title: Endogenous Small-Noncoding RNAs and Potential Functions in Desiccation Tolerance in Physcomitrella Patens.
abstract: Early land plants like moss Physcomitrella patens have developed remarkable drought tolerance. Phytohormone abscisic acid (ABA) protects seeds during water stress by activating genes through transcription factors such as ABSCISIC ACID INSENSITIVE (ABI3). Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs), are key gene regulators in eukaryotes, playing critical roles in stress tolerance in plants. Combining next-generation sequencing and computational analysis, we profiled and characterized sncRNA species from two ABI3 deletion mutants and the wild type P. patens that were subject to ABA treatment in dehydration and rehydration stages. Small RNA profiling using deep sequencing helped identify 22 novel miRNAs and 6 genomic loci producing trans-acting siRNAs (ta-siRNAs) including TAS3a to TAS3e and TAS6. Data from degradome profiling showed that ABI3 genes (ABI3a/b/c) are potentially regulated by the plant-specific miR536 and that other ABA-relevant genes are regulated by miRNAs and ta-siRNAs. We also observed broad variations of miRNAs and ta-siRNAs expression across different stages, suggesting that they could potentially influence desiccation tolerance. This study provided evidence on the potential roles of sncRNA in mediating desiccation-responsive pathways in early land plants.
authors.affiliation: Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.|Department of Computer Science and Engineering, Washington University, St. Louis, MO 63130, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Xia
authors.affiliation: College of Life Sciences, Capital Normal University, Beijing 100048, China.|Department of Biology, Washington University, St. Louis, MO 63130, USA.
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Biology, Washington University, St. Louis, MO 63130, USA.
authors.forename: Pierre-François
authors.initials: PF
authors.lastname: Perroud
authors.affiliation: College of Life Sciences, Capital Normal University, Beijing 100048, China.
authors.forename: Yikun
authors.initials: Y
authors.lastname: He
authors.affiliation: Department of Biology, Washington University, St. Louis, MO 63130, USA.
authors.forename: Ralph
authors.initials: R
authors.lastname: Quatrano
authors.affiliation: Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.|Department of Computer Science and Engineering, Washington University, St. Louis, MO 63130, USA.|Department of Genetics, Washington University, St. Louis, MO 63130, USA.
authors.forename: Weixiong
authors.initials: W
authors.lastname: Zhang
mesh_terms: D000040:Abscisic Acid; D017360:Arabidopsis / Q000235:genetics; D019068:Bryopsida / Q000235:genetics*; D003890:Desiccation / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics; D010937:Plant Growth Regulators / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*; D012639:Seeds / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D015533:Transcriptional Activation / Q000235:genetics
chemical_list: D035683:MicroRNAs; D010937:Plant Growth Regulators; D010940:Plant Proteins; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated; D014157:Transcription Factors; D000040:Abscisic Acid