Journal Article

Recursive splicing in long vertebrate genes

Sibley, Christopher R., Ryten, Mina, Blazquez, Lorea, Trabzuni, Daniah, Briese, Michael, Plagnol, Vincent, Hardy, John, Ule, Jernej, Emmett, Warren, Wilson, Stephen W., Curk, Tomaž, Weale, Michael E., Modic, Miha, Faro, Ana, Haberman, Nejc

2015

Overview

Highly conserved recursive splice sites are identified in vertebrates, particularly within long genes encoding proteins that are involved in neuronal development; analysis of the splicing mechanism reveals that such recursive splicing sites can be used to dictate different mRNA isoforms. Recursive splicing in insects and vertebrates The mechanisms by which the very longest genes in eukaryotic genomes are accurately processed are poorly understood. It was thought that intron removal generally involved a single excisive step. Later studies showed that, in flies, some introns contain internal splice sites that cause 'recursive splicing', in which single introns are removed 'bit-by-bit' in several sequential splicing reactions. Brenton Graveley and coworkers demonstrate that the scope of this regulatory mechanism is much more extensive in flies than had been appreciated. They identify nearly 200 zero-nucleotide exons in Drosophila that are the products of recursive splicing. Jernej Ule and colleagues identify recursive splicing sites in vertebrates, particularly within long genes encoding proteins that are involved in neuronal development. Analysis of the mechanism of their splicing reveals that such splicing sites can be used to dictate different mRNA isoforms. It is generally believed that splicing removes introns as single units from precursor messenger RNA transcripts. However, some long Drosophila melanogaster introns contain a cryptic site, known as a recursive splice site (RS-site), that enables a multi-step process of intron removal termed recursive splicing 1 , 2 . The extent to which recursive splicing occurs in other species and its mechanistic basis have not been examined. Here we identify highly conserved RS-sites in genes expressed in the mammalian brain that encode proteins functioning in neuronal development. Moreover, the RS-sites are found in some of the longest introns across vertebrates. We find that vertebrate recursive splicing requires initial definition of an ‘RS-exon’ that follows the RS-site. The RS-exon is then excluded from the dominant mRNA isoform owing to competition with a reconstituted 5′ splice site formed at the RS-site after the first splicing step. Conversely, the RS-exon is included when preceded by cryptic promoters or exons that fail to reconstitute an efficient 5′ splice site. Most RS-exons contain a premature stop codon such that their inclusion can decrease mRNA stability. Thus, by establishing a binary splicing switch, RS-sites demarcate different mRNA isoforms emerging from long genes by coupling cryptic elements with inclusion of RS-exons.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 13/105 / 38/39 / 38/77 / 38/88 / 38/91 / 631/114/2184 / 631/337/1645/1769 / 631/337/1645/1792 / 631/378/340 / Animals / Ankyrins - genetics / Base Sequence / Brain / Brain - cytology / Brain - metabolism / Cell adhesion & migration / Cell Adhesion Molecule-1 / Cell Adhesion Molecules - genetics / Codon, Terminator - genetics / Drosophila melanogaster - genetics / Exons - genetics / Female / Frontal Lobe - cytology / Frontal Lobe - metabolism / Genes / Genetic aspects / Humanities and Social Sciences / Humans / Immunoglobulins - genetics / Introns - genetics / letter / Male / Methods / multidisciplinary / Mutation / Nervous system / Promoter Regions, Genetic - genetics / Regression analysis / RNA Isoforms - genetics / RNA Isoforms - metabolism / RNA Splice Sites - genetics / RNA splicing / RNA Splicing - genetics / RNA Stability - genetics / Science / Vertebrates / Vertebrates - genetics / Zebrafish - embryology / Zebrafish - genetics / Zebrafish Proteins - genetics