Annotation of the local context of RNA secondary structure improves the classification and prediction of A-minors

Abstract

Noncoding RNAs play a crucial role in various cellular processes in living organisms, and RNA functions heavily depend on molecule structures composed of stems, loops, and various tertiary motifs. Among those, the most frequent are A-minor interactions, which are often involved in the formation of more complex motifs such as kink-turns and pseudoknots. We present a novel classification of A-minors in terms of RNA secondary structure where each nucleotide of an A-minor is attributed to the stem or loop, and each pair of nucleotides is attributed to their relative position within the secondary structure. By analyzing classes of A-minors in known RNA structures, we found that the largest classes are mostly homogeneous and preferably localize with known A-minor co-motifs, such as tetraloop–tetraloop receptor and coaxial stacking. Detailed analysis of local A-minors within internal loops revealed a novel recurrent RNA tertiary motif, the across-bulged motif. Interestingly, the motif resembles the previously known GAAA/11nt motif but with the local adenines performing the role of the GAAA-tetraloop. By using machine learning, we show that particular classes of local A-minors can be predicted from sequence and secondary structure. The proposed classification is the first step toward automatic annotation of not only A-minors and their co-motifs but various types of RNA tertiary motifs as well.

A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures

“…We observed and demonstrated a number of topology-independent structural similarities, e.g., between a long-range D-loop/T-loop interaction motif and a GAAA-tetraloop hairpin. Previously, similar cases were described e.g., in [20] between an internal loop forming the across-bulged motif and the long-range GAAA/11nt interaction motif. The possibility of the kink-turn motif usually being an internal loop to occur in the context of a multiple junction is another example [61].…”

“…To annotate RNA secondary structure elements and nucleotide doublets we used the urslib2 python library [20], which relies on DSSR annotations of canonical base pairs. We defined a nucleotide doublet as any two ribonucleotides that have any non-hydrogen atoms within 6.0 Å of each other.…”

“…Then, we defined a long-range nucleotide doublet as a nucleotide doublet of two ribonucleotides that belong to distant RNA secondary structure elements, stems or loops. For that, we used the definitions from [20] (Scheme 1). According to these definitions, a stem is defined as a maximal set of N ≥ 2 consecutive Watson-Crick (A-U, G-C) or Wobble (G-U) base pairs.…”

“…E.g., on Scheme 1 HC2 and S3 are distant, but HP3 and JI0 are not distant as they are both adjacent to S3. For the strict formal description of the used definitions see Supplementary Text in [20].…”

RNA multimerization as an organizing force for liquid–liquid phase separation

“…Figure 1B, image 3). The A-minor motif is common in tertiary interactions, including structures such as pseudoknots (Shalybkova et al 2021). This motif is more plastic than the aforementioned major groove triplexes because A's can interact with GC, CG, AU, and UA pairs, as well as with non-Watson-Crick pairs to make base triples in the wide and accessible minor groove of RNA.…”