A manually curated annotation characterises genomic features of P. falciparum lncRNAs

Hoshizaki, J., Adjalley, S. H., Thathy, V., Judge, K., Berriman, M., Reid, A. J. and Lee, M. C. S. (2022) A manually curated annotation characterises genomic features of P. falciparum lncRNAs. BMC Genomics, 23, 780. (doi: 10.1186/s12864-022-09017-2) (PMID:36451097) (PMCID:PMC9710153)

Abstract

Background: Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum. Results: We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1119 novel lncRNAs and validated and refined 1250 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes. Conclusions: The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.

• Item Type: Articles
• Additional Information: This research was funded by Wellcome [206194].
• Keywords: Plasmodium falciparum, lncRNA, noncoding, annotation, manual curation, long-read RNA sequencing.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Berriman, Professor Matt
• Authors: Hoshizaki, J., Adjalley, S. H., Thathy, V., Judge, K., Berriman, M., Reid, A. J., and Lee, M. C. S.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: BMC Genomics
• Publisher: BioMed Central
• ISSN: 1471-2164
• ISSN (Online): 1471-2164
• Copyright Holders: Copyright © 2022 The Authors
• First Published: First published in BMC Genomics 23: 780
• Publisher Policy: Reproduced under a Creative Commons License