Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite
Abstract
:1. Introduction
2. Materials and Methods
2.1. Parasite Culture Conditions and Synchronization
2.2. Extraction of RNA and cDNA Synthesis
2.3. Selection of Genes for the RNA Editing Study
2.4. Primer Design
2.5. Sequencing of PCR Products
2.6. Quantification of Different RNA Editing Events
2.7. Prediction of mRNA and Protein Structures
2.8. Tight Synchronization and RNA Extraction for NGS
2.9. RNA Integrity Test to Check for Hidden Breaks (HBs)
2.10. Library Preparation for Total mRNA Sequencing
2.10.1. Quality Control
2.10.2. Data Analyses
2.11. RNA Seq Data Analysis and Integrated Genomics Viewer (IGV) Analysis for RNA Editing Event Detection and Quantification
2.12. Stage-Specific Expression of RNA Editing-Related Genes
3. Results
3.1. RNA Editing Event Detection
3.2. RNA Integrity Test to Check for Hidden Breaks (HBs)
3.3. RNA Editing Affects RNA and Protein Secondary Structures
3.4. RNA Seq Data Analysis and IGV Analysis for RNA Editing Event Detection
3.5. Stage-Specific Expression of RNA Editing-Related Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Variation/Editing Site in Transcript; Gene ID PF3D7_0112700 | Variation/Editing Types | Genomic Sequence | Stage-Specific Editing% | |||||
---|---|---|---|---|---|---|---|---|
8 h | 16 h | 24 h | 32 h | 40 h | 46 h | |||
751 | G>C | TCGTC | 0% | 0% | 0% | 0% | 12% | 0% |
773 | G>A | GAGTC | 0% | 0% | 0% | 0% | 10% | 0% |
2633 | A>C | AAATT | 100% | 100% | 100% | 100% | 100% | 100% |
2645 | T>C | TTTAA | 100% | 100% | 100% | 100% | 100% | 100% |
2649 | T>C | ATTAA | 100% | 100% | 100% | 100% | 100% | 100% |
2649 | C>G | ATCAA | 20% | 35% | 0% | 0% | 0% | 0% |
2737 | T>G | ATTAA | 17% | 28% | 0% | 0% | 0% | 0% |
2761 | T>C | ACTTG | 20% | 31% | 0% | 0% | 0% | 0% |
2763 | G>A | TTGCT | 0% | 24% | 0% | 0% | 0% | 0% |
2769 | T>C | TCTAG | 22% | 31% | 0% | 0% | 0% | 0% |
2800 | G>C | TGGCA | 0% | 0% | 16% | 0% | 0% | 0% |
2802 | A>G | GCAAA | 20% | 25% | 0% | 0% | 0% | 0% |
2803 | A>G | CAAAA | 17% | 27% | 0% | 0% | 0% | 0% |
2814 | G>A | GGGAA | 0% | 0% | 0% | 0% | 0% | 11% |
2818 | G>A | AAGAA | 17% | 29% | 0% | 0% | 0% | 0% |
2821 | G>A | AAGAC | 0% | 0% | 0% | 0% | 0% | 7% |
2836 | T>G | TTTAC | 18% | 31% | 0% | 0% | 0% | 0% |
2850 | T>A | CTTT | 3% | 17% | 0% | 0% | 0% | 0% |
2851 | T>C | CTTTG | 9% | 20% | 0% | 0% | 0% | 0% |
2852 | T>G | TTTGT | 0% | 5% | 0% | 0% | 0% | 0% |
Editing Site in Transcript; Gene ID PF3D7_0112700 | Editing Types | Genomic Sequence | Editing% in Time Course/NGS Data on IGV View | |||
---|---|---|---|---|---|---|
16 h | 24 h | 32 h | 40 h | |||
2737 | T>G | ATTAA | 20% | 9% | 3% | 3% |
2761 | T>C | ACTTG | 19% | 7% | 2% | 3% |
2763 | G>A | TTGCT | 20% | 7% | 2% | 3% |
2769 | T>C | TCTAG | 19% | 8% | 2% | 4% |
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Azad, M.T.A.; Sugi, T.; Qulsum, U.; Kato, K. Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite. Microorganisms 2024, 12, 137. https://doi.org/10.3390/microorganisms12010137
Azad MTA, Sugi T, Qulsum U, Kato K. Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite. Microorganisms. 2024; 12(1):137. https://doi.org/10.3390/microorganisms12010137
Chicago/Turabian StyleAzad, Md Thoufic Anam, Tatsuki Sugi, Umme Qulsum, and Kentaro Kato. 2024. "Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite" Microorganisms 12, no. 1: 137. https://doi.org/10.3390/microorganisms12010137
APA StyleAzad, M. T. A., Sugi, T., Qulsum, U., & Kato, K. (2024). Detection of Developmental Asexual Stage-Specific RNA Editing Events in Plasmodium falciparum 3D7 Malaria Parasite. Microorganisms, 12(1), 137. https://doi.org/10.3390/microorganisms12010137