pRNA: NoRC-associated RNA of rRNA operons

Citation

Wehner S, Dorrich AK, Ciba P, Wilde A & Marz M (2014) pRNA: NoRC-associated RNA of rRNA operons. RNA Biology, 11 (1), pp. 3-9. https://doi.org/10.4161/rna.27448

Abstract
Promoter-associated RNAs (pRNAs) are a family of ~90–100 nt-long divergent RNAs overlapping the promoter of the rRNA (rDNA) operon. pRNA transcripts interact with TIP5, a component of the chromatin remodeling complex NoRC, which recruits enzymes for heterochromatin formation and mediates silencing of rRNA genes. Here we present a comprehensive analysis of pRNA homologs, including different versions per species, as result of in silico studies in available metazoan genome assemblies. Comparative sequence analysis and secondary structure prediction ended up in two possible secondary structures, which let us assume a possible dual function of pRNAs for regulation of rRNA operons. Furthermore, we validated parts of our computational predictions experimentally by RT-PCR and sequencing. A representative seed alignment of the pRNA family, annotated with possible secondary structures was released to the Rfam database.

Keywords
promoter-associated RNA; non-coding RNA; ribosomal RNA; gene silencing

Journal
RNA Biology: Volume 11, Issue 1