Structural basis of long non-coding RNA PVT1 interactions with select mRNAs universal in pan-cancer system: A...

PVT1 lncRNA can regulate multi-gene expression through diverse mechanisms, one of which is through binding interactions with mRNAs. Our previous study highlighted its regulatory role in pan-cancer systems through predicted interactions with select mRNAs that are significantly differentially expressed across 15 cancer types. The structural basis of these interactions are yet to be propounded. Here, in order to identify and compare secondary structural features that may mediate PVT1 binding to select cancer-relevant mRNAs, and to determine evidence of evolutionary conservation, if any, we adopted the secondary structure folding information to identify key intermolecular interactions mediating the binding of PVT1 to specific regions, 5'UTR, coding region, and 3'UTR, of these select mRNAs, which may influence the translation process. Forming stable secondary structures, using both Watson-Crick and non-Watson-Crick base pairs, the flexibility of PVT1 lncRNA in interacting with these varied molecules at specific locations is deduced at the secondary structure level. To demonstrate the possible presence of conserved structural elements in PVT1 secondary structure generated based on 7SL non-coding RNA seed sequences, covariation analysis identified 10 significantly co-varying base pairs, suggesting structural conservation. The location of the start point of these lncRNA-mRNA interactions is majorly in the open loop regions. A-U nucleotides in the loops are observed to be higher in number than G-C nucleotides in PVT1 secondary structure. This may initiate multiple base-pairing interactions with other macromolecules more readily, owing to a lesser strength of the hydrogen bonding interactions between A-U base pairs. In the case of these mRNAs, comparatively speaking, there is a variability in the number of purines in the loop regions in their respective secondary structures. Since GC content correlates with the stability of mRNA secondary structures, our analysis shows that even though there is a variable sequence length, some of these mRNAs may demonstrate a higher stability of their specific secondary structures based on a higher GC content. Further, in order to potentially correlate with high protein expression, the distal segment of CDS and the 3'UTR regions of mRNAs require the presence of increased secondary structure. In our analysis, we found the same underlying pattern in a few of our select mRNA molecules. Exploration of the sequence and structural details of these lncRNA-mRNA interactions led us to an insight on a probable mechanism of a single PVT1 molecule being able to bind multiple mRNAs simultaneously or sequentially, in a spatio-temporal manner. Our research also seeks to further elucidate the contribution of bases and intermolecular interactions in the formation of these complexes.