Not surprisingly, several lncRNAs possess characteristics from multiple archetypes that, in combination, are critical to its eventual biological function. For example, COLDAIR and COOLAIR are transcribed in response to the environmental cue of cold temperature—their transcription serves as a signal of a significant biological event, in this case the preparations for competence to flower after a prolonged winter. Epigenetic repression of floral repressors is then achieved through binding of PRC2 by COLDAIR, with the lncRNA serving as a guide to affect silencing at the FLC locus to bring about the biological effect of vernalization. The lncRNA HOTTIP is another example of a “signal plus guide” combination archetype—it is transcribed in a temporal and spatial manner along with the rest of the distal HOXA genes to convey positional identity, and functions by binding to and targeting the trithorax protein complex Mixed Lineage in Leukemia-1 (MLL-1) to the 5‘ HOXA locus to drive histone methylation and gene transcription.
Another combinatorial archetype is exemplified by HOTAIR. Like HOTTIP, HOTAIR is transcribed in posterior and distal cells, acting as a signal for anatomic specificity. By bindings to both the PRC2 and LSD1 complexes, HOTAIR serves as a modular scaffold, and by targeting PRC2 to its proper genomic locations it acts as a guide. Thus, the desired biological outcome—positional identity and appropriate chromatin modifications leading to proper gene expression—is ultimately achieved through a functional multi-functional lncRNA.
One emerging theme from the analysis of the four lncRNA archetypes is that of stepwise complexity. When one considers each of the archetype classes from an evolutionary perspective, it is a strikingly simple process of incremental modifications that confer alterations in molecular utility. The simple signal archetype lncRNA, such as eRNAs, merely requires the transcription of a regulatory DNA element. If the lncRNA that is produced also binds a protein due to the formation of a RNA motif mimicking its DNA counterpart, as is the case for Gas5, then the lncRNA develops into a molecular decoy. If the lncRNA then gains the ability to target the bound effectors to a specific DNA sequence either in cis or trans, it transitions to become a guide. With nucleic acid duplication, fusion, and recombination events, it is not far-fetched to imagine that lncRNAs may subsequently acquire multiple effector binding sites to turn into a scaffold. This step-wise scenario is potentially quite likely because the regulatory DNA being transcribed, such as enhancers, by definition possess high affinity transcription factor binding sequences, and often in tandem and combinatorial arrangements. Thus, the primordial lncRNA “signals” may often contain functional seeds to become decoys, guides, and scaffolds.
In fact, experimental evolution hints at the feasibility of evolving many new lncRNA regulators of gene expression. Work by Kehayova and Liu (2007)
highlights the value of RNA evolution, and argue that the polyanionic characteristic, in combination with the great structural and functional diversity of RNA, makes it especially well suited to mediate processes that involve proteins with cationic patches (Kehayova and Liu, 2007
). In fact, RNA-based transcript regulators are relatively easy to evolve, on the order of 104
, in contrast to in vitro selections for RNA aptamers for a specific ligand or protein, in which the rate of active RNAs among random library members is approximately 1 in 1010
(Kehayova and Liu, 2007
Polymorphisms and mutations in regulatory regions are increasingly shown to be associated with human disease. However, currently, we are only observing the tip of the iceberg. It is becoming clear that many common disease-association studies are identifying noncoding region variants as the underlying cause of these later onset disorders. It will be exciting, and potentially useful for disease management and treatment, to see what aspects of fine tuning are altered in different anomalies. Areas for future exploration will include the mechanisms through which physiological and environmental changes are translated into altered gene function through lncRNAs and their regulatory networks. We hope that we have provided logic and experimental evidence to support the archetypal classifications of lncRNAs as a useful framework. As more examples of regulation by long ncRNA are uncovered, one might predict that the large transcripts will eventually rival small RNAs and proteins in their versatility as regulators of genetic information.