title: Regulation of MicroRNA-Mediated Developmental Changes by the SWR1 Chromatin Remodeling Complex.
abstract: The ATP-dependent SWR1 chromatin remodeling complex (SWR1-C) exchanges the histone H2A-H2B dimer with the H2A.Z-H2B dimer, producing variant nucleosomes. Arabidopsis thaliana SWR1-C contributes to the active transcription of many genes, but also to the repression of genes that respond to environmental and developmental stimuli. Unlike other higher eukaryotic H2A.Z deposition mutants (which are embryonically lethal), Arabidopsis SWR1-C component mutants, including arp6, survive and display a pleiotropic developmental phenotype. However, the molecular mechanisms of early flowering, leaf serration, and the production of extra petals in arp6 have not been completely elucidated. We report here that SWR1-C is required for miRNA-mediated developmental control via transcriptional regulation. In the mutants of the components of SWR1-C such as arp6, sef, and pie1, miR156 and miR164 levels are reduced at the transcriptional level, which results in the accumulation of target mRNAs and associated morphological changes. Sequencing of small RNA libraries confirmed that many miRNAs including miR156 decreased in arp6, though some miRNAs increased. The arp6 mutation suppresses the accumulation of not only unprocessed primary miRNAs, but also miRNA-regulated mRNAs in miRNA processing mutants, hyl1 and serrate, which suggests that arp6 has a transcriptional effect on both miRNAs and their targets. We consistently detected that the arp6 mutant exhibits increased nucleosome occupancy at the tested MIR gene promoters, indicating that SWR1-C contributes to transcriptional activation via nucleosome dynamics. Our findings suggest that SWR1-C contributes to the fine control of plant development by generating a balance between miRNAs and target mRNAs at the transcriptional level.
authors.affiliation: Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.).
authors.forename: Kyuha
authors.identifier: 0000-0002-4072-3807
authors.initials: K
authors.lastname: Choi
authors.affiliation: Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.).
authors.forename: Juhyun
authors.identifier: 0000-0001-5462-3391
authors.initials: J
authors.lastname: Kim
authors.affiliation: Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.).
authors.forename: Sebastian Y
authors.identifier: 0000-0002-0148-7020
authors.initials: SY
authors.lastname: Müller
authors.affiliation: Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.).
authors.forename: Mijin
authors.initials: M
authors.lastname: Oh
authors.affiliation: Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.).
authors.forename: Charles
authors.identifier: 0000-0001-5730-6279
authors.initials: C
authors.lastname: Underwood
authors.affiliation: Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.).
authors.forename: Ian
authors.initials: I
authors.lastname: Henderson
authors.affiliation: Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.) ilhalee@snu.ac.kr kc404@cam.ac.uk.
authors.forename: Ilha
authors.identifier: 0000-0002-3516-4326
authors.initials: I
authors.lastname: Lee
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D019521:Body Patterning / Q000187:drug effects / Q000235:genetics; D042002:Chromatin Assembly and Disassembly / Q000187:drug effects / Q000235:genetics*; D003517:Cyclopentanes / Q000494:pharmacology; D004777:Environment; D035264:Flowers / Q000187:drug effects / Q000235:genetics / Q000502:physiology; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D009154:Mutation / Q000235:genetics; D009707:Nucleosomes / Q000187:drug effects / Q000378:metabolism; D054883:Oxylipins / Q000494:pharmacology; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics / Q000254:growth & development; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site; D015533:Transcriptional Activation / Q000187:drug effects / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D003517:Cyclopentanes; D035683:MicroRNAs; D009707:Nucleosomes; D054883:Oxylipins; D012333:RNA, Messenger; C011006:jasmonic acid