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

Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing

RNA begins to fold as it is transcribed by an RNA polymerase. Consequently, RNA folding is constrained by the direction and rate of transcription. Understanding how RNA folds into secondary and tertiary structures therefore requires methods for determining the structure of cotranscriptional folding intermediates. Cotranscriptional RNA chemical probing methods accomplish this by systematically probing the structure of nascent RNA that is displayed from an RNA polymerase. Here, we describe a concise, high-resolution cotranscriptional RNA chemical probing procedure called variable length Transcription Elongation Complex RNA structure probing (TECprobe-VL). We demonstrate the accuracy and resolution of TECprobe-VL by replicating and extending previous analyses of ZTP and fluoride riboswitch folding and mapping the folding pathway of a ppGpp-sensing riboswitch. In each system, we show that TECprobe-VL identifies coordinated cotranscriptional folding events that mediate transcription antitermination. Our findings establish TECprobe-VL as an accessible method for mapping cotranscriptional RNA folding pathways.

Observation of coordinated cotranscriptional RNA folding events

RNA begins to fold as it is transcribed by an RNA polymerase. Consequently, RNA folding is constrained by the direction and rate of transcription. Understanding how RNA folds into secondary and tertiary structures therefore requires methods for determining the structure of cotranscriptional folding intermediates. Cotranscriptional RNA chemical probing methods accomplish this by systematically probing the structure of nascent RNA that is displayed from RNA polymerase. Here, we have developed a concise, high-resolution cotranscriptional RNA chemical probing procedure called Transcription Elongation Complex RNA structure probing-Multilength (TECprobe-ML). We validated TECprobe-ML by replicating and extending previous analyses of ZTP and fluoride riboswitch folding, and mapped the folding pathway of a ppGpp-sensing riboswitch. In each system, TECprobe-ML identified coordinated cotranscriptional folding events that mediate transcription antitermination. Our findings establish TECprobe-ML as an accessible method for mapping cotranscriptional RNA folding pathways.

Women in the European Virus Bioinformatics Center

Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.

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.