title: Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis.
abstract: Plant's response and adaptation to abiotic stresses involve sophisticated genetic and epigenetic regulatory systems. To obtain a global view of molecular response to osmotic stresses, including the non-coding portion of genome, we conducted a total leaf transcriptome analysis on maize plants subjected to prolonged drought and salt stresses. Stress application to both B73 wild type and the epiregulator mutant rpd1-1/rmr6 allowed dissection of the epigenetic component of stress response. Coupling total RNA-Seq and transcriptome re-assembly we annotated thousands of new maize transcripts, together with 13,387 lncRNAs that may play critical roles in regulating gene expression. Differential expression analysis revealed hundreds of genes modulated by long-term stress application, including also many lncRNAs and transposons specifically induced by stresses. The amplitude and dynamic of the stress-modulated gene sets are very different between B73 and rpd1-1/rmr6 mutant plants, as result of stress-like effect on genome regulation caused by the mutation itself, which activates many stress-related genes even in control condition. The analyzed extensive set of total RNA-Seq data, together with the improvement of the transcriptome and the identification of the non-coding portion of the transcriptome give a revealing insight into the genetic and epigenetic mechanism responsible for maize molecular response to abiotic stresses.
authors.affiliation: Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD)-Italy.
authors.forename: Cristian
authors.initials: C
authors.lastname: Forestan
authors.affiliation: Sequentia Biotech SL, Calle Comte D'Urgell, 240, Barcelona, Spain.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Aiese Cigliano
authors.affiliation: Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD)-Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Farinati
authors.affiliation: Department of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802 USA.
authors.forename: Alice
authors.initials: A
authors.lastname: Lunardon
authors.affiliation: Sequentia Biotech SL, Calle Comte D'Urgell, 240, Barcelona, Spain.
authors.forename: Walter
authors.initials: W
authors.lastname: Sanseverino
authors.affiliation: Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD)-Italy.
authors.forename: Serena
authors.initials: S
authors.lastname: Varotto
mesh_terms: D000595:Amino Acid Sequence; D004251:DNA Transposable Elements / Q000235:genetics; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D056426:Genetic Loci; D005838:Genotype; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D009154:Mutation / Q000235:genetics; D009997:Osmotic Pressure; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D003313:Zea mays / Q000235:genetics* / Q000502:physiology*
chemical_list: D004251:DNA Transposable Elements; D010940:Plant Proteins; D020033:Protein Isoforms; D012333:RNA, Messenger; D022661:RNA, Untranslated