The landscape of human mutually exclusive splicing.

Klas Hatje,Ashish Rajput,Björn Hammesfahr,Ramon O Vidal,Martin Kollmar,Raza‐Ur Rahman,Vikas Bansal,Ting Sun,Stefan Bonn,Dominic Simm,Michel Edwar Mickael

doi:10.15252/msb.20177728

Abstract

Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA‐Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi‐cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio‐temporal expression might predict human disease pathology.

Highlights

Alternative splicing of pre-messenger RNAs is a mechanism common to almost all eukaryotes to generate a plethora of protein variants out of a limited number of genes (Matlin et al, 2005; Nilsen & Graveley, 2010; Lee & Rio, 2015)
The human genome contains 855 high-confidence mutually exclusive exons (MXEs) Compared to other splicing mechanisms, mutually exclusive splicing in humans seems to be a rare event
Our analysis showed that 29 of the 158 annotated MXEs are not mutually exclusively spliced but represent constitutively spliced exons or other types of alternative splicing (Supplementary Fig. S2)

Summary

Introduction

Alternative splicing of pre-messenger RNAs is a mechanism common to almost all eukaryotes to generate a plethora of protein variants out of a limited number of genes (Matlin et al, 2005; Nilsen & Graveley, 2010; Lee & Rio, 2015). Vertebrate MXEs have been reported to only occur in pairs (Matlin et al, 2005; Gerstein et al, 2014; Abascal et al, 2015a), and genome-wide estimates in human range from 118 (Suyama, 2013) to at most 167 cases (Wang et al, 2008) Despite these relatively few reported cases, mutually exclusive splicing might be far more frequent in humans than currently anticipated, as has been recently revealed in the model organism D.melanogaster (Hatje & Kollmar, 2013). Mutations in MXEs have been shown to cause diseases such as Timothy syndrome (missense mutation in the CACNA1C gene) (Splawski et al, 2004, 2005),, cardiomyopathy (defect of the mitochondrial phosphate carrier SLC25A3) (Mayr et al, 2011) or cancer (mutations in e.g. the pyruvate kinase PKM and the zinc transporter SLC39A14) (David et al, 2010)

Methods

Results

Conclusion