title: Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses.
abstract: Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis, but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV complex and is responsible for accumulation of most 24-nucleotide (nt) small interfering RNAs (siRNAs). We identified novel MIRNA loci and verified miR399 target conservation in maize. RMR6-dependent 23-24 nt siRNA loci were specifically enriched in the upstream region of the most highly expressed genes. Most genes misregulated in rmr6-1 did not show a significant correlation with loss of flanking siRNAs, but we identified one gene supporting existing models of direct gene regulation by TE-derived siRNAs. Long-term drought correlated with changes of miRNA and sRNA accumulation, in particular inducing down-regulation of a set of sRNA loci in the wild-typeleaf.
authors.affiliation: Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.).
authors.forename: Alice
authors.initials: A
authors.lastname: Lunardon
authors.affiliation: Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.).
authors.forename: Cristian
authors.initials: C
authors.lastname: Forestan
authors.affiliation: Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.).
authors.forename: Silvia
authors.initials: S
authors.lastname: Farinati
authors.affiliation: Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.).
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Axtell
authors.affiliation: Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.) serena.varotto@unipd.it.
authors.forename: Serena
authors.initials: S
authors.lastname: Varotto
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000222:Adaptation, Physiological / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D055864:Droughts; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D018519:Meristem / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics; D009154:Mutation; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics*; D018520:Plant Shoots / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*; D013312:Stress, Physiological; D013997:Time Factors; D003313:Zea mays / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated; D012321:DNA-Directed RNA Polymerases