title: RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway.
abstract: In Arabidopsis, pericentromeric repeats, retroelements, and silenced rRNA genes are assembled into heterochromatin within nuclear structures known as chromocenters. The mechanisms governing higher-order heterochromatin organization are poorly understood but 24-nt small interfering RNAs (siRNAs) are known to play key roles in heterochromatin formation. Nuclear RNA polymerase IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2), and DICER-LIKE 3 (DCL3) are required for biogenesis of 24-nt siRNAs that associate with ARGONAUTE 4 (AGO4). Nuclear RNA polymerase V (Pol V) collaborates with DRD1 (DEFICIENT IN RNA-DEPENDENT DNA METHYLATION 1) to generate transcripts at heterochromatic loci that are hypothesized to bind to siRNA-AGO4 complexes and subsequently recruit the de-novo DNA methylation and/or histone modifying machinery. Here, we report that decondensation of the major pericentromeric repeats and depletion of the heterochromatic mark histone H3 lysine 9 dimethylation at chromocenters occurs specifically in pol V and drd1 mutants. Disruption of pericentromeric repeats condensation is coincident with transcriptional reactivation of specific classes of pericentromeric 180-bp repeats. We further demonstrate that Pol V functions independently of Pol IV, RDR2, and DCL3-mediated siRNA production to affect interphase heterochromatin organization, possibly by involving RNAs that recruit structural or chromatin-modifying proteins.
authors.affiliation: Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA. Electronic address: opontes@biology2.wustl.edu.
authors.forename: Olga
authors.initials: O
authors.lastname: Pontes
authors.affiliation: Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA.
authors.forename: Pedro
authors.initials: P
authors.lastname: Costa-Nunes
authors.affiliation: Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Vithayathil
authors.affiliation: Biology Department, Washington University, 1 Brookings Drive, St Louis, MO 63130, USA.
authors.forename: Craig S
authors.initials: CS
authors.lastname: Pikaard
mesh_terms: D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D019175:DNA Methylation / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D005455:Fluorescent Antibody Technique; D018506:Gene Expression Regulation, Plant; D006570:Heterochromatin / Q000378:metabolism*; D017403:In Situ Hybridization; D008856:Microscopy, Fluorescence; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D029681:Arabidopsis Proteins; D006570:Heterochromatin; D034741:RNA, Small Interfering; C499181:RNA polymerase IV, Arabidopsis; C538841:RNA polymerase V, Arabidopsis; C519655:RDR2 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase; D012321:DNA-Directed RNA Polymerases; C504888:DRD1 protein, Arabidopsis; C519654:DCL3 protein, Arabidopsis; D043244:Ribonuclease III