RNA articles from across Nature Portfolio

Trans-splicing enables the ligation of exons from different pre-mRNAs into a single transcript. A recent study harnesses this process and develops riboregulators that, upon binding programmable external guide sequences (EGSs), allow customizable, orthogonal and predictable gene circuit construction.

Eucaryotic EndoU are endoribonucleases that require calcium ions to cleave RNA substrates. Here, the authors solved the structure of calcium-activated human EndoU and proposed a structural model for U-rich RNA recognition, revealing how calcium ions allosterically activate the enzyme.

A method called UltraSelex for identifying RNA aptamers has been developed. UltraSelex is noniterative and can combine biochemical partitioning, high-throughput sequencing and computational signal-to-background rank modeling of hits in approximately 1 day.

Here authors use RNA interference to identify circular RNAs involved in synaptogenesis. They report that the candidate circRERE inhibits the formation of silent synapses via microRNA miR-128-3p stabilization.

Zhang, Mille-Fragoso and colleagues developed a synthetic receptor platform named LIDAR (Ligand-Induced Dimerization-Activating RNA editing), which enables ligand-responsive gene regulation without the need of DNA promoters and is, thus, compatible with mRNA delivery.

RNA is a promising reservoir of new drug targets. Here, the authors introduce RNAmigos2, a structure-based deep learning model that speeds up screening by 10,000x while rivaling docking accuracy, showing success in identifying RNA-binding compounds in vitro.

Trans-splicing enables the ligation of exons from different pre-mRNAs into a single transcript. A recent study harnesses this process and develops riboregulators that, upon binding programmable external guide sequences (EGSs), allow customizable, orthogonal and predictable gene circuit construction.

Biomolecules morph between conformations with distinct lifetimes according to their functional requirements. Mosquito-borne flaviviruses encode exoribonuclease-resistant RNAs (xrRNAs) that fold into knot-like structures to prevent exonuclease Xrn1 digestion. To achieve high Xrn1 resistance, xrRNAs contain molecular interactions with lifetimes that persist up to ten million times longer than canonical base pairs.

The mechanism of translation initiation in linear and circular mRNAs influences translation efficiency. Covalent attachment of an N⁷-methylguanosine (m⁷G) cap increases protein production from circular mRNAs in mice. Hybridization with capped endogenous RNAs also promotes protein production in cells, suggesting that this interaction might also occur between endogenous RNAs.

Using trans-ribozyme-mediated circularization, we have produced circular RNAs that are not limited by RNA sequence or length and that allow for modifications. The synthesized RNAs increase protein expression more than 7,000-fold.

We present an RNA language model-based deep learning pipeline for accurate and rapid de novo RNA 3D structure prediction, demonstrating strong accuracy in modeling single-stranded RNAs and excellent generalization across RNA families and types while also being capable of capturing local features such as interhelical angles and secondary structures.