title: Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis.
abstract: The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE Synthase (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.
authors.affiliation: The Genome Center, University of California, Davis, Davis, California 95616, USA tadeusz.academicus@gmail.com.
authors.forename: Tadeusz
authors.initials: T
authors.lastname: Wroblewski
authors.affiliation: The Genome Center, University of California, Davis, Davis, California 95616, USA.
authors.forename: Marta
authors.initials: M
authors.lastname: Matvienko
authors.affiliation: The Genome Center, University of California, Davis, Davis, California 95616, USA.
authors.forename: Urszula
authors.initials: U
authors.lastname: Piskurewicz
authors.affiliation: The Genome Center, University of California, Davis, Davis, California 95616, USA.
authors.forename: Huaqin
authors.initials: H
authors.lastname: Xu
authors.affiliation: The Genome Center, University of California, Davis, Davis, California 95616, USA.
authors.forename: Belinda
authors.initials: B
authors.lastname: Martineau
authors.affiliation: The Genome Center, University of California, Davis, Davis, California 95616, USA.
authors.forename: Joan
authors.initials: J
authors.lastname: Wong
authors.affiliation: The Genome Center, University of California, Davis, Davis, California 95616, USA.
authors.forename: Manjula
authors.initials: M
authors.lastname: Govindarajulu
authors.affiliation: The Genome Center, University of California, Davis, Davis, California 95616, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Kozik
authors.affiliation: The Genome Center, University of California, Davis, Davis, California 95616, USA Department of Plant Science, University of California, Davis, Davis, California 95616, USA Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California 95616, USA.
authors.forename: Richard W
authors.initials: RW
authors.lastname: Michelmore
mesh_terms: D000217:Acyltransferases / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D059014:High-Throughput Nucleotide Sequencing; D055029:Inverted Repeat Sequences / Q000235:genetics; D030821:Plants, Genetically Modified / Q000235:genetics; D034622:RNA Interference; D020871:RNA Stability / Q000235:genetics; D012330:RNA, Double-Stranded / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D015398:Signal Transduction
chemical_list: D012330:RNA, Double-Stranded; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D000217:Acyltransferases; C020141:flavanone synthetase
keywords: RNA decay; chalcone synthase; hairpin RNA; heterochromatic siRNA; transitivity; translation