Sequence and epigenetic landscapes of active and silenced nucleolus organizers in Arabidopsis

Abstract

AbstractArabidopsis thalianahas two ribosomal RNA gene loci, nucleolus organizer regionsNOR2andNOR4, whose complete sequences remain undefined. Ultra-long DNA sequences assembled using an unconventional approach yielded 5.5 and 3.9 Mbp sequences forNOR2andNOR4(in the reference strain, Col-0), revealing their distinct gene subtype compositions. RNA sequencing and identification of genes associated with flow-sorted nucleoli of wild-type or silencing-defective mutant plants shows that most ofNOR4is comprised of active genes whereas most, but not all,NOR2genes are epigenetically silenced. Long intervals of low CG and CHG methylation overlap regions of gene activity and gene subtype homogenization. Collectively, the data reveal the genetic and epigenetic landscapes of the NORs and implicate transcription in rRNA gene concerted evolution.One Sentence SummaryNOR2andNOR4sequences fill genome gaps and enable megabase-scale analyses of rRNA gene regulation and concerted evolution.