An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

Abstract

Alternative splicing (AS) generates remarkable regulatory and proteomic complexity in metazoans. However, the functions of most AS events are not known, and programs of regulated splicing remain to be identified. To address these challenges, we describe the Vertebrate Alternative Splicing and Transcription Database (VastDB), the largest resource of genome-wide, quantitative profiles of AS events assembled to date. VastDB provides readily accessible quantitative information on the inclusion levels and functional associations of AS events detected in RNA-seq data from diverse vertebrate cell and tissue types, as well as developmental stages. The VastDB profiles reveal extensive new intergenic and intragenic regulatory relationships among different classes of AS and previously unknown and conserved landscapes of tissue-regulated exons. Contrary to recent reports concluding that nearly all human genes express a single major isoform, VastDB provides evidence that at least 48% of multiexonic protein-coding genes express multiple splice variants that are highly regulated in a cell/tissue-specific manner, and that >18% of genes simultaneously express multiple major isoforms across diverse cell and tissue types. Isoforms encoded by the latter set of genes are generally coexpressed in the same cells and are often engaged by translating ribosomes. Moreover, they are encoded by genes that are significantly enriched in functions associated with transcriptional control, implying they may have an important and wide-ranging role in controlling cellular activities. VastDB thus provides an unprecedented resource for investigations of AS function and regulation.

A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes

“…AS analysis of RNA-Seq data was performed with vasttools version 1 (Tapial et al, 2017). RNA was purified using RNeasy kit from three independent differentiation experiments.…”

“…Reads were mapped to the mouse (mm9) genome. AS analysis of RNA-Seq data was performed with vasttools version 1 (Tapial et al, 2017). From the primary output, events with poor coverage or junction balance were filtered out (vast-tools quality score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC], and alternative 5 0 or 3 0 splice site [Alt5/3] events or coverage < 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events and score 5 of < 0.05 for IR events).…”

Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain

“…Splicing varies extensively across human development and aging 7 , and between tissues. The brain exhibits one of the highest levels of splicing diversity and prominent use of tissue specific exons, microexons and splicing factors [14][15][16][17][18] .…”

MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development

“…Another strategy for increasing the sensitivity of microexon discovery is to directly map RNA-seq reads to libraries of annotated splice junctions (Irimia et al, 2014;Li et al, 2015) , but the bioinformatic pipelines used in these seminal studies have not been released to the public domain. Today, VAST-TOOLS is the most widely used tool for microexon quantification from RNA-seq data (Tapial et al, 2017) . However, a significant restriction of VAST-TOOLS is that it can only identify microexons that are annotated in VastDB (Tapial et al, 2017) , which is only available for a limited number of species.…”