ArticleNucleic acids research2018
Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Integration of ATAC-seq and RNA-seq reveals temperature-responsive regulatory regions in Plasmodium falciparum asexual stages.Parasites & vectors · 2026Article
- Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle.BMC genomics · 2026Article
- Epigenetic regulation as a therapeutic target in the malaria parasite Plasmodium falciparum.Malaria journal · 2024Review
- ARID5B-mediated LINC01128 epigenetically activated pyroptosis and apoptosis by promoting the formation of the BTF3/STAT3 complex in β2GPI/anti-β2GPI-treated monocytes.Clinical and translational medicine · 2024Article
- Epigenetic Regulation and Chromatin Remodeling in Malaria Parasites.Annual review of microbiology · 2023Review
- Decoding the impact of nuclear organization on antigenic variation in parasites.Nature microbiology · 2023Review
- Review
- Histone modification analysis reveals common regulators of gene expression in liver and blood stage merozoites of Plasmodium parasites.Epigenetics & chromatin · 2023Article
- A manually curated annotation characterises genomic features of P. falciparum lncRNAs.BMC genomics · 2022Article
- Integrated multi-omics approach revealed cellular senescence landscape.Nucleic acids research · 2022Article
- Review
- Characterization of chromatin accessibility in psoriasis.Frontiers of medicine · 2022Article
- Genome-wide landscape of ApiAP2 transcription factors reveals a heterochromatin-associated regulatory network during Plasmodium falciparum blood-stage development.Nucleic acids research · 2022Article
- Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification.NAR genomics and bioinformatics · 2022Article
- Decrypting the complexity of the human malaria parasite biology through systems biology approaches.Frontiers in systems biology · 2022Article
- Shared Mechanisms for Mutually Exclusive Expression and Antigenic Variation by Protozoan Parasites.Frontiers in cell and developmental biology · 2022Review
- Article
- Peculiarities ofInternational journal of molecular sciences · 2021Review
- Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.PLoS computational biology · 2021Article
- Dynamic Chromatin Structure and Epigenetics Control the Fate of Malaria Parasites.Trends in genetics : TIG · 2021Review
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6 authors.
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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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