title: Chromosome-specific NOR inactivation explains selective rRNA gene silencing and dosage control in Arabidopsis.
abstract: In eukaryotes, scores of excess ribosomal RNA (rRNA) genes are silenced by repressive chromatin modifications. Given the near sequence identity of rRNA genes within a species, it is unclear how specific rRNA genes are reproducibly chosen for silencing. Using Arabidopsis thaliana ecotype (strain) Col-0, a systematic search identified sequence polymorphisms that differ between active and developmentally silenced rRNA gene subtypes. Recombinant inbred mapping populations derived from three different ecotype crosses were then used to map the chromosomal locations of silenced and active RNA gene subtypes. Importantly, silenced and active rRNA gene subtypes are not intermingled. All silenced rRNA gene subtypes mapped to the nucleolus organizer region (NOR) on chromosome 2 (NOR2). All active rRNA gene subtypes mapped to NOR4. Using an engineered A. thaliana line in which a portion of Col-0 chromosome 4 was replaced by sequences of another ecotype, we show that a major rRNA gene subtype silenced at NOR2 is active when introgressed into the genome at NOR4. Collectively, these results reveal that selective rRNA gene silencing is not regulated gene by gene based on mechanisms dependent on subtle gene sequence variation. Instead, we propose that a subchromosomal silencing mechanism operates on a multimegabase scale to inactivate NOR2.
authors.affiliation: Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
authors.forename: Chinmayi
authors.initials: C
authors.lastname: Chandrasekhara
authors.affiliation: Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
authors.forename: Gireesha
authors.initials: G
authors.lastname: Mohannath
authors.affiliation: Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Todd
authors.initials: T
authors.lastname: Blevins
authors.affiliation: Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
authors.forename: Frederic
authors.initials: F
authors.lastname: Pontvianne
authors.affiliation: Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Craig S
authors.initials: CS
authors.lastname: Pikaard
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D001947:Breeding; D032461:Chromosomes, Plant / Q000235:genetics; D018628:Gene Dosage; D020868:Gene Silencing; D020459:Genes, rRNA / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D009697:Nucleolus Organizer Region / Q000235:genetics*; D011110:Polymorphism, Genetic / Q000235:genetics
keywords: chromatin; gene silencing; nucleolus organizer region; rRNA gene subtypes; transcription