Post-transcriptional Regulation of Gene Expression via Unproductive Splicing

Unproductive splicing is a mechanism of post-transcriptional gene expression control in which premature stop codons are inserted into protein-coding transcripts as a result of regulated alternative splicing, leading to their degradation via the nonsense-mediated decay pathway. This mechanism is especially characteristic of RNA-binding proteins, which regulate each other's expression levels and those of other genes in multiple auto- and cross-regulatory loops. Deregulation of unproductive splicing is a cause of serious human diseases, including cancers, and is increasingly being considered as a prominent therapeutic target. This review discusses the types of unproductive splicing events, the mechanisms of auto- and cross-regulation, nonsense-mediated decay escape, and problems in identifying unproductive splice isoforms. It also provides examples of deregulation of unproductive splicing in human diseases and discusses therapeutic strategies for its correction using antisense oligonucleotides and small molecules.

Cooperation and Competition of RNA Secondary Structure and RNA-Protein Interactions in the Regulation of Alternative Splicing

The regulation of alternative splicing in eukaryotic cells is carried out through the coordinated action of a large number of factors, including RNA-binding proteins and RNA structure. The RNA structure influences alternative splicing by blocking cis-regulatory elements, or bringing them closer or farther apart. In combination with RNA-binding proteins, it generates transcript conformations that help to achieve the necessary splicing outcome. However, the binding of regulatory proteins depends on RNA structure and, vice versa, the formation of RNA structure depends on the interaction with regulators. Therefore, RNA structure and RNA-binding proteins are inseparable components of common regulatory mechanisms. This review highlights examples of alternative splicing regulation by RNA-binding proteins, the regulation through local and long-range RNA structures, as well as how these elements work together, cooperate, and compete.

RNAcontacts: A Pipeline for Predicting Contacts from RNA Proximity Ligation Assays

High-throughput RNA proximity ligation assays are molecular methods that are used to simultaneously analyze the spatial proximity of many RNAs in living cells. Their principle is based on cross-linking, fragmentation, and subsequent religation of RNAs, followed by high-throughput sequencing. The generated fragments have two different types of splits, one resulting from pre-mRNA splicing and the other formed by the ligation of spatially close RNA strands. Here, we present RNAcontacts, a universal pipeline for detecting RNA-RNA contacts in high-throughput RNA proximity ligation assays. RNAcontacts circumvents the inherent problem of mapping sequences with two distinct types of splits using a two-pass alignment, in which splice junctions are inferred from a control RNA-seq experiment on the first pass and then provided to the aligner as bona fide introns on the second pass. Compared to previously developed methods, our approach allows for a more sensitive detection of RNA contacts and has a higher specificity with respect to splice junctions that are present in the biological sample. RNAcontacts automatically extracts contacts, clusters their ligation points, computes the read support, and generates tracks for visualizing through the UCSC Genome Browser. The pipeline is implemented in Snakemake, a reproducible and scalable workflow management system for rapid and uniform processing of multiple datasets. RNAcontacts is a generic pipeline for the detection of RNA contacts that can be used with any proximity ligation method as long as one of the interacting partners is RNA. RNAcontacts is available via the GitHub repository https://github.com/smargasyuk/ RNAcontacts/.

Tandem Exon Duplications Expanding the Alternative Splicing Repertoire

Tandem exon duplications play an important role in the evolution of eukaryotic genes, providing a generic mechanism for adaptive regulation of protein function. In recent studies, tandem exon duplications have been linked to mutually exclusive exon choice, a pattern of alternative splicing in which one and only one exon from a group of tandemly arranged exons is included in the mature transcript. Here, we revisit the problem of identifying tandem exon duplications in eukaryotic genomes using bioinformatic methods and show that tandemly duplicated exons are abundant not only in the coding parts, but also in the untranslated regions. We present a number of remarkable examples of tandem exon duplications, identify unannotated duplicated exons, and provide statistical support for their expression using large panels of RNA-seq experiments.

Neuronal metabolism governs cortical network response state

The level of arousal in mammals is correlated with metabolic state and specific patterns of cortical neuronal responsivity. In particular, rhythmic transitions between periods of high activity (up phases) and low activity (down phases) vary between wakefulness and deep sleep/anesthesia. Current opinion about changes in cortical response state between sleep and wakefulness is split between neuronal network-mediated mechanisms and neuronal metabolism-related mechanisms. Here, we demonstrate that slow oscillations in network state are a consequence of interactions between both mechanisms. Specifically, recurrent networks of excitatory neurons, whose membrane potential is partly governed by ATP-modulated potassium (K(ATP)) channels, mediate response-state oscillations via the interaction between excitatory network activity involving slow, kainate receptor-mediated events and the resulting activation of ATP-dependent homeostatic mechanisms. These findings suggest that K(ATP) channels function as an interface between neuronal metabolic state and network responsivity in mammalian cortex.