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| Status |
Public on Apr 05, 2021 |
| Title |
The RNA Structurome in the Asexual Blood Stages of Malaria Pathogen Plasmodium falciparum |
| Organism |
Plasmodium falciparum |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Plasmodium falciparum is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and noncoding transcripts from the asexual developmental cycle in P. falciparum in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite’s development. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, approximately 71% of the genes with secondary structures are found to be protein coding mRNAs. The mapping pattern of these base-paired RNAs corresponded to all regions of protein-coding mRNAs, including the 5’ UTR, CDS and 3’ UTR as well as the start and stop codons. Histone family genes which are known to form secondary structures in their mRNAs and transcripts from genes which are important for transcriptional and post-transcriptional control, such as the unique plant-like transcription factor family, ApiAP2, DNA/RNA binding protein, Alba3 and proteins important for RBC invasion and malaria cytoadherence also showed strong accumulation of duplex RNA reads in various asexual stages in P. falciparum. Intriguingly, our study determined a positive relationship between mRNA structural contents and translation efficiency in P. falciparum asexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs.
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| Overall design |
Duplex RNA-seq of Ring, Trophozoite and Schizont stages in P. falciparum
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| Contributor(s) |
Kadri S, Chakrabarti K |
| Citation missing |
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| Submission date |
Dec 29, 2020 |
| Last update date |
Apr 05, 2021 |
| Contact name |
Sabah Kadri |
| Organization name |
Broad institute
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| Department |
Computational Biology
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| Street address |
7 Cambridge Center
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (2) |
| GPL21078 |
Illumina HiSeq 2500 (Plasmodium falciparum) |
| GPL21298 |
Illumina NextSeq 500 (Plasmodium falciparum) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA688427 |
| SRA |
SRP299338 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE163965_duplex_rnaseq_raw_counts.txt.gz |
58.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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