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This may give the genome and the transcriptome unusual structural features. Recent progress in sequencing techniques has made it possible to study the secondary structures of RNA molecules at the transcriptomic level. Thus, in this study we produced the\n                    <jats:italic>in vivo<\/jats:italic>\n                    RNA structurome of a protozoan parasite with a highly A\/U-biased transcriptome. We showed that it is possible to probe the secondary structures of\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>falciparum<\/jats:italic>\n                    RNA molecules\n                    <jats:italic>in vivo<\/jats:italic>\n                    using two different chemical probes, and obtained structures for more than half of all transcripts in the transcriptome. These showed greater stability (lower free energy) than the same structures modelled\n                    <jats:italic>in silico<\/jats:italic>\n                    , and structural features appeared to influence translation efficiency and RNA decay. Finally, we compared the\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>falciparum<\/jats:italic>\n                    RNA structurome with the predicted RNA structurome of an A\/U-balanced species,\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>knowlesi<\/jats:italic>\n                    , finding a bias towards lower overall transcript stability and more hairpins and multi-stem loops in\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>falciparum<\/jats:italic>\n                    .\n                  <\/jats:p>\n                  <jats:p>This unusual protozoan RNA structurome will provide a basis for similar studies in other protozoans and also in other unusual genomes.<\/jats:p>","DOI":"10.1371\/journal.pone.0270863","type":"journal-article","created":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T13:43:07Z","timestamp":1662039787000},"page":"e0270863","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["The in vivo RNA structurome of the malaria parasite Plasmodium falciparum, a protozoan with an A\/U-rich transcriptome"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8790-9986","authenticated-orcid":true,"given":"Franck","family":"Dumetz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anton J.","family":"Enright","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jieyu","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chun Kit","family":"Kwok","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7583-2176","authenticated-orcid":true,"given":"Catherine J.","family":"Merrick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,9,1]]},"reference":[{"key":"pone.0270863.ref001","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","article-title":"Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure","volume":"288","author":"DH Mathews","year":"1999","journal-title":"J Mol Biol"},{"key":"pone.0270863.ref002","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.cell.2009.02.007","article-title":"The Centrality of RNA","volume":"136","author":"PA Sharp","year":"2009","journal-title":"Cell"},{"key":"pone.0270863.ref003","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.cell.2014.03.008","article-title":"The noncoding RNA revolution-trashing old rules to forge new ones","volume":"157","author":"TR Cech","year":"2014","journal-title":"Cell"},{"key":"pone.0270863.ref004","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1038\/nrg3049","article-title":"Understanding the transcriptome through RNA structure","volume":"12","author":"Y Wan","year":"2011","journal-title":"Nat Rev Genet"},{"key":"pone.0270863.ref005","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1146\/annurev-arplant-043015-111754","article-title":"The Conservation and Function of RNA Secondary Structure in Plants","volume":"67","author":"LE Vandivier","year":"2016","journal-title":"Annu Rev Plant Biol"},{"key":"pone.0270863.ref006","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1038\/s41594-019-0200-7","article-title":"RNA structure maps across mammalian cellular compartments","volume":"26","author":"L Sun","year":"2019","journal-title":"Nat Struct Mol Biol"},{"key":"pone.0270863.ref007","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-16555-4","article-title":"The RNA fold interactome of evolutionary conserved RNA structures in S. cerevisiae","volume":"11","author":"N Casas-Vila","year":"2020","journal-title":"Nat Commun"},{"key":"pone.0270863.ref008","doi-asserted-by":"crossref","first-page":"2354","DOI":"10.1002\/1873-3468.12294","article-title":"From tRNA to miRNA: RNA-folding contributes to correct entry into noncoding RNA pathways","volume":"590","author":"D Hasler","year":"2016","journal-title":"FEBS Lett"},{"key":"pone.0270863.ref009","doi-asserted-by":"crossref","DOI":"10.4161\/rna.7.1.10489","article-title":"Riboswitch-mediated control of gene expression in eukaryotes","volume":"7","author":"A. 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