yR1n

yR1n is the designation of a hypothetical small non-coding RNA used to illustrate RNA-based regulation in prokaryotes. In this article, yR1n refers to a conserved RNA of roughly 90–120 nucleotides located in intergenic regions near metabolism-related genes. The yR1n family is posited to occur in several bacterial lineages based on computational analyses of transcriptomes.

It is predicted to fold into a compact structure with a conserved hairpin in the 3' region and an apical loop containing invariant nucleotides. Comparative analyses suggest core motifs are preserved, although flanking sequences vary between species.

The proposed function of yR1n is post-transcriptional regulation by base pairing with target mRNAs to influence translation efficiency or mRNA stability. In simulations and limited experiments, yR1n activity correlates with nutrient limitation and stress responses, implying a role in environmental adaptation. Associated RNA-binding proteins are thought to facilitate target recognition.

Transcription is carried out by RNA polymerase and, in some models, processed from longer primary transcripts. Expression responds to environmental cues via transcription factors and regulatory networks, and some models propose auto-regulation through feedback from its targets.

Detection and study rely on RNA sequencing and northern blotting, coupled with conservation analyses. Target predictions use computational pairing algorithms and are typically validated by reporter assays or loss- or gain-of-function experiments in model systems. As a prototype regulatory RNA, yR1n features in discussions of RNA-based regulation and synthetic biology.