pRNA: NoRC-associated RNA of rRNA operons.
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.
Department for Bioinformatics; Faculty of Mathematics and Computer Science; Friedrich-Schiller-University Jena; Jena, Germany.
Stefanie
S
Wehner
Institute for Microbiology and Molecular Biology; Justus-Liebig-University Giessen; Giessen, Germany.
Anja K
AK
Dörrich
Fraunhofer Research Institution for Marine Biotechnology; Lübeck, Germany.
Philipp
P
Ciba
Faculty of Biology; University of Freiburg; Freiburg, Germany.
Annegret
A
Wilde
Department for Bioinformatics; Faculty of Mathematics and Computer Science; Friedrich-Schiller-University Jena; Jena, Germany.
Manja
M
Marz
D000818:Animals; D001483:Base Sequence; D004275:DNA, Ribosomal / Q000737:chemistry*; D020459:Genes, rRNA; D016678:Genome; D006570:Heterochromatin / Q000378:metabolism*; D006801:Humans; D055029:Inverted Repeat Sequences; D015394:Molecular Structure; D010802:Phylogeny; D015203:Reproducibility of Results; D012689:Sequence Homology, Nucleic Acid; D012407:rRNA Operon / Q000235:genetics*
D004275:DNA, Ribosomal; D006570:Heterochromatin
gene silencing; non-coding RNA; promoter-associated RNA; ribosomal RNA