title: Stress-induced endogenous siRNAs targeting regulatory intron sequences in Brachypodium.
abstract: Exposure to abiotic stresses triggers global changes in the expression of thousands of eukaryotic genes at the transcriptional and post-transcriptional levels. Small RNA (smRNA) pathways and splicing both function as crucial mechanisms regulating stress-responsive gene expression. However, examples of smRNAs regulating gene expression remain largely limited to effects on mRNA stability, translation, and epigenetic regulation. Also, our understanding of the networks controlling plant gene expression in response to environmental changes, and examples of these regulatory pathways intersecting, remains limited. Here, to investigate the role of smRNAs in stress responses we examined smRNA transcriptomes of Brachypodium distachyon plants subjected to various abiotic stresses. We found that exposure to different abiotic stresses specifically induced a group of novel, endogenous small interfering RNAs (stress-induced, UTR-derived siRNAs, or sutr-siRNAs) that originate from the 3' UTRs of a subset of coding genes. Our bioinformatics analyses predicted that sutr-siRNAs have potential regulatory functions and that over 90% of sutr-siRNAs target intronic regions of many mRNAs in trans. Importantly, a subgroup of these sutr-siRNAs target the important intron regulatory regions, such as branch point sequences, that could affect splicing. Our study indicates that in Brachypodium, sutr-siRNAs may affect splicing by masking or changing accessibility of specific cis-elements through base-pairing interactions to mediate gene expression in response to stresses. We hypothesize that this mode of regulation of gene expression may also serve as a general mechanism for regulation of gene expression in plants and potentially in other eukaryotes.
authors.affiliation: School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
authors.forename: Hsiao-Lin V
authors.initials: HL
authors.lastname: Wang
authors.affiliation: School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
authors.forename: Brandon L
authors.initials: BL
authors.lastname: Dinwiddie
authors.affiliation: School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
authors.forename: Herman
authors.initials: H
authors.lastname: Lee
authors.affiliation: School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA chekanovaj@gmail.com.
authors.forename: Julia A
authors.initials: JA
authors.lastname: Chekanova
mesh_terms: D020413:3' Untranslated Regions; D000222:Adaptation, Physiological; D001483:Base Sequence; D058431:Brachypodium / Q000235:genetics* / Q000378:metabolism; D016384:Consensus Sequence; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D007438:Introns; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference; D018749:RNA, Plant / Q000502:physiology*; D034741:RNA, Small Interfering / Q000502:physiology*; D012045:Regulatory Sequences, Nucleic Acid; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D010940:Plant Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering
keywords: Brachypodium; abiotic stresses; smRNAs; splicing; splicing regulation