{"data":{"id":"10.6084/m9.figshare.1613867","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1613867","prefix":"10.6084","suffix":"m9.figshare.1613867","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"López-Carrasco, Amparo","nameType":"Personal","givenName":"Amparo","familyName":"López-Carrasco","affiliation":[],"nameIdentifiers":[]},{"name":"Gago-Zachert, Selma","nameType":"Personal","givenName":"Selma","familyName":"Gago-Zachert","affiliation":[],"nameIdentifiers":[]},{"name":"Mileti, Giuseppe","nameType":"Personal","givenName":"Giuseppe","familyName":"Mileti","affiliation":[],"nameIdentifiers":[]},{"name":"Minoia, Sofia","nameType":"Personal","givenName":"Sofia","familyName":"Minoia","affiliation":[],"nameIdentifiers":[]},{"name":"Flores, Ricardo","nameType":"Personal","givenName":"Ricardo","familyName":"Flores","affiliation":[],"nameIdentifiers":[]},{"name":"Delgado, Sonia","nameType":"Personal","givenName":"Sonia","familyName":"Delgado","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"The transcription initiation sites of eggplant latent viroid strands map within distinct motifs in their \u003ci\u003ein vivo\u003c/i\u003e RNA conformations"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2016,"subjects":[{"subject":"Biophysics"},{"subject":"Biochemistry"},{"subject":"29999 Physical Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Physical sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Physical sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Molecular Biology"},{"subject":"59999 Environmental Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Earth and related environmental sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Earth and related environmental sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"39999 Chemical Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Chemical sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Chemical sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"69999 Biological Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"110309 Infectious Diseases","subjectScheme":"FOR"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Health sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Plant Biology"},{"subject":"60506 Virology","subjectScheme":"FOR"},{"subject":"Computational Biology"}],"contributors":[],"dates":[{"date":"2015-11-30","dateType":"Created"},{"date":"2016-02-19","dateType":"Updated"},{"date":"2016","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15476286.2015.1119365","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["340034 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Eggplant latent viroid (ELVd), like other members of family \u003ci\u003eAvsunviroidae\u003c/i\u003e, replicates in plastids through a symmetric rolling-circle mechanism in which elongation of RNA strands is most likely catalyzed by a nuclear-encoded polymerase (NEP) translocated to plastids. Here we have addressed where NEP initiates transcription of viroid strands. Because this step is presumably directed by sequence/structural motifs, we have previously determined the conformation of the monomeric linear (+) and (−) RNAs of ELVd resulting from hammerhead-mediated self-cleavage. \u003ci\u003eIn silico\u003c/i\u003e predictions with 3 softwares led to similar bifurcated conformations for both ELVd strands. \u003ci\u003eIn vitro\u003c/i\u003e examination by non-denaturing PAGE showed that they migrate as prominent single bands, with the ELVd (+) RNA displaying a more compact conformation as revealed by its faster electrophoretic mobility. \u003ci\u003eIn vitro\u003c/i\u003e SHAPE analysis corroborated the ELVd conformations derived from thermodynamics-based predictions \u003ci\u003ein silico\u003c/i\u003e. Moreover, sequence analysis of 94 full-length natural ELVd variants disclosed co-variations, and mutations converting canonical into wobble pairs or vice versa, which confirmed \u003ci\u003ein vivo\u003c/i\u003e most of the stems predicted \u003ci\u003ein silico\u003c/i\u003e and \u003ci\u003ein vitro\u003c/i\u003e, and additionally helped to introduce minor structural refinements. Therefore, results from the 3 experimental approaches were essentially consistent among themselves. Application to RNA preparations from ELVd-infected tissue of RNA ligase-mediated rapid amplification of cDNA ends, combined with pretreatments to modify the 5′ ends of viroid strands, mapped the transcription initiation sites of ELVd (+) and (−) strands \u003ci\u003ein vivo\u003c/i\u003e at different sequence/structural motifs, in contrast with the situation previously observed in 2 other members of the family \u003ci\u003eAvsunviroidae\u003c/i\u003e.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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