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Review
.2021 Dec 15;7(4):81.
doi: 10.3390/ncrna7040081.

Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions

Affiliations
Review

Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions

Ilias Skeparnias et al. Noncoding RNA..

Abstract

Complex RNA-RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation. By contrast, the nature of these interactions and characteristics of their interfaces, especially those that involve partially or wholly structured RNAs, remain elusive. Herein, we discuss different modalities of RNA-RNA interactions with an emphasis on those that depend on secondary, tertiary, or quaternary structure. We dissect recently structurally elucidated RNA-RNA complexes including RNA triplexes, riboswitches, ribozymes, and reverse transcription complexes. These analyses highlight a reciprocal relationship that intimately links RNA structure formation with RNA-RNA interactions. The interactions not only shape and sculpt RNA structures but also are enabled and modulated by the structures they create. Understanding this two-way relationship between RNA structure and interactions provides mechanistic insights into the expanding repertoire of noncoding RNA functions, and may inform the design of novel therapeutics that target RNA structures or interactions.

Keywords: RNA; RNA structure; RNA–RNA interactions; RNase P; T-box; base pair; base stacking; riboswitch; ribozyme; tRNA.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 3
Figure 3
Interaction between structured RNAs. (A) Host tRNALys3 refolds and binds HIV-1 PBS genomic RNA region forming the reverse transcription initiation complex (RTIC). HIV-1 Reverse transcriptase (RT) bound to the RNA–RNA complex is omitted for clarity. Bottom: cryo-EM structure of the RTIC. tRNA is in green whereas the partner RNA is in blue. Interaction regions are highlighted in red. (B) Pre-tRNAs bind RNase P ribozymes through three base-pairing interactions to the tRNA 3′ region and stacking interactions with its elbow. Ribozyme catalytic center is indicated by the red scissors. Bottom: cryo-EM structure of human RNase P holoenzyme (upper) [93] and co-crystal structure ofThermotoga maritima RNase P holoenzyme (lower) [12]. (C) T-box riboswitches encase their cognate tRNA ligands via coordinated contacts at three distant interfaces: codon–anticodon base-pairing interactions stabilized by cross-stranding stacking and A-minor interactions with the Stem II S-turn, stacking interactions with the tRNA elbow, and both pairing and stacking interactions with the tRNA termini. Bottom: composite structural model of a full-length, feature-complete T-box riboswitch based on several co-crystal and cryo-EM structures [97]. Intermolecular base-pairing interactions are indicated by red sticks perpendicular to the RNA strands, intermolecular stacking interactions by two red sticks parallel to the RNA strands. RNA–RNA interfaces on structural renderings are highlighted in red.
Figure 1
Figure 1
ssRNA–ssRNA interactions (A) Bacterial sRNAs form extensive base-pairing interactions with partially or wholly complementary segments of mRNAs, assisted by RNA chaperones such as Hfq, ProQ, FinO. sRNA binding remodels the mRNA structure to regulate its transcription, translation, stability, or decay, etc. (B) Eukaryotic small ssRNAs such as miRNAs, siRNAs, and piRNAs assemble with Ago proteins to form RNA-induced silencing complexes (RISC), and form perfect or imperfect base pairing with the target mRNA. Base pairing occurs first in the seed region and then in the supplementary pairing region. Such targeting leads to mRNA degradation or translation suppression. (C) RNA-targeting CRISPR-Cas13 binds the dsRNA duplex between the crispr RNA (crRNA) and the target mRNA, causing mRNA degradation and activating Cas13′s collateral RNase activity [34]. (D) Codon–anticodon base-pairing interactions between tRNA and mRNA are further stabilized by adjacent contacts from the rRNA and tRNA. Intermolecular base-pairing interactions are indicated by red sticks. Target mRNAs are shown in blue, sRNAs and other targeting or guiding RNAs in orange, and tRNAs in green. Proteins that facilitate the RNA interactions are shown as orange bodies.
Figure 2
Figure 2
ssRNA interaction with structured RNAs. (A) Circular lncRNAs can associate with multiple miRNAs via base-pairing and store them until conditional release. (B) Expression and nuclear retention elements (ENEs) binds polyA ssRNAs forming RNA triplexes, leading to protection of the mRNA 3′ end from deadenylases and RNases. (C) The CCR5 pseudoknot is stabilized by miR-1224 forming an RNA triplex, promoting −1 programed ribosome frameshift. (D) SnoRNAs guide snoRNPs to their rRNA targets via base pairing and likely other tertiary interactions. (E) Crystal structures of the BWYV frameshifting pseudoknot and three ENE triplexes from KSHV PAN RNA, human MALAT-1 lncRNA, and rice double ENE RNA.
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References

    1. Breaker R.R. Riboswitches and the RNA World. Cold Spring Harb. Perspect. Biol. 2012;4:a003566. doi: 10.1101/cshperspect.a003566. - DOI - PMC - PubMed
    1. Cech T.R., Steitz J.A. The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones. Cell. 2014;157:77–94. doi: 10.1016/j.cell.2014.03.008. - DOI - PubMed
    1. Yao R.-W., Wang Y., Chen L.-L. Cellular functions of long noncoding RNAs. Nat. Cell Biol. 2019;21:542–551. doi: 10.1038/s41556-019-0311-8. - DOI - PubMed
    1. Ulyanov N.B., James T.L. RNA structural motifs that entail hydrogen bonds involving sugar–phosphate backbone atoms of RNA. New J. Chem. 2010;34:910–917. doi: 10.1039/b9nj00754g. - DOI - PMC - PubMed
    1. Ferré-D’Amaré A.R., Winkler W.C. The roles of metal ions in regulation by riboswitches. Struct. Catal. Roles Met. Ions RNA. 2011;9:141–173. - PMC - PubMed

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