Selective nucleolus organizer inactivation in Arabidopsis is a chromosome position effect phenomenon
Significance For decades, rRNA genes have been known to be differentially regulated during growth and development, with some genes being expressed and other genes being inactive. However, rRNA genes are so similar in sequence that the basis for choosing among them to differentially express some, but not others, has long been a puzzle. This study demonstrates that entire clusters of rRNA genes, known as nucleolus organizer regions, are silenced based on the chromosome on which they reside. Nucleolus organizer regions (NORs) are chromosomal loci where hundreds of rRNA genes are clustered. Despite being nearly identical in sequence, specific rRNA genes are selected for silencing during development via choice mechanism(s) that remain unclear. In Arabidopsis thaliana, rRNA gene subtypes that are silenced during development were recently mapped 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, we show that millions of base pairs of chromosome 4, including the telomere, TEL4N, and much of NOR4, have been converted to the corresponding sequences of chromosome 2. This genomic change places rRNA genes of NOR2, which are normally silenced, at the position on chromosome 4 where active rRNA genes are normally located. At their new location, 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.
Proceedings of the National Academy of Sciences