I’ll See Your Double Helix and Raise You One!
RNA generally undergoes extensive processing following transcription (or co-transcriptionally), and these processing events are both tightly regulated and critical for the function and stability of the RNA molecule. Some common types of RNA processing are 5’ end capping, splicing, and polyadenylation of the 3’ end of the transcript. Polyadenylation of mRNAs is thought to be critical to stabilize these molecules by inhibiting 3’ to 5’ exonuclease activity of RNase enzymes and also increases the efficiency of their translation. Historically, nearly all RNA molecules that are transcribed by RNA Polymerase II (Pol II) were thought to be processed to contain a poly(A) tail. However, more recent whole-transcriptome studies have indicated that there may be more non-polyadenylated Pol II transcripts than previously thought. One prominent example of a stable RNA that is not polyadenylated is MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), which is a long non-coding RNA that is expressed at higher levels than most protein-coding RNAs and that is often misregulated in human cancers. A recent report by Wilusz et al. suggests that MALAT1 utilizes an RNA triple helix, rather than a poly(A) tail, to promote its stability.
The authors began their study by generating an in vitro model to recapitulate the previously observed 3’ processing of the MALAT1 transcript and then used this model system to determine the role of cis-acting elements in the 3’ end of the MALAT1 RNA. Evolutionarily conserved regions were identified at the 3’ end of the MALAT1 transcript (two U-rich motifs and one A-rich tract) and mutational analysis showed that all three motifs were required for MALAT1 RNA stability. Extensive additional mutagenesis studies, as well as tertiary RNA structure modeling performed using a powerful algorithm known as FARFAR, led the authors to conclude that the three highly conserved motifs at the 3’ end of MALAT1 adopt a stable triple helix structure. In addition to promoting RNA stability, the RNA triple helix was also found to promote translation of transcripts to a similar extent as poly(A) tails. The authors suggested that triple helix structures, or other related structures, at the 3’ termini of RNAs might be a widely-used mechanism to promote the stability and/or translation efficiency of non-polyadenylated RNAs.
As the result of recent genome-wide transcriptome studies, we now know that the vast majority of most genomes are actively transcribed, and that most of these transcripts originate from regions outside of protein-coding genes. A larger than previously anticipated proportion of Pol II-transcribed long RNAs (~25%) lack a canonical poly(A) tail, and the authors argue that these non-polyadenylated RNAs might be protected from degradation by triple helices or other complex RNA structures at their 3’ end. This would be quite a paradigm shift from our previous understanding of mRNA stabilization, which suggested that RNA processing to add poly(A) tails was the primary mechanism involved in promoting transcript stability. If confirmed, these new findings will greatly expand our knowledge of RNA processing events and how they can regulate gene expression. Do you think that the presence of triple helices in the 3’ end of transcripts will allow us to artificially control the stability of specific RNA molecules as a novel therapeutic approach?
Wilusz JE et al. (2012) A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev. 2012 Oct 16. (Published online October 16, 2012)