RNA technologies 

Abstract: Unlike other large biomolecules, RNA carries two main tasks: an informational coding potential governed by its sequence and a catalytic/regulatory role, determined by its secondary and tertiary structure. During the last decade, a significant improvement in biophysical and biochemical techniques has enabled researchers to initiate exploratory studies on the relationship between RNA structure and its function. Among other technological improvements, the explosion of next generation sequencing (NGS) tools has allowed the transcriptome-wide investigation of RNA folding in cells. Deeper knowledge of 2D and 3D structures is extremely important for understanding the mechanisms of RNA function as well as for designing synthetic RNAs and the development of RNA-targeted drugs. RNA molecules can adopt specific 3D motifs that are now considered druggable and offer untapped potential to therapeutically modulate numerous cellular processes, including those linked to ‘undruggable’ protein targets. In parallel to the growing interest for the RNA targetome in the pharmaceutical sector, the in-silico modelling of RNA folds is developing complementary methods. Currently, RNA structure probing methods can only capture partial structure information. The ability to directly measure intact RNA structures could facilitate investigations of the functions and regulation mechanisms as well as druggability. In this chapter, we will summarize biophysical and biochemical strategies for determining RNA structures/motifs, including latest approaches that combine molecular biology strategies with NGS readouts.

Abstract: G-quadruplexes are four-stranded nucleic acid structures, the bases of which are linked through Hoogsteen hydrogen bonding. RNA G-quadruplex is shown to take part in a wide range of cellular events such as telomere maintenance, gene expression mechanisms, etc. RNA G-quadruplex is found to be present in a significant portion of the non-coding transcriptome, thus acting as a biomarker for several diseases. RNA quadruplex is also shown to be associated with neurogenerative diseases and cancer; thus, it is a potential therapeutic target. For these reasons, it is necessary to understand the sequence, structure and functional relevance of RNA G-quadruplex. A comprehensive analysis of the structural and folding characteristics of RNA G-quadruplex structures deposited in the PDB has therefore been carried out. A total of 10 unique folds are found to be present in RNA quadruplex. Together with the existing algorithms for the transcriptome-wide prediction of G-quadruplexes, the structural features discussed here would help in the modeling of G-quadruplex structures.

Abstract: The genome is pervasively transcribed and produces various messenger RNAs and noncoding RNAs. Defective transcripts are also produced, which are cleared by RNA surveillance and quality control systems. Nuclear RNA degradation pathways play important roles in these systems and in shaping the transcriptome and preventing diseases. In this review, we summarize current knowledge of nuclear noncoding RNAs. We then discuss nuclear RNA degradation factors involved in RNA surveillance and RNA quality control systems.

Abstract: Like proteins, an RNA is only functional when it is folded into its native conformation and adopts a specific secondary and tertiary structure. Hence, the analysis of RNA structure is essential to understand the cellular roles of distinct RNA molecules. Technical approaches used to study RNA structure comprise bioinformatics tools, structural probing, and biophysical methods to integrate sequence and 3D structure information. In this review, I focus on structural probing techniques of RNA secondary structure. I discuss basic enzymatic and chemical probing techniques, and present novel approaches in combination with high-throughput sequencing. A focus is laid on SHAPE techniques and its various developments and applications. Finally, at the example of RNA G-quadruplexes, it is highlighted how an array of probing techniques can be combined to study a specific RNA structural motif in vitro and in vivo.