A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA

Abstract

The ubiquitous presence of long noncoding RNAs (lncRNAs) in eukaryotes points to the importance of understanding how their sequences impact function. As many lncRNAs regulate nuclear events and thus must localize to nuclei, we analyzed the sequence requirements for nuclear localization in an intergenic lncRNA named BORG (BMP2-OP1-responsive gene), which is both spliced and polyadenylated but is strictly localized in nuclei. Subcellular localization of BORG was not dependent on the context or level of its expression or decay but rather depended on the sequence of the mature, spliced transcript. Mutational analyses indicated that nuclear localization of BORG was mediated through a novel RNA motif consisting of the pentamer sequence AGCCC with sequence restrictions at positions ؊8 (T or A) and ؊3 (G or C) relative to the first nucleotide of the pentamer. Mutation of the motif to a scrambled sequence resulted in complete loss of nuclear localization, while addition of even a single copy of the motif to a cytoplasmically localized RNA was sufficient to impart nuclear localization. Further, the presence of this motif in other cellular RNAs showed a direct correlation with nuclear localization, suggesting that the motif may act as a general nuclear localization signal for cellular RNAs.

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

“…Nevertheless, through this classification we have managed to discover features that distinguish lncRNAs and have laid a foundation for predicting lncRNA localization de novo. Similarly, a recent study discovered an RNA motif that predicts and appears to confer nuclear localization (Zhang et al 2014). We find that lncRNAs localized in the light polysomal fraction tend to have mRNA-like 5 ′ features, more specifically a nonrandom long "pseudo-5…”

Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications

“…These structures and motifs are important for the stabilization, subcellular localization, and function of these lncRNAs. For example, a small motif involved in restricting lncRNA localization to the nucleus was identified [185]. …”

The Long Non-Coding RNAs in Neurodegenerative Diseases: Novel Mechanisms of Pathogenesis

“…Localization of lncRNAs is mainly nuclear, but they can also shuttle in the cytoplasm. Although the signals driving cytoplasmic localization are at now unknown [10][11][12], an RNA motif consisting of the pentamer sequence AGCCC has been recently reported to mediate the nuclear localization of BORG lncRNA [13]. LncRNAs can be broadly classified into two large categories, based on their position in respect to protein-coding genes: 1) intergenic lncRNAs, including pseudogenes, long intergenic non-coding RNAs (lincRNAs), and very long intergenic non-coding RNAs (vlincRNAs/macroRNAs); 2) coding gene-overlapping lncRNAs, represented by intronic lncRNAs, natural antisense transcripts (NATs), expressed non-coding regions (ENORs), enhancer RNAs (eRNAs), and promoter-associated long RNAs (PALRs) [14].…”