Transcriptome analysis reveals a de novo DNA element that may interact with chromatin-associated proteins in Plasmodium berghei during erythrocytic development
Abstract The life cycle of Plasmodium parasites involves intricate, multistage processes that are tightly regulated by stage-specific transcription factors. These factors bind to regulatory regions within gene promoters, enabling the precise expression of genes required for each developmental stage....
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Nature Portfolio
2025-05-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-03586-4 |
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| author | Adaobi Okafor Yagoub Adam Benedikt Brors Ezekiel Adebiyi |
| author_facet | Adaobi Okafor Yagoub Adam Benedikt Brors Ezekiel Adebiyi |
| author_sort | Adaobi Okafor |
| collection | DOAJ |
| description | Abstract The life cycle of Plasmodium parasites involves intricate, multistage processes that are tightly regulated by stage-specific transcription factors. These factors bind to regulatory regions within gene promoters, enabling the precise expression of genes required for each developmental stage. Despite the importance of these transcriptional mechanisms, our understanding remains limited, particularly in the rodent model organism P. berghei. To address this, we conducted a genome-wide analysis of RNA-Seq data from different developmental stages of P. berghei by initially integrating data from human malaria parasites P. falciparum and P. vivax. We identified unique transcriptional signatures across Plasmodium species. Our analysis of P. berghei revealed stage-specific gene sets clustered by expression profiles and predicted regulatory motifs involved in their control. We interpreted these motifs using known binding sites for eukaryotic transcription factors including ApiAP2 proteins. Additionally, we expanded the annotation of the AGGTAA motif which resembles a de novo motif linked to erythrocytic development in P. falciparum, and identified its potential interacting proteins including members of the PfMORC and GCN5 complexes. This study enhances our understanding of gene regulation in P. berghei and provides new insights into the transcriptional dynamics underlying Plasmodium development. |
| format | Article |
| id | doaj-art-e27e22960a624266aa04593e14c92c2b |
| institution | OA Journals |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-e27e22960a624266aa04593e14c92c2b2025-08-20T02:00:03ZengNature PortfolioScientific Reports2045-23222025-05-0115111810.1038/s41598-025-03586-4Transcriptome analysis reveals a de novo DNA element that may interact with chromatin-associated proteins in Plasmodium berghei during erythrocytic developmentAdaobi Okafor0Yagoub Adam1Benedikt Brors2Ezekiel Adebiyi3Applied Bioinformatics, German Cancer Research Center (DKFZ)Covenant University Bioinformatics Research (CUBRe), Covenant UniversityApplied Bioinformatics, German Cancer Research Center (DKFZ)Applied Bioinformatics, German Cancer Research Center (DKFZ)Abstract The life cycle of Plasmodium parasites involves intricate, multistage processes that are tightly regulated by stage-specific transcription factors. These factors bind to regulatory regions within gene promoters, enabling the precise expression of genes required for each developmental stage. Despite the importance of these transcriptional mechanisms, our understanding remains limited, particularly in the rodent model organism P. berghei. To address this, we conducted a genome-wide analysis of RNA-Seq data from different developmental stages of P. berghei by initially integrating data from human malaria parasites P. falciparum and P. vivax. We identified unique transcriptional signatures across Plasmodium species. Our analysis of P. berghei revealed stage-specific gene sets clustered by expression profiles and predicted regulatory motifs involved in their control. We interpreted these motifs using known binding sites for eukaryotic transcription factors including ApiAP2 proteins. Additionally, we expanded the annotation of the AGGTAA motif which resembles a de novo motif linked to erythrocytic development in P. falciparum, and identified its potential interacting proteins including members of the PfMORC and GCN5 complexes. This study enhances our understanding of gene regulation in P. berghei and provides new insights into the transcriptional dynamics underlying Plasmodium development.https://doi.org/10.1038/s41598-025-03586-4Plasmodium bergheiRNA-SeqApiAP2 proteinsRegulatory motifsPlasmodium falciparumPlasmodium vivax |
| spellingShingle | Adaobi Okafor Yagoub Adam Benedikt Brors Ezekiel Adebiyi Transcriptome analysis reveals a de novo DNA element that may interact with chromatin-associated proteins in Plasmodium berghei during erythrocytic development Scientific Reports Plasmodium berghei RNA-Seq ApiAP2 proteins Regulatory motifs Plasmodium falciparum Plasmodium vivax |
| title | Transcriptome analysis reveals a de novo DNA element that may interact with chromatin-associated proteins in Plasmodium berghei during erythrocytic development |
| title_full | Transcriptome analysis reveals a de novo DNA element that may interact with chromatin-associated proteins in Plasmodium berghei during erythrocytic development |
| title_fullStr | Transcriptome analysis reveals a de novo DNA element that may interact with chromatin-associated proteins in Plasmodium berghei during erythrocytic development |
| title_full_unstemmed | Transcriptome analysis reveals a de novo DNA element that may interact with chromatin-associated proteins in Plasmodium berghei during erythrocytic development |
| title_short | Transcriptome analysis reveals a de novo DNA element that may interact with chromatin-associated proteins in Plasmodium berghei during erythrocytic development |
| title_sort | transcriptome analysis reveals a de novo dna element that may interact with chromatin associated proteins in plasmodium berghei during erythrocytic development |
| topic | Plasmodium berghei RNA-Seq ApiAP2 proteins Regulatory motifs Plasmodium falciparum Plasmodium vivax |
| url | https://doi.org/10.1038/s41598-025-03586-4 |
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