Restricted chromosomal silencing in nucleolar dominance

Failure of one parent's chromosomes to organize nucleoli in an interspecifi c hybrid is an epigenetic phenomenon known as nucleolar dominance. Selectiv e gene silencing on a scale of millions of by is known to be involved, but the full extent to which nucleolus organizer region (NOR)-bearing chromosom es are inactivated beyond the NORs is unknown. Aided by genome sequence dat a for Arabidopsis thaliana, we have mapped the extent of nucleolar dominanc e-induced silencing in Arabidopsis suecica, the allotetraploid hybrid of A. thaliana and Arabidopsis arenosa. Using a sensitive reverse transcription PCR assay, we show that the four A. thaliana NORs, each approximate to4 Mbp in size, are approximate to 99.5% silenced in A. suecica vegetative leaves , whereas the NORs inherited from A. arenosa remain fully active. The two A . thaliana NORs, NOR2 and NOR4, abut the telomeres on chromosomes 2 and 4, thus there are no genes distal to the NORs. The three protein-coding genes nearest NOR4 on its centromere-proximal side, the closest of which is only 3.1 kb from rRNA gene sequences, are shown to be transcribed in the hybrid despite the silencing of the adjacent approximate to 4-Mbp NOR. These data argue against hypotheses in which NOR inactivation is attributed to the spr ead of silencing from adjacent chromosomal regions, but favor models in whi ch NORs or rRNA genes are the targets of regulation.