organization in parasitic protozoa: Specializations associated with disease. Mol Biochem Parasitol 2016; 209:104-113. [PMID: 27475118 DOI: 10.1016/j.molbiopara.2016.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/12/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022]
Abstract
The parasitic protozoa Trypanosoma brucei and Plasmodium falciparum are lethal human parasites that have developed elegant strategies of immune evasion by antigenic variation. Despite the vast evolutionary distance between the two taxa, both parasites employ strict monoallelic expression of their membrane proteins, variant surface glycoproteins in Trypanosomes and the var, rif and stevor genes in Plasmodium, in order to evade their host's immune system. Additionally, both telomeric location and epigenetic controls are prominent features of these membrane proteins. As such, telomeres, chromatin structure and nuclear organization all contribute to control of gene expression and immune evasion. Here, we discuss the importance of epigenetics and sub-nuclear context for the survival of these disease-causing parasites.
Collapse
|
50
|
Saraf A, Cervantes S, Bunnik EM, Ponts N, Sardiu ME, Chung DWD, Prudhomme J, Varberg JM, Wen Z, Washburn MP, Florens L, Le Roch KG. Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite. J Proteome Res 2016; 15:2787-801. [PMID: 27291344 DOI: 10.1021/acs.jproteome.6b00366] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A major obstacle in understanding the complex biology of the malaria parasite remains to discover how gene transcription is controlled during its life cycle. Accumulating evidence indicates that the parasite's epigenetic state plays a fundamental role in gene expression and virulence. Using a comprehensive and quantitative mass spectrometry approach, we determined the global and dynamic abundance of histones and their covalent post-transcriptional modifications throughout the intraerythrocytic developmental cycle of Plasmodium falciparum. We detected a total of 232 distinct modifications, of which 160 had never been detected in Plasmodium and 88 had never been identified in any other species. We further validated over 10% of the detected modifications and their expression patterns by multiple reaction monitoring assays. In addition, we uncovered an unusual chromatin organization with parasite-specific histone modifications and combinatorial dynamics that may be directly related to transcriptional activity, DNA replication, and cell cycle progression. Overall, our data suggest that the malaria parasite has a unique histone modification signature that correlates with parasite virulence.
Collapse
Affiliation(s)
- Anita Saraf
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Serena Cervantes
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Evelien M Bunnik
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Nadia Ponts
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Duk-Won D Chung
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| | - Joseph M Varberg
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Zhihui Wen
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Michael P Washburn
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center , 3901 Rainbow Boulevard, Kansas City, Kansas 66160, United States
| | - Laurence Florens
- Stowers Institute for Medical Research , 1000 E. 50th Street, Kansas City, Missouri 64110, United States
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California , 900 University Avenue, Riverside, California 92521, United States
| |
Collapse
|