Riboswitches articles from across Nature Portfolio

CaCoFold-R3D is a probabilistic model that simultaneously predicts the RNA 3D motifs jointly with the secondary structure in a structural RNA using evolutionary information.

150 years ago, guanidine was found to affect muscle function via unknown mechanisms. Here, Kavita et al. provide evidence that guanine-sensing RNAs are present in many eukaryotic transcripts relevant to Ca2+ signaling and neuromuscular function.

RNA switches are a promising tool for cell type-specific gene regulation but often suffer from insufficient specificity. Here authors developed “split RNA switches”, which integrate outputs from multiple RNA switches by exploiting protein splicing, improving specificity and increasing the ON/OFF ratio.

Cotranscriptional RNA folding pathways often involve the sequential formation of folding intermediates as RNA emerges from an RNA polymerase. Here the authors develop an RNA chemical probing method that directly measures the cotranscriptional rearrangement of nascent RNA structures.

Understanding how RNA folds into functional structures requires methods that can systematically assess how sequence perturbations affect RNA structure and function. Here, the authors develop a broadly accessible platform for performing high-throughput cotranscriptional RNA functional assays.

Riboswitches are RNA sensors that allow bacteria to sense and respond to their environment. Here, Bushhouse et al. demonstrate that the sensitivity of several riboswitches can be tuned by manipulating how the riboswitch RNAs fold during transcription.

To understand the complex dynamics and diverse functions of RNA, robust technologies for labeling and imaging RNA are highly desirable. A newly developed green fluorescent aptamer named Okra enables the imaging of mRNA dynamics in living cells.

Nano-DMS-MaP focuses in on the structures of individual RNA isoforms, enabling direct examination of the structural diversity of different RNAs inside cells.

In the post-genomic era, many genes and regulatory elements remain uncharacterized, including riboswitches — RNA structures that control gene expression by directly binding metabolites. Here, a new type of metal-responsive riboswitch that senses sodium cations expands the bacterial Na⁺ metabolic repertoire.

Hiroshide Saito discusses two seminal papers that provided foundational evidence for the hypothesis that RNA with both genetic information and catalytic activity had an essential role in the origin of life.

Reliable quantification and tracing of RNA molecules remain challenging goals. A new fluorescent RNA tag, developed based on a natural adenine-sensing riboswitch and named Squash, offers superior imaging properties and accurate quantification in living cells.