Chromosome Position-Effect in Megabase-Scale Silencing of Nucleolus Organizer Regions

Nucleolus organizer regions (NORs) are chromosomal loci where ribosomal RNA (rRNA) genes are clustered in hundreds of copies. Despite being nearly identical in sequence, approximately half of the rRNA genes are selectively silencing via repressive chromatin modifications during development, via choice mechanism(s) that remain unclear. In the Arabidopsis thaliana strain Col-0 we recently defined more than a dozed rRNA gene subtypes that are defined by single nucleotide polymorphisms or short insertions/deletions. We then identified strain-specific rRNA subtypes and exploitied recombinant inbred lines in order to genetically map silenced versus active rRNA gene subtypes. rRNA gene subtypes that are silenced during development map to the NOR on chromosome 2, NOR2, whereas active rRNA genes map to NOR4, on chromosome 4. In a mutant line deficient for ATXR5 or ATXR6-dependent histone H3 lysine 27 (H3K27) monomethylation, a translocation event resulted in millions of basepairs of chromosome 4, including the telomere, TEL4N and much of NOR4, being converted to the corresponding sequences of chromosome 2. This genomic change moved rRNA genes of NOR2, which are normally silenced, to the position on chromosome 4 where active rRNA genes are normally located. At their new location, the NOR2-derived rRNA genes escape silencing, independent of the atxr mutations, indicating that selective rRNA gene silencing is chromosome 2-specific. The chromosome 2 position effect is not explained by the NOR2-associated telomere, TEL2N, which remains linked to the translocated NOR, implicating centromere-proximal sequences in silencing. Genetic mapping of recombinant inbred loci required for NOR2 silencing reveals evidence for NOR2 and NOR4 crosstalk.