Anything but Ordinary – Emerging Splicing Mechanisms in Eukaryotic Gene Regulation

Abstract

Splicing of precursor mRNAs (pre-mRNA) is an important step during eukaryotic gene expression. The identification of the actual splice sites and the proper removal of introns are essential for the production of the desired mRNA isoforms and their encoded proteins. While the basic mechanisms of splicing regulation are well understood, recent work has uncovered a growing number of noncanonical splicing mechanisms that play key roles in the regulation of gene expression. In this review, we summarize the current principles of splicing regulation, including the impact of cis and trans regulatory elements, as well as the influence of chromatin structure, transcription, and RNA modifications. We further discuss the recent development of emerging splicing mechanisms, such as recursive and back splicing, and their impact on gene expression. Significance of Splicing for Gene ExpressionThe genomes of all eukaryotes contain introns, but their number, size, and distribution vary considerably between different species [1]. In humans, for example, the average gene contains about eight introns, whereas genes in Drosophila melanogaster have fewer introns, which on average are also shorter (5.8 kb versus 1.5 kb) [1-3]. The correct identification and removal of introns by the splicing machinery is a central, conserved step during gene expression in all eukaryotes, and mutations that alter the sequence of splice sites or elicit splicing errors are often associated with disease [4,5]. Furthermore, the noncontinuous exon-intron structure of eukaryotic genes allows the formation of alternative mRNA isoforms. During this process the exons of a pre-mRNA are assembled in different ways; for example, by skipping one or several exons or using alternative splice sites [6]. Alternative splice variants of one gene may encode different protein isoforms, which in extreme cases can have opposite functions [7]. The occurrence of alternative splicing provides exciting new possibilities for gene regulation and is responsible for the remarkable transcriptome and proteome diversity in metazoans [8,9]. Of all human genes, only 5% consist of a single exon [10] and >90% are alternatively spliced [11][12][13]. Alternative splicing is regulated by interactions of RNA-binding proteins (RBPs; see Glossary) and splicing factors with sequences in the pre-mRNA, and by base-pairing between complementary RNA sequences in cis and in trans [6,14]. Since most splicing decisions occur concomitantly to transcription, the interaction of RBPs with pre-mRNAs can be impacted by chromatin structure, transcription factors as well as RNA modifications. In this review, we first summarize the general mechanisms of splicing regulation that integrate all these parameters, and in the second part, we discuss the emergence of new splicing mechanisms, also referred to as noncanonical splicing. General Principles of Splicing RegulationRegulation by the Spliceosome and Other RBPs Pre-mRNA splicing in eukaryotes is carried out by the spliceosome [15][16][17]. This large RNA-protein com...

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