1
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Interplay Between the Histone Variant H2A.Z and the Epigenome in Pancreatic Cancer. Arch Med Res 2022; 53:840-858. [PMID: 36470770 DOI: 10.1016/j.arcmed.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/25/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND The oncogenic process is orchestrated by a complex network of chromatin remodeling elements that shape the cancer epigenome. Histone variant H2A.Z regulates DNA control elements such as promoters and enhancers in different types of cancer; however, the interplay between H2A.Z and the pancreatic cancer epigenome is unknown. OBJECTIVE This study analyzed the role of H2A.Z in different DNA regulatory elements. METHODS We performed Chromatin Immunoprecipitation Sequencing assays (ChiP-seq) with total H2A.Z and acetylated H2A.Z (acH2A.Z) antibodies and analyzed published data from ChIP-seq, RNA-seq, bromouridine labeling-UV and sequencing (BruUV-seq), Hi-C and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) in the pancreatic cancer cell line PANC-1. RESULTS The results indicate that total H2A.Z facilitates the recruitment of RNA polymerase II and transcription factors at promoters and enhancers allowing the expression of pro-oncogenic genes. Interestingly, we demonstrated that H2A.Z is enriched in super-enhancers (SEs) contributing to the transcriptional activation of key genes implicated in tumor development. Importantly, we established that H2A.Z contributes to the three-dimensional (3D) genome organization of pancreatic cancer and that it is a component of the Topological Associated Domains (TADs) boundaries in PANC-1 and that total H2A.Z and acH2A.Z are associated with A and B compartments, respectively. CONCLUSIONS H2A.Z participates in the biology and development of pancreatic cancer by generating a pro-oncogenic transcriptome through its posttranslational modifications, interactions with different partners, and regulatory elements, contributing to the oncogenic 3D genome organization. These data allow us to understand the molecular mechanisms that promote an oncogenic transcriptome in pancreatic cancer mediated by H2A.Z.
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2
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Shang X, Wang C, Shen L, Sheng F, He X, Wang F, Fan Y, He X, Jiang M. PfAP2-EXP2, an Essential Transcription Factor for the Intraerythrocytic Development of Plasmodium falciparum. Front Cell Dev Biol 2022; 9:782293. [PMID: 35083215 PMCID: PMC8785209 DOI: 10.3389/fcell.2021.782293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmodium falciparum undergoes a series of asexual replications in human erythrocytes after infection, which are effective targets for combatting malaria. Here, we report roles of an ApiAP2 transcription factor PfAP2-EXP2 (PF3D7_0611200) in the intraerythrocytic developmental cycle of P. falciparum. PfAP2-EXP2 conditional knockdown resulted in an asexual growth defect but without an appreciable effect on parasite morphology. Further ChIP-seq analysis revealed that PfAP2-EXP2 targeted genes related to virulence and interaction between erythrocytes and parasites. Especially, PfAP2-EXP2 regulation of euchromatic genes does not depend on recognizing specific DNA sequences, while a CCCTAAACCC motif is found in its heterochromatic binding sites. Combined with transcriptome profiling, we suggest that PfAP2-EXP2 is participated in the intraerythrocytic development by affecting the expression of genes related to cell remodeling at the schizont stage. In summary, this study explores an ApiAP2 member plays an important role for the P. falciparum blood-stage replication, which suggests a new perspective for malaria elimination.
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Affiliation(s)
- Xiaomin Shang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Changhong Wang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Li Shen
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fei Sheng
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui He
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Fei Wang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yanting Fan
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Mei Jiang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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3
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Shang X, Wang C, Fan Y, Guo G, Wang F, Zhao Y, Sheng F, Tang J, He X, Yu X, Zhang M, Zhu G, Yin S, Mu J, Culleton R, Cao J, Jiang M, Zhang Q. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3413-3431. [PMID: 35288749 PMCID: PMC8989538 DOI: 10.1093/nar/gkac176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/13/2022] Open
Abstract
Heterochromatin-associated gene silencing controls multiple physiological processes in malaria parasites, however, little is known concerning the regulatory network and cis-acting sequences involved in the organization of heterochromatin and how they modulate heterochromatic gene expression. Based on systematic profiling of genome-wide occupancy of eighteen Apicomplexan AP2 transcription factors by ChIP-seq analysis, we identify and characterize eight heterochromatin-associated factors (PfAP2-HFs), which exhibit preferential enrichment within heterochromatic regions but with differential coverage profiles. Although these ApiAP2s target euchromatic gene loci via specific DNA motifs, they are likely integral components of heterochromatin independent of DNA motif recognition. Systematic knockout screenings of ApiAP2 factors coupled with RNA-seq transcriptomic profiling revealed three activators and three repressors of heterochromatic gene expression including four PfAP2-HFs. Notably, expression of virulence genes is either completely silenced or significantly reduced upon the depletion of PfAP2-HC. Integrated multi-omics analyses reveal autoregulation and feed-forward loops to be common features of the ApiAP2 regulatory network, in addition to the occurrence of dynamic interplay between local chromatin structure and ApiAP2s in transcriptional control. Collectively, this study provides a valuable resource describing the genome-wide landscape of the ApiAP2 family and insights into functional divergence and cooperation within this family during the blood-stage development of malaria parasites.
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Affiliation(s)
| | | | | | | | - Fei Wang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yuemeng Zhao
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Fei Sheng
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Meihua Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Shigang Yin
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892-8132, USA
| | - Richard Culleton
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Jun Cao
- Correspondence may also be addressed to Jun Cao. Tel: +05 10 6878 1007;
| | - Mei Jiang
- Correspondence may also be addressed to Mei Jiang. Tel: +86 21 6598 5138;
| | - Qingfeng Zhang
- To whom correspondence should be addressed. Tel: +86 21 6598 5138;
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Gurung P, Gomes AR, Martins RM, Juranek SA, Alberti P, Mbang-Benet DE, Urbach S, Gazanion E, Guitard V, Paeschke K, Lopez-Rubio JJ. PfGBP2 is a novel G-quadruplex binding protein in Plasmodium falciparum. Cell Microbiol 2021; 23:e13303. [PMID: 33340385 DOI: 10.1111/cmi.13303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 11/27/2022]
Abstract
Guanine-quadruplexes (G4s) are non-canonical DNA structures that can regulate key biological processes such as transcription, replication and telomere maintenance in several organisms including eukaryotes, prokaryotes and viruses. Recent reports have identified the presence of G4s within the AT-rich genome of Plasmodium falciparum, the protozoan parasite causing malaria. In Plasmodium, potential G4-forming sequences (G4FS) are enriched in the telomeric and sub-telomeric regions of the genome where they are associated with telomere maintenance and recombination events within virulence genes. However, there is a little understanding about the biological role of G4s and G4-binding proteins. Here, we provide the first snapshot of G4-interactome in P. falciparum using DNA pull-down assay followed by LC-MS/MS. Interestingly, we identified ~24 potential G4-binding proteins (G4-BP) that bind to a stable G4FS (AP2_G4). Furthermore, we characterised the role of G-strand binding protein 2 (PfGBP2), a putative telomere-binding protein in P. falciparum. We validated the interaction of PfGBP2 with G4 in vitro as well as in vivo. PfGBP2 is expressed throughout the intra-erythrocytic developmental cycle and is essential for the parasites in the presence of G4-stabilising ligand, pyridostatin. Gene knockout studies showed the role of PfGBP2 in the expression of var genes. Taken together, this study suggests that PfGBP2 is a bona fide G4-binding protein, which is likely to be involved in the regulation of G4-related functions in these malarial parasites. In addition, this study sheds light on this understudied G4 biology in P. falciparum.
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Affiliation(s)
- Pratima Gurung
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Ana Rita Gomes
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Rafael M Martins
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Patrizia Alberti
- Laboratory Genome Structure and Instability, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U 1154, Paris, France
| | - Diane-Ethna Mbang-Benet
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Serge Urbach
- BioCampus Montpellier, CNRS UMR 5203, IGF, Montpellier, France
| | - Elodie Gazanion
- Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Vincent Guitard
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jose-Juan Lopez-Rubio
- LPHI, UMR 5235, CNRS, INSERM, University of Montpellier, Montpellier, France.,Laboratory of Parasitology and Mycology, CNRS UMR 5290 MIVEGEC, University of Montpellier, Montpellier, France
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5
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Liu H, Cui XY, Xu DD, Wang F, Meng LW, Zhao YM, Liu M, Shen SJ, He XH, Fang Q, Tao ZY, Jiang CZ, Zhang QF, Gu L, Xia H. Actin-related protein Arp4 regulates euchromatic gene expression and development through H2A.Z deposition in blood-stage Plasmodium falciparum. Parasit Vectors 2020; 13:314. [PMID: 32552779 PMCID: PMC7301494 DOI: 10.1186/s13071-020-04139-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/21/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Malaria caused by Plasmodium spp. is still a major threat to public health globally. The various approaches to developing new antimalarial agents rely on the understanding of the complex regulatory mechanisms of dynamic gene expression in the life-cycle of these malaria parasites. The nuclear members of the evolutionarily conserved actin-related protein nuclear (ARP) superfamily are the major components of nucleosome remodelling complexes. In the human malaria parasite Plasmodium falciparum, bioinformatics analysis has predicted three ARP orthologues: PfArp1, PfArp4 and PfArp6. However, little is known about the biological functions of putative PfArp4. In this study, we aimed to investigate the function and the underlying mechanisms of PfArp4 gene regulation. METHODS A conditional gene knockdown approach was adopted by incorporating the glucosamine-inducible glmS ribozyme sequence into the 3' UTR of the PfArp4 and PfArp6 genes. The transgenic parasites PfArp4-Ty1-Ribo, PfArp6-Ty1-Ribo and pL6-PfArp4-Ty1::PfArp6-HA were generated by the CRISPR-Cas9 technique. The knockdown effect in the transgenic parasite was measured by growth curve assay and western blot (WB) analysis. The direct interaction between PfArp4 and PfArp6 was validated by co-IFA and co-IP assays. The euchromatic gene expression mediated through H2A.Z (histone H2A variant) deposition and H3K9ac modification at promoters and regulated by PfArp4, was determined by RNA-seq and ChIP-seq. RESULTS The inducible knockdown of PfArp4 inhibited blood-stage development of P. falciparum. PfArp4 and PfArp6 were colocalized in the nucleus of P. falciparum parasites. PfArp4 gene knockdown altered the global transcriptome. PfArp4 protein colocalized with the histone variant H2A.Z and euchromatic marker H3K9ac in intergenic regions. The inducible downregulation of PfArp4 resulted in the depletion of H2A.Z and lower H3K9ac levels at the upstream regions of eukaryotic genes, thereby repressing the transcriptional abundance of H2A.Z-dependent genes. CONCLUSIONS Our findings suggest that PfArp4 regulates the cell cycle by controlling H2A.Z deposition and affecting centromere function, contributing to the understanding the complex epigenetic regulation of gene expression and the development of P. falciparum.
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Affiliation(s)
- Hui Liu
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, 233030, China
| | - Xin-Yu Cui
- The School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Dan-Dan Xu
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, 233030, China
| | - Fei Wang
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Lin-Wen Meng
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, 233030, China
| | - Yue-Meng Zhao
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Meng Liu
- The School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shi-Jun Shen
- The School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xiao-Hui He
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Qiang Fang
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, 233030, China.,Anhui Provincial Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, 233000, China
| | - Zhi-Yong Tao
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, 233030, China
| | - Ci-Zong Jiang
- The School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.,Tsingtao Advanced Research Institute, Tongji University, Qingdao, 266071, China
| | - Qing-Feng Zhang
- Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Liang Gu
- The School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Hui Xia
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, 233030, China. .,Anhui Provincial Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, 233000, China.
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6
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Abstract
Heterochromatin plays a central role in the process of immune evasion, pathogenesis, and transmission of the malaria parasite Plasmodium falciparum during blood stage infection. Here, we use ChIP sequencing to demonstrate that sporozoites from mosquito salivary glands expand heterochromatin at subtelomeric regions to silence blood-stage-specific genes. Our data also revealed that heterochromatin enrichment is predictive of the transcription status of clonally variant genes members that mediate cytoadhesion in blood stage parasites. A specific member (here called NF54varsporo) of the var gene family remains euchromatic, and the resultant PfEMP1 (NF54_SpzPfEMP1) is expressed at the sporozoite surface. NF54_SpzPfEMP1-specific antibodies efficiently block hepatocyte infection in a strain-specific manner. Furthermore, human volunteers immunized with infective sporozoites developed antibodies against NF54_SpzPfEMP1. Overall, we show that the epigenetic signature of var genes is reset in mosquito stages. Moreover, the identification of a strain-specific sporozoite PfEMP1 is highly relevant for vaccine design based on sporozoites. Sporozoites expand subtelomeric heterochromatin to silence blood-stage-specific genes A strain-specific PfEMP1 is expressed on the surface of sporozoites NF54_SpzPfEMP1 is immunogenic in sporozoite-infected human volunteers Antibodies against NF54_SpzPfEMP1 block sporozoite infection of hepatocytes
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7
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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.
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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
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8
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Herrera-Solorio AM, Vembar SS, MacPherson CR, Lozano-Amado D, Meza GR, Xoconostle-Cazares B, Martins RM, Chen P, Vargas M, Scherf A, Hernández-Rivas R. Clipped histone H3 is integrated into nucleosomes of DNA replication genes in the human malaria parasite Plasmodium falciparum. EMBO Rep 2019; 20:embr.201846331. [PMID: 30833341 PMCID: PMC6446197 DOI: 10.15252/embr.201846331] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 01/15/2023] Open
Abstract
Post-translational modifications of histone H3 N-terminal tails are key epigenetic regulators of virulence gene expression and sexual commitment in the human malaria parasite Plasmodium falciparum Here, we identify proteolytic clipping of the N-terminal tail of nucleosome-associated histone H3 at amino acid position 21 as a new chromatin modification. A cathepsin C-like proteolytic clipping activity is observed in nuclear parasite extracts. Notably, an ectopically expressed version of clipped histone H3, PfH3p-HA, is targeted to the nucleus and integrates into mononucleosomes. Furthermore, chromatin immunoprecipitation and next-generation sequencing analysis identified PfH3p-HA as being highly enriched in the upstream region of six genes that play a key role in DNA replication and repair: In these genes, PfH3p-HA demarcates a specific 1.5 kb chromatin island adjacent to the open reading frame. Our results indicate that, in P. falciparum, the process of histone clipping may precede chromatin integration hinting at preferential targeting of pre-assembled PfH3p-containing nucleosomes to specific genomic regions. The discovery of a protease-directed mode of chromatin organization in P. falciparum opens up new avenues to develop new anti-malarials.
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Affiliation(s)
- Abril Marcela Herrera-Solorio
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
| | - Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Cameron Ross MacPherson
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Daniela Lozano-Amado
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
| | - Gabriela Romero Meza
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
| | - Beatriz Xoconostle-Cazares
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de México, México
| | - Rafael Miyazawa Martins
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Patty Chen
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Miguel Vargas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France .,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Rosaura Hernández-Rivas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (IPN), Ciudad de Mexico, México
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9
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Sindikubwabo F, Ding S, Hussain T, Ortet P, Barakat M, Baumgarten S, Cannella D, Palencia A, Bougdour A, Belmudes L, Couté Y, Tardieux I, Botté CY, Scherf A, Hakimi MA. Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites. eLife 2017; 6:29391. [PMID: 29101771 PMCID: PMC5685513 DOI: 10.7554/elife.29391] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/02/2017] [Indexed: 12/22/2022] Open
Abstract
An unusual genome architecture characterizes the two related human parasitic pathogens Plasmodium falciparum and Toxoplasma gondii. A major fraction of the bulk parasite genome is packaged as transcriptionally permissive euchromatin with few loci embedded in silenced heterochromatin. Primary chromatin shapers include histone modifications at the nucleosome lateral surface close to the DNA but their mode of action remains unclear. We now identify versatile modifications at Lys31 within the globular domain of histone H4 that crucially determine genome organization and expression in Apicomplexa parasites. H4K31 acetylation at the promoter correlates with, and perhaps directly regulates, gene expression in both parasites. By contrast, monomethylated H4K31 is enriched in the core body of T. gondii active genes but inversely correlates with transcription, whereas it is unexpectedly enriched at transcriptionally inactive pericentromeric heterochromatin in P. falciparum, a region devoid of the characteristic H3K9me3 histone mark and its downstream effector HP1.
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Affiliation(s)
- Fabien Sindikubwabo
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Shuai Ding
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, CNRS, ERL 9195, INSERM, Unit U1201, Paris, France
| | - Tahir Hussain
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Philippe Ortet
- Aix-Marseille Univ, CEA, CNRS, UMR 7265, BIAM-LEMIRE, St-Paul-lez-Durance, France
| | - Mohamed Barakat
- Aix-Marseille Univ, CEA, CNRS, UMR 7265, BIAM-LEMIRE, St-Paul-lez-Durance, France
| | - Sebastian Baumgarten
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, CNRS, ERL 9195, INSERM, Unit U1201, Paris, France
| | - Dominique Cannella
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Alexandre Bougdour
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Lucid Belmudes
- Université Grenoble Alpes, CEA, INSERM, Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, Grenoble, France
| | - Isabelle Tardieux
- Institute for Advanced Biosciences (IAB), Team Membrane and Cell Dynamics of Host Parasite Interactions, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Cyrille Y Botté
- Institute for Advanced Biosciences (IAB), Team ApicoLipid, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Artur Scherf
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, CNRS, ERL 9195, INSERM, Unit U1201, Paris, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-pathogen interactions and immunity to infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
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10
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Garcia-Silva MR, Sollelis L, MacPherson CR, Stanojcic S, Kuk N, Crobu L, Bringaud F, Bastien P, Pagès M, Scherf A, Sterkers Y. Identification of the centromeres of Leishmania major: revealing the hidden pieces. EMBO Rep 2017; 18:1968-1977. [PMID: 28935715 DOI: 10.15252/embr.201744216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/15/2017] [Accepted: 08/28/2017] [Indexed: 01/16/2023] Open
Abstract
Leishmania affects millions of people worldwide. Its genome undergoes constitutive mosaic aneuploidy, a type of genomic plasticity that may serve as an adaptive strategy to survive distinct host environments. We previously found high rates of asymmetric chromosome allotments during mitosis that lead to the generation of such ploidy. However, the underlying molecular events remain elusive. Centromeres and kinetochores most likely play a key role in this process, yet their identification has failed using classical methods. Our analysis of the unconventional kinetochore complex recently discovered in Trypanosoma brucei (KKTs) leads to the identification of a Leishmania KKT gene candidate (LmKKT1). The GFP-tagged LmKKT1 displays "kinetochore-like" dynamics of intranuclear localization throughout the cell cycle. By ChIP-Seq assay, one major peak per chromosome is revealed, covering a region of 4 ±2 kb. We find two largely conserved motifs mapping to 14 of 36 chromosomes while a higher density of retroposons are observed in 27 of 36 centromeres. The identification of centromeres and of a kinetochore component of Leishmania chromosomes opens avenues to explore their role in mosaic aneuploidy.
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Affiliation(s)
- Maria-Rosa Garcia-Silva
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Lauriane Sollelis
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Cameron Ross MacPherson
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Slavica Stanojcic
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Nada Kuk
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Lucien Crobu
- CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), University of Bordeaux, Bordeaux, France.,CNRS, UMR 5234, Bordeaux, France
| | - Patrick Bastien
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France.,Department of Parasitology-Mycology, University Hospital Centre (CHU), Montpellier, France
| | - Michel Pagès
- CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Artur Scherf
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Yvon Sterkers
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France .,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France.,Department of Parasitology-Mycology, University Hospital Centre (CHU), Montpellier, France
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11
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Sierra-Miranda M, Vembar SS, Delgadillo DM, Ávila-López PA, Herrera-Solorio AM, Lozano Amado D, Vargas M, Hernandez-Rivas R. PfAP2Tel, harbouring a non-canonical DNA-binding AP2 domain, binds to Plasmodium falciparum telomeres. Cell Microbiol 2017; 19. [PMID: 28376558 DOI: 10.1111/cmi.12742] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 03/18/2017] [Accepted: 03/21/2017] [Indexed: 12/11/2022]
Abstract
The telomeres of the malaria parasite Plasmodium falciparum are essential not only for chromosome end maintenance during blood stage development in humans but also to generate genetic diversity by facilitating homologous recombination of subtelomeric, multigene virulence families such as var and rifin. However, other than the telomerase PfTERT, proteins that act at P. falciparum telomeres are poorly characterised. To isolate components that bind to telomeres, we performed oligonucleotide pulldowns and electromobility shift assays with a telomeric DNA probe and identified a non-canonical member of the ApiAP2 family of transcription factors, PfAP2Tel (encoded by PF3D7_0622900), as a component of the P. falciparum telomere-binding protein complex. PfAP2Tel is expressed throughout the intra-erythrocytic life cycle and localises to the nuclear periphery, co-localising with telomeric clusters. Furthermore, EMSAs using the recombinant protein demonstrated direct binding of PfAP2Tel to telomeric repeats in vitro, while genome-wide chromatin immunoprecipitation followed by next generation sequencing corroborated the high specificity of this protein to telomeric ends of all 14 chromosomes in vivo. Taken together, our data describe a novel function for ApiAP2 proteins at chromosome ends and open new avenues to study the molecular machinery that regulates telomere function in P. falciparum.
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Affiliation(s)
- Miguel Sierra-Miranda
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México, México
| | - Shruthi-Sridhar Vembar
- Unité de Biologie des Interactions Hôte-Parasite, CNRS URA 2581, Institut Pasteur Paris, Paris, France.,CNRS ERL9195, Paris, France.,INSERM U1201, Paris, France
| | - Dulce María Delgadillo
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México, México
| | - Pedro A Ávila-López
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México, México
| | - Abril-Marcela Herrera-Solorio
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México, México
| | - Daniela Lozano Amado
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México, México
| | - Miguel Vargas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México, México
| | - Rosaura Hernandez-Rivas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México, México
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12
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Gómez-Díaz E, Yerbanga RS, Lefèvre T, Cohuet A, Rowley MJ, Ouedraogo JB, Corces VG. Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae. Sci Rep 2017; 7:40655. [PMID: 28091569 PMCID: PMC5238449 DOI: 10.1038/srep40655] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/09/2016] [Indexed: 12/17/2022] Open
Abstract
P. falciparum phenotypic plasticity is linked to the variant expression of clonal multigene families such as the var genes. We have examined changes in transcription and histone modifications that occur during sporogonic development of P. falciparum in the mosquito host. All var genes are silenced or transcribed at low levels in blood stages (gametocyte/ring) of the parasite in the human host. After infection of mosquitoes, a single var gene is selected for expression in the oocyst, and transcription of this gene increases dramatically in the sporozoite. The same PF3D7_1255200 var gene was activated in 4 different experimental infections. Transcription of this var gene during parasite development in the mosquito correlates with the presence of low levels of H3K9me3 at the binding site for the PF3D7_1466400 AP2 transcription factor. This chromatin state in the sporozoite also correlates with the expression of an antisense long non-coding RNA (lncRNA) that has previously been shown to promote var gene transcription during the intraerythrocytic cycle in vitro. Expression of both the sense protein-coding transcript and the antisense lncRNA increase dramatically in sporozoites. The findings suggest a complex process for the activation of a single particular var gene that involves AP2 transcription factors and lncRNAs.
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