Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans

Abstract

Epigenetic silencing of a fraction of ribosomal DNA (rDNA) requires association of the nucleolar chromatin-remodelling complex NoRC to 150-250 nucleotide RNAs (pRNA) that originate from an RNA polymerase I promoter located in the intergenic spacer separating rDNA repeats. Here, we show that NoRC-associated pRNA is transcribed from a sub-fraction of hypomethylated rRNA genes during mid S phase, acting in trans to inherit DNA methylation and transcriptional repression of late-replicating silent rDNA copies. The results reveal variability between individual rDNA clusters with distinct functional consequences.

Nucleoli: Composition, Function, and Dynamics

“…Further confirmation that nucleolar dominance in plants involves RNA-directed DNA methylation was obtained by knockdown of RNA Dependent RNA Polymerase2, Dicer-like3, and DRM2, which disrupted the silencing of the Arabidopsisderived rRNA genes in A. suecica (Preuss et al, 2008). In mammals, rRNA genes are silenced by the nucleolar remodeling complex, NoRC, which is recruited to rRNA genes by 200-to 300-nt RNA species, termed pRNA, derived from intergenic regions of the rDNA (Guetg et al, 2010;Santoro et al, 2010).…”

pRNA

“…1 The intergenic transcripts are short-lived and degraded by the exosome, except a 150-250 nt transcript that matches the promoter of the ribosomal genes (rDNA), termed promoter-associated RNA. 2 These pRNAs are stabilized by binding to TIP5 (transcription termination factor I interacting protein 5), the large subunit of the nucleolar remodeling complex NoRC, which mediates heterochromatin formation and transcriptional silencing. 3 This interaction is a prerequisite for the function of NoRC, because antisense-mediated depletion of pRNA leads to decreased rDNA methylation and activation of Pol I transcription.…”

The expanding role ofPARPs in the establishment and maintenance of heterochromatin

“…After replication of silent rDNA sequences, TIP5 binds to and re-establishes rDNA heterochromatin [71,72]. Re-assembly of these repressive chromatin structures requires association of TIP5 with the non-coding RNA pRNA, a transcript that originates from an alternative rDNA promoter in early S phase [73,74]. Recently, PARP1 was identified as an interaction partner of TIP5 [12].…”