Search

To maintain genome stability, the specialised reverse transcriptase telomerase processively adds telomeric DNA repeats to chromosome ends. Here the authors reported structures of human telomerase at three stages of telomeric repeat synthesis, providing key insights into its mechanism.

This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.

Here, Rangan et al. characterize S. cerevisiae intron structures with in vivo transcriptome-wide structure probing, showing that certain introns exhibit structural features that distinguish pre-mRNA from spliced mRNA and contain structures that regulate gene expression.

Cryo-electron microscopy structures of three large ornate natural bacterial RNA molecules reveal their quaternary structures and intra- and intermolecular interactions that stabilize them.

Designing single molecules capable of complex sensing functions is challenging. Now, using crowdsourced RNA designs from the online game Eterna, compact single-molecule sensors have been demonstrated for a variety of tasks, including a complex three-input tuberculosis diagnostic. The development of a Monte Carlo Tree Search algorithm enabled automated design of similarly sophisticated nucleic-acid sensors.

The authors develop an RNA sequencing-based platform, PERSIST-seq, to simultaneously delineate in-cell mRNA stability, ribosome load, and in-solution stability of a diverse mRNA library to derive design principles for improved mRNA therapeutics.

The conformational heterogeneity of RNA molecules makes their structure determination by X-ray crystallography and NMR challenging. Here the authors show that RNA structures can be solved by cryo-EM and present the structures of a 40 kDa SAM-IV riboswitch in the apo form and bound to its ligand S-adenosylmethionine.

The results of the Fifth RNA-Puzzles contest highlights advances in RNA three-dimensional structure prediction and uncovers new insights into RNA folding and structure.

Using cryogenic electron microscopy and a modelling approach, complex water networks in a ribozyme are visualized.

While the ribosome has been harnessed for synthetic biology, designing ribosomes has remained challenging. Here, the authors demonstrate a community science approach for rational design of ribosomes with beneficial properties.

The Ribosolve pipeline combines single-particle cryo-EM, M2-seq biochemical analysis and Rosetta auto-DRRAFTER modeling to guide three-dimensional RNA structure determination.

Predicting RNA degradation is a fundamental task in designing RNA-based therapeutics. Two crowdsourcing platforms, Kaggle and Eterna, united to develop accurate deep learning models for RNA degradation on a timescale of 6 months.

Cryo-electron microscopy has been used to determine the structure of the Tetrahymena ribozyme (a catalytic RNA) at sufficiently high resolution to model side chains and metal ions.

The EternaBench dataset of synthetic RNA constructs was used to directly compare RNA secondary structure prediction software packages on ensemble-oriented prediction tasks and used to train the EternaFold model for improved performance.

DRRAFTER, a method for RNA modeling into cryo-EM maps, generates accurate models for diverse RNA–protein complexes.

A new computational approach that can be used to refine the three dimensional structural models of proteins is described. When used to refine models generated from nuclear magnetic resonance data, the method can improve the accuracy of the structures in terms of the backbone conformations and the placement of core side chains. In addition, the approach can be used to generate significantly better solutions to the X-ray crystallographic phase problem in molecular replacement trials.

The frameshift stimulation element (FSE) of coronaviruses is an RNA structure that is required for balanced expression of viral proteins and is thus a promising drug target. A structure of the SARS-CoV-2 FSE serves as a guide for the development of antisense oligonucleotides that impair virus replication.

Automated 3D design produces rapid and near-atomically accurate predictions of RNA tertiary structure as well as the ability to generate complex RNA machines such as functional single-stranded tethered ribosomes, and enhancement of the binding properties of small-molecule RNA aptamers.

Non-coding RNAs are ubiquitous biomolecules with intricate three-dimensional folds that are difficult to characterize. This Article presents an information-rich strategy for inferring RNA structure by combining nucleotide-by-nucleotide mutagenesis with single-nucleotide-resolution chemical mapping.

Computational methods are becoming an increasingly important part of biological research. Using the Rosetta framework as an example, the authors demonstrate how community-driven development of computational methods can be done in a reproducible and reliable fashion.

CS-Rosetta-RNA is a web tool for determining high-resolution structures of noncoding RNA motifs using ¹H NMR chemical shift data coupled with Rosetta-based modeling.

Advances in cryo-EM technology will open a new era of RNA-only 3D structure determination.

Complex RNA three-dimensional structures undergo functionally important programmed conformational changes. Here, the authors report how two structurally and functionally coupled RNA domains within a viral 3′-UTR sense the ribosome through conformational changes and respond by modulating translation.

Targeting conserved secondary structure of RNA viruses offers the potential for a customizable therapeutic approach to viral variants.

Evolink, a method developed to co-evolve structurally adjacent but sequence-distant sites in molecular machines, was used in concert with computational modeling to evolve an improved tethered ribosome variant.

A high-resolution structure of human telomerase bound to telomeric DNA reveals details of telomerase assembly and its active site, and sheds light on how mutations alter telomerase function.

The RNA sequence and secondary structure regulate RNA editing by ADAR. Here the authors employ a CRISPR/Cas9-mediated saturation mutagenesis and machine learning to predict RNA editing efficiency of specific substrates.

Extremely conserved 5′ UTRs act as cis-regulatory elements, playing an unsuspected role in translation regulation. A new in-cell mutational method, icM², shows that these 5′ UTRs adopt alternative structures that depend on RNA helicase activity.

Structures in 5′ untranslated regions of eukaryotic mRNAs contribute to gene regulation by controlling cap-dependent and cap-independent translation initiation through diverse mechanisms. New structure probing technologies coupled with techniques such as compensatory mutagenesis will likely identify new structured RNA elements and help elucidate their function.

The cryo-electron microscopy structures of an early spliceosome complex in yeast reveal a unified mechanism for defining introns and exons and also for back-splicing to generate circular RNA.

Picornaviruses use modular RNA domains in their internal ribosome entry sites (IRESs) for translation through non-canonical, cap-independent mechanisms. Here the authors report the crystal structure of domain V from the IRES of hepatitis A virus (HAV) ssRNA genome, suggesting that the functional homology among different types of picornaviral IRESs is structure-based.

Specialized ribosomes (with a particular protein composition) carry out translation of specific transcripts; analysis of Hox mRNA translation in mice reveals that unique RNA structural elements within their 5′ UTRs, including internal ribosome entry sites and translation inhibitory elements, are responsible for this specialized mode of translation.

A Rosetta algorithm improves RNA structure by scoring each nucleotide's possible conformations based on an energy function and electron-density data.

A Rosetta full-atom framework, called fragment assembly of RNA with full-atom refinement (FARFAR), allows the de novo structure prediction and design of noncanonical RNA motifs with near-atomic resolution.

A hybrid molecular motor made of an engineered protein and an RNA lever arm shows bidirectional transport controlled by oligonucleotide signals.