Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states

Abstract

Eukaryotes can have thousands of 45S ribosomal RNA (rRNA) genes, many of which are silenced during development. Using fluorescence-activated sorting techniques, we show that active rRNA genes in Arabidopsis thaliana are present within sorted nucleoli, whereas silenced rRNA genes are excluded. DNA methyltransferase (met1), histone deacetylase (hda6), or chromatin assembly (caf1) mutants that disrupt silencing abrogate this nucleoplasmic-nucleolar partitioning. Bisulfite sequencing data indicate that active nucleolar rRNA genes are nearly completely demethylated at promoter CGs, whereas silenced genes are nearly fully methylated. Collectively, the data reveal that rRNA genes occupy distinct but changeable nuclear territories according to their epigenetic state.

Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

“…There was extensive demethylation of some rRNA genes, particularly in root tissue, involving the Pol I promoter region in 3 (8%) P-genome and 1 (100%) D-genome genes. Given that transcriptionally active rDNA units are extensively demethylated in Arabidopsis (Pontvianne et al, 2013), we suggest that about 10% of P-genome rRNA genes become activated in plant 33A. Thus, there are about 130 active rDNA genes, corresponding to 70 D-genome rRNA genes and 60 P-genome rRNA genes.…”

The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes

“…In somatic leaf nuclei, condensed silent heterochromatic portions of rDNA loci coincide with chromocenters that contain centromeric heterochromatin at the external periphery of the nucleolus, a subnuclear compartment where rDNA transcription and ribosome assembly take place, and only relatively few rRNA genes are located within the nucleolus to be transcribed (22). Distinct megabase-sized clusters of rRNA gene variant repeats are selectively silenced during early embryonic development; are excluded from the nucleolus; and are not transcribed in somatic tissues, including leaves (23,24).…”

The many faces of plant chromatin: Meeting summary of the 4th European workshop onplantchromatin 2015, Uppsala, Sweden

“…Distinct sequence variants of the 45S rRNA genes exist, which have either extra-or intra-nucleolar localization. 30 This homeostasis is compromised in the CAF-1 mutants fasciata, where rDNA copies are progressively lost and the originally inactive rRNA gene copies translocate into the nucleolus and are expressed. 30,31 Jiri Fajkus (Brno, Czech Republic) showed that the reintroduction of a wild-type FAS allele into fas mutant plants that have been inbred for several generations can lead to reversion of the rRNA gene copy-number but causes major changes in the bulk variant composition, their transcriptional state and nuclear localization, suggesting reprogramming and establishment of a novel epigenetic equilibrium at the nucleolus organizer regions in these plants.…”

“…32 A potential role of the nucleolus as a compartment sequestering transcriptionally repressed parts of genome away from the RNAP II territory was presented by Frederic Pontvianne (Perpignan, France). Fluorescence-assisted sorting of nucleoli 30 followed by DNA sequencing revealed that, in addition to rRNA genes, also RNAP II-transcribed genomic DNA sequences can localize within the nucleolus, defining nucleolus-associated domains (NADs) in plants (Fig. 3).…”

“…Development of biosensors for different chromatin marks combined with live-cell imaging techniques will be a great asset to chromatin dynamics research. Novel tools for studying the organization of chromatin within the nuclear space were presented, 30,34 which can help to address the molecular mechanisms governing the 3-dimensional nuclear organization, its dynamics and role in plant development.…”