Apple miRNAs and tasiRNAs with novel regulatory networks

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dc.contributor.authorXia, Ruien
dc.contributor.authorZhu, Hongen
dc.contributor.authorAn, Yong-qiangen
dc.contributor.authorBeers, Eric P.en
dc.contributor.authorLiu, Zongrangen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.contributor.departmentVirginia Agricultural Experiment Stationen
dc.date.accessioned2012-08-24T10:48:27Zen
dc.date.available2012-08-24T10:48:27Zen
dc.date.issued2012-06-15en
dc.date.updated2012-08-24T10:48:27Zen
dc.description.abstractBackground MicroRNAs (miRNAs) and their regulatory functions have been extensively characterized in model species but whether apple has evolved similar or unique regulatory features remains unknown. Results We performed deep small RNA-seq and identified 23 conserved, 10 less-conserved and 42 apple-specific miRNAs or families with distinct expression patterns. The identified miRNAs target 118 genes representing a wide range of enzymatic and regulatory activities. Apple also conserves two TAS gene families with similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profiles and target specificities. Importantly, we found that miR159, miR828 and miR858 can collectively target up to 81 MYB genes potentially involved in diverse aspects of plant growth and development. These miRNA target sites are differentially conserved among MYBs, which is largely influenced by the location and conservation of the encoded amino acid residues in MYB factors. Finally, we found that 10 of the 19 miR828-targeted MYBs undergo small interfering RNA (siRNA) biogenesis at the 3' cleaved, highly divergent transcript regions, generating over 100 sequence-distinct siRNAs that potentially target over 70 diverse genes as confirmed by degradome analysis. Conclusions Our work identified and characterized apple miRNAs, their expression patterns, targets and regulatory functions. We also discovered that three miRNAs and the ensuing siRNAs exploit both conserved and divergent sequence features of MYB genes to initiate distinct regulatory networks targeting a multitude of genes inside and outside the MYB family.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationGenome Biology. 2012 Jun 15;13(6):R47en
dc.identifier.doihttps://doi.org/10.1186/gb-2012-13-6-r47en
dc.identifier.urihttp://hdl.handle.net/10919/18772en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderRui Xia et al.; licensee BioMed Central Ltd.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleApple miRNAs and tasiRNAs with novel regulatory networksen
dc.title.serialGenome Biologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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