Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions

Abstract

In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing (“kissing”) interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.

RNA Granules: A View from the RNA Perspective

“…RNA assemblies can also form via RNA base stacking, which can happen both with and without the Watson-Crick base pairing [132]. Within the adjacent base-pairings, the bases may stack on each other either within the same strand or the opposite strand, possibly helping to stabilize the RNA dimerization as demonstrated for HIV dimers, bacterial Host factor-I bound RNAs as well as bicoid mRNA dimers [132][133][134]. The G-quadruplex, on the other hand, is based on the interactions among the aromatic rings of the guanines via Hoogsteen-type hydrogen bonding.…”

Global mapping of RNA homodimers in living cells

“…Figure 6. Summary of known and newly identified RNA-RNA homodimers (Micklem, et al 2000;Wittenhagen and Kelley 2002;Irion and St Johnston 2007;Ishikawa, et al 2013;Qu, et al 2014;Franken, et al 2017;Dubois, et al 2018;Tosar, et al 2018;Bou-Nader and Zhang 2020). Counts of gapped and ungapped chimeras (orange) and overlapping chimeras (green) in individual genes in human PARIS data (Lu, et al 2016); yeast RPL (Ramani, et al 2015) human RIC-Seq (Cai, et al 2020); Zika COMRADES (Ziv, et al 2018); human Ago1 CLASH (Helwak, et al 2013); yeast SPLASH (Aw, et al 2016) and human RPL (Ramani, et al 2015).…”

“…A special case of intermolecular interaction between two identical molecules is known as homodimerization. Although homodimers are common in proteins (Bergendahl and Marsh 2017), relatively few homodimers of RNA molecules have been described in vivo (reviewed in (Bou-Nader and Zhang 2020)). Perhaps the best studied are dimers of the HIV genome, which are initiated by an interaction between two copies of the palindromic sequence known as DIS (Berkhout and van Wamel 1996).…”

Three‐Color Imaging Enables Simultaneous Screening of Multiple RNA Targets on Small Molecule Microarrays

“…It is imperative that the fluorophore be linked to a site on the RNA target that causes minimal perturbation of the native 3D structure of the target. Common sites for RNA labeling are either the 5′ or 3′ end, although internal sites of labeling can also be used (especially in the case of multimers) (Bou‐Nader & Zhang, 2020; Kolesnikova, Hubálek, Bednárová, Cvacka, & Curtis, 2017).…”