Transient RNA structure features are evolutionarily conserved and can be computationally predicted

How does RNA fold dynamically?

Recent advances in interrogating RNA folding dynamics have shown the classical model of RNA folding to be incomplete. Here, we pose three prominent questions for the field that are at the forefront of our understanding of the importance of RNA folding dynamics for RNA function. The first centers on the most appropriate biophysical framework to describe changes to the RNA folding energy landscape that a growing RNA chain encounters during transcriptional elongation. The second focuses on the potential ubiquity of strand displacement - a process by which RNA can rapidly change conformations - and how this process may be generally present in broad classes of seemingly different RNAs. The third raises questions about the potential importance and roles of cellular protein factors in RNA conformational switching. Answers to these questions will greatly improve our fundamental knowledge of RNA folding and function, drive biotechnological advances that utilize engineered RNAs, and potentially point to new areas of biology yet to be discovered.

ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence

There is an increased interest in the determination of RNA structures in vivo as it is now possible to probe them in a high-throughput manner, e.g. using SHAPE protocols. By now, there exist a range of computational methods that integrate experimental SHAPE-probing evidence into computational RNA secondary structure prediction. The state-of-the-art in this field is currently provided by computational methods that employ the minimum-free energy strategy for prediction RNA secondary structures with SHAPE-probing evidence. These methods, however, rely on the assumption that transcripts in vivo fold into the thermodynamically most stable configuration and ignore evolutionary evidence for conserved RNA structure features. We here present a new computational method, ShapeSorter, that predicts RNA structure features without employing the thermodynamic strategy. Instead, ShapeSorter employs a fully probabilistic framework to identify RNA structure features that are supported by evolutionary and SHAPE-probing evidence. Our method can capture RNA structure heterogeneity, pseudo-knotted RNA structures as well as transient and mutually exclusive RNA structure features. Moreover, it estimates P-values for the predicted RNA structure features which allows for easy filtering and ranking. We investigate the merits of our method in a comprehensive performance benchmarking and conclude that ShapeSorter has a significantly superior performance for predicting base-pairs than the existing state-of-the-art methods.

Thermal adaptation of mRNA secondary structure: stability versus lability

Macromolecular function commonly involves rapidly reversible alterations in three-dimensional structure (conformation). To allow these essential conformational changes, macromolecules must possess higher order structures that are appropriately balanced between rigidity and flexibility. Because of the low stabilization free energies (marginal stabilities) of macromolecule conformations, temperature changes have strong effects on conformation and, thereby, on function. As is well known for proteins, during evolution, temperature-adaptive changes in sequence foster retention of optimal marginal stability at a species' normal physiological temperatures. Here, we extend this type of analysis to messenger RNAs (mRNAs), a class of macromolecules for which the stability-lability balance has not been elucidated. We employ in silico methods to determine secondary structures and estimate changes in free energy of folding (ΔG_fold) for 25 orthologous mRNAs that encode the enzyme cytosolic malate dehydrogenase in marine mollusks with adaptation temperatures spanning an almost 60 °C range. The change in free energy that occurs during formation of the ensemble of mRNA secondary structures is significantly correlated with adaptation temperature: ΔG_fold values are all negative and their absolute values increase with adaptation temperature. A principal mechanism underlying these adaptations is a significant increase in synonymous guanine + cytosine substitutions with increasing temperature. These findings open up an avenue of exploration in molecular evolution and raise interesting questions about the interaction between temperature-adaptive changes in mRNA sequence and in the proteins they encode.

CoBold: a method for identifying different functional classes of transient RNA structure features that can impact RNA structure formation in vivo

RNA structure formation in vivo happens co-transcriptionally while the transcript is being made. The corresponding co-transcriptional folding pathway typically involves transient RNA structure features that are not part of the final, functional RNA structure. These transient features can play important functional roles of their own and also influence the formation of the final RNA structure in vivo. We here present CoBold, a computational method for identifying different functional classes of transient RNA structure features that can either aid or hinder the formation of a known reference RNA structure. Our method takes as input either a single RNA or a corresponding multiple-sequence alignment as well as a known reference RNA secondary structure and identifies different classes of transient RNA structure features that could aid or prevent the formation of the given RNA structure. We make CoBold available via a web-server which includes dedicated data visualisation.

Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates

The series of RNA folding events that occur during transcription can critically influence cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a method to uncover details of cotranscriptional RNA folding. We model the folding of the Escherichia coli signal recognition particle (SRP) RNA and show that it requires specific local structural fluctuations within a key hairpin to engender efficient cotranscriptional conformational rearrangement into the functional structure. All-atom molecular dynamics simulations suggest that this rearrangement proceeds through an internal toehold-mediated strand-displacement mechanism, which can be disrupted with a point mutation that limits local structural fluctuations and rescued with compensating mutations that restore these fluctuations. Moreover, a cotranscriptional folding intermediate could be cleaved in vitro by recombinant E. coli RNase P, suggesting potential cotranscriptional processing. These results from experiment-guided multi-scale modeling demonstrate that even an RNA with a simple functional structure can undergo complex folding and processing during synthesis.

The International Virus Bioinformatics Meeting 2020

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.

Viroid research and its significance for RNA technology and basic biochemistry

Viroids were described 47 years ago as the smallest RNA molecules capable of infecting plants and autonomously self-replicating without an encoded protein. Work on viroids initiated the development of a number of innovative methods. Novel chromatographic and gelelectrophoretic methods were developed for the purification and characterization of viroids; these methods were later used in molecular biology, gene technology and in prion research. Theoretical and experimental studies of RNA folding demonstrated the general biological importance of metastable structures, and nuclear magnetic resonance spectroscopy of viroid RNA showed the partially covalent nature of hydrogen bonds in biological macromolecules. RNA biochemistry and molecular biology profited from viroid research, such as in the detection of RNA as template of DNA-dependent polymerases and in mechanisms of gene silencing. Viroids, the first circular RNA detected in nature, are important for studies on the much wider spectrum of circular RNAs and other non-coding RNAs.

Fixed-parameter tractable sampling for RNA design with multiple target structures

Background

The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which substantially reduce the need for costly wet-lab experiments.

Results

We devise a novel approach to a central ingredient of most in-silico design methods: the generation of sequences that fold well into multiple target structures. Based on constraint networks, our approach supports generic Boltzmann-weighted sampling, which enables the positive design of RNA sequences with specific free energies (for each of multiple, possibly pseudoknotted, target structures) and GC-content. Moreover, we study general properties of our approach empirically and generate biologically relevant multi-target Boltzmann-weighted designs for an established design benchmark. Our results demonstrate the efficacy and feasibility of the method in practice as well as the benefits of Boltzmann sampling over the previously best multi-target sampling strategy—even for the case of negative design of multi-stable RNAs. Besides empirically studies, we finally justify the algorithmic details due to a fundamental theoretic result about multi-stable RNA design, namely the #P-hardness of the counting of designs.

Conclusion

introduces a novel, flexible, and effective approach to multi-target RNA design, which promises broad applicability and extensibility.

Our free software is available at: https://github.com/yannponty/RNARedPrint Supplementary data are available online.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2784-7) contains supplementary material, which is available to authorized users.

Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing

A physics-based method for the prediction of the structures of nucleic acids, which is based on the physics-based 2-bead NARES-2P model of polynucleotides and global-optimization Conformational Space Annealing (CSA) algorithm has been proposed. The target structure is sought as the global-energy-minimum structure, which ignores the entropy component of the free energy but spares expensive multicanonical simulations necessary to find the conformational ensemble with the lowest free energy. The CSA algorithm has been modified to optimize its performance when treating both single and multi-chain nucleic acids. It was shown that the method finds the native fold for simple RNA molecules and DNA duplexes and with limited distance restraints, which can easily be obtained from the secondary-structure-prediction servers, complex RNA folds can be treated with using moderate computer resources.

Computational approaches for alternative and transient secondary structures of ribonucleic acids

Transient and alternative structures of ribonucleic acids (RNAs) play essential roles in various regulatory processes, such as translation regulation in living cells. Because experimental analyses for RNA structures are difficult and time-consuming, computational approaches based on RNA secondary structures are promising. In this article, we review computational methods for detecting and analyzing transient/alternative secondary structures of RNAs, including static approaches based on probabilistic distributions of RNA secondary structures and dynamic approaches such as kinetic folding and folding pathway predictions.

Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts

Lentiviral RNA genomes contain structural elements that play critical roles in viral replication. Although structural features of 5'-untranslated regions have been well characterized, attempts to identify important structures in other genomic regions by Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) have led to conflicting structural and mechanistic conclusions. Previous approaches accounted neither for sequence heterogeneity that is ubiquitous in viral populations, nor for selective constraints operating at the protein level. We developed an approach that augments SHAPE with phylogenetic analyses and applied it to investigate structure in coding regions (cRNA) within the HIV and SIV envelope genes. Analysis of single-genome SHAPE data with phylogenetic information from diverse lentiviral sequences argues against the conservation of a putative global gp120 RNA structure but points to the existence of core RNA sub-structures. Our findings establish a framework for considering sequence heterogeneity and protein function in de novo RNA structure inference approaches.

RNA-mediated signal perception in pathogenic bacteria

Bacterial pathogens encounter several different environments during an infection, many of them possibly being detrimental. In order to sense its surroundings and adjust the gene expression accordingly, different regulatory schemes are undertaken. With these, the bacterium appropriately can differentiate between various environmental cues to express the correct virulence factor at the appropriate time and place. An attractive regulator device is RNA, which has an outstanding ability to alter its structure in response to external stimuli, such as metabolite concentration or alterations in temperature, to control its downstream gene expression. This review will describe the function of riboswitches and thermometers, with a particular emphasis on regulatory RNAs being important for bacterial pathogenicity. WIREs RNA 2017, 8:e1429. doi: 10.1002/wrna.1429 For further resources related to this article, please visit the WIREs website.

In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression

RNA transcripts are the primary products of active genes in any living organism, including many viruses. Their cellular destiny not only depends on primary sequence signals, but can also be determined by RNA structure. Recent experimental evidence shows that many transcripts can be assigned more than a single functional RNA structure throughout their cellular life and that structure formation happens co-transcriptionally, i.e. as the transcript is synthesised in the cell. Moreover, functional RNA structures are not limited to non-coding transcripts, but can also feature in coding transcripts. The picture that now emerges is that RNA structures constitute an additional layer of information that can be encoded in any RNA transcript (and on top of other layers of information such as protein-context) in order to exert a wide range of functional roles. Moreover, different encoded RNA structures can be expressed at different stages of a transcript's life in order to alter the transcript's behaviour depending on its actual cellular context. Similar to the concept of alternative splicing for protein-coding genes, where a single transcript can yield different proteins depending on cellular context, it is thus appropriate to propose the notion of alternative RNA structure expression for any given transcript. This review introduces several computational strategies that my group developed to detect different aspects of RNA structure expression in vivo. Two aspects are of particular interest to us: (1) RNA secondary structure features that emerge during co-transcriptional folding and (2) functional RNA structure features that are expressed at different times of a transcript's life and potentially mutually exclusive.

Regulatory effects of cotranscriptional RNA structure formation and transitions

RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA-RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5'-capping, splicing, 3'-polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure-mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562-574. doi: 10.1002/wrna.1350 For further resources related to this article, please visit the WIREs website.

Four RNA families with functional transient structures

Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5' flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5' UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All transient and dominant structures are mapped to our new alignments introduced here.

How to find RNA thermometers

Temperature is one of the decisive signals that a mammalian pathogen has entered its warm-blooded host. Among the many ways to register temperature changes, bacteria often use temperature-modulated structures in the untranslated region of mRNAs. In this article, we describe how such RNA thermometers (RNATs) have been discovered one by one upstream of heat shock and virulence genes in the past, and how next-generation sequencing approaches are able to reveal novel temperature-responsive RNA structures on a global scale.

e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation

e-RNA offers a free and open-access collection of five published RNA sequence analysis tools, each solving specific problems not readily addressed by other available tools. Given multiple sequence alignments, Transat detects all conserved helices, including those expected in a final structure, but also transient, alternative and pseudo-knotted helices. RNA-Decoder uses unique evolutionary models to detect conserved RNA secondary structure in alignments which may be partly protein-coding. SimulFold simultaneously co-estimates the potentially pseudo-knotted conserved structure, alignment and phylogenetic tree for a set of homologous input sequences. CoFold predicts the minimum-free energy structure for an input sequence while taking the effects of co-transcriptional folding into account, thereby greatly improving the prediction accuracy for long sequences. R-chie is a program to visualise RNA secondary structures as arc diagrams, allowing for easy comparison and analysis of conserved base-pairs and quantitative features. The web site server dispatches user jobs to a cluster, where up to 100 jobs can be processed in parallel. Upon job completion, users can retrieve their results via a bookmarked or emailed link. e-RNA is located at http://www.e-rna.org.

On the importance of cotranscriptional RNA structure formation

The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.