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Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts

Plasmodium vivax infections often consist of heterogenous populations of parasites at different developmental stages and with distinct transcriptional profiles, which complicates gene expression analyses. The advent of single cell RNA sequencing (scRNA-seq) enabled disentangling this complexity and...

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Autores principales: Hazzard, Brittany, Sá, Juliana M., Ellis, Angela C., Pascini, Tales V., Amin, Shuchi, Wellems, Thomas E., Serre, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9803293/
https://www.ncbi.nlm.nih.gov/pubmed/36525464
http://dx.doi.org/10.1371/journal.pntd.0010991
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author Hazzard, Brittany
Sá, Juliana M.
Ellis, Angela C.
Pascini, Tales V.
Amin, Shuchi
Wellems, Thomas E.
Serre, David
author_facet Hazzard, Brittany
Sá, Juliana M.
Ellis, Angela C.
Pascini, Tales V.
Amin, Shuchi
Wellems, Thomas E.
Serre, David
author_sort Hazzard, Brittany
collection PubMed
description Plasmodium vivax infections often consist of heterogenous populations of parasites at different developmental stages and with distinct transcriptional profiles, which complicates gene expression analyses. The advent of single cell RNA sequencing (scRNA-seq) enabled disentangling this complexity and has provided robust and stage-specific characterization of Plasmodium gene expression. However, scRNA-seq information is typically derived from the end of each mRNA molecule (usually the 3’-end) and therefore fails to capture the diversity in transcript isoforms documented in bulk RNA-seq data. Here, we describe the sequencing of scRNA-seq libraries using Pacific Biosciences (PacBio) chemistry to characterize full-length Plasmodium vivax transcripts from single cell parasites. Our results show that many P. vivax genes are transcribed into multiple isoforms, primarily through variations in untranslated region (UTR) length or splicing, and that the expression of many isoforms is developmentally regulated. Our findings demonstrate that long read sequencing can be used to characterize mRNA molecules at the single cell level and provides an additional resource to better understand the regulation of gene expression throughout the Plasmodium life cycle.
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spelling pubmed-98032932022-12-31 Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts Hazzard, Brittany Sá, Juliana M. Ellis, Angela C. Pascini, Tales V. Amin, Shuchi Wellems, Thomas E. Serre, David PLoS Negl Trop Dis Research Article Plasmodium vivax infections often consist of heterogenous populations of parasites at different developmental stages and with distinct transcriptional profiles, which complicates gene expression analyses. The advent of single cell RNA sequencing (scRNA-seq) enabled disentangling this complexity and has provided robust and stage-specific characterization of Plasmodium gene expression. However, scRNA-seq information is typically derived from the end of each mRNA molecule (usually the 3’-end) and therefore fails to capture the diversity in transcript isoforms documented in bulk RNA-seq data. Here, we describe the sequencing of scRNA-seq libraries using Pacific Biosciences (PacBio) chemistry to characterize full-length Plasmodium vivax transcripts from single cell parasites. Our results show that many P. vivax genes are transcribed into multiple isoforms, primarily through variations in untranslated region (UTR) length or splicing, and that the expression of many isoforms is developmentally regulated. Our findings demonstrate that long read sequencing can be used to characterize mRNA molecules at the single cell level and provides an additional resource to better understand the regulation of gene expression throughout the Plasmodium life cycle. Public Library of Science 2022-12-16 /pmc/articles/PMC9803293/ /pubmed/36525464 http://dx.doi.org/10.1371/journal.pntd.0010991 Text en © 2022 Hazzard et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Hazzard, Brittany
Sá, Juliana M.
Ellis, Angela C.
Pascini, Tales V.
Amin, Shuchi
Wellems, Thomas E.
Serre, David
Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts
title Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts
title_full Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts
title_fullStr Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts
title_full_unstemmed Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts
title_short Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts
title_sort long read single cell rna sequencing reveals the isoform diversity of plasmodium vivax transcripts
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9803293/
https://www.ncbi.nlm.nih.gov/pubmed/36525464
http://dx.doi.org/10.1371/journal.pntd.0010991
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