RNA-Seq reveals the landscape of human mutually exclusive splicing

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, researchers at the Max-Planck-Institute for Biophysical Chemistry predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA-Seq datasets. Here, they 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.

 The human genome contains 1,399 high‐confidence MXEs

A. Schematic representation of the various annotated and predicted exon types included in the MXE candidate list. For MXE validation, at least three restraints must be fulfilled: the absence of an MXE‐joining read (R1), except for those leading to frame shift, and the presence of two MXE‐bridging SJ reads (R2 and R3).

B. Prediction and validation of 1,399 1SJ (855 3SJ) human MXEs. Top: Dataset of 6,541 MXE candidates from annotated and predicted exons. Bottom left: MXE candidates for which splice junction data are currently missing hindering their annotation as MXE or other splice variant. Bottom right: Validation of the MXE candidates using over 15 billion RNA‐Seq reads.

C. MXE saturation analysis.

D. Distribution of validated MXEs in two‐exon and multi‐exon clusters.

E. Size and distribution of multi‐cluster MXEs.

F. The CUX1 gene (cut‐like homeobox 1) contains two interleaved clusters of MXEs (clusters 1 and 2) and two standard clusters each with two MXEs (clusters 3 and 4).