Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing.

Szi Kay Leung,Zeshan Ahmed,Michael J Gandal,Shyam Prabhakar,Leonard Schalkwyk,Paul O’Neill,Connor Jops,Isabel Castanho,Elizabeth Tseng,Jonathan Mill,David A Collier,Karen Moore,Aaron R Jeffries,Emma Dempster ,Eilís Hannon ,Jonathan Davies ,Nicholas John Bray ,B Jordan ,Erin Jeffery ,Gloria Sheynkman

doi:10.1016/j.celrep.2021.110022

Abstract

SummaryAlternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community.

Highlights

Alternative splicing (AS) is a post-transcriptional regulatory mechanism producing multiple RNA isoforms from a single mRNA precursor
All downstream analyses and statistics reported in our manuscript are based on the subset of SQANTI2-filtered transcripts unless otherwise indicated, the extended datasets are available as genome browser tracks as a resource
We identified 32,802 unique transcripts in the human cortex (Table 1); as expected, these were enriched near Cap Analysis Gene Expression (CAGE) peaks from the FANTOM5 dataset (Lizio et al, 2019) (Figure 1B) and were located proximally to annotated transcription start sites and transcription termination sites (Figures S4B and S4C)

Summary

Introduction

Alternative splicing (AS) is a post-transcriptional regulatory mechanism producing multiple RNA isoforms from a single mRNA precursor. The mechanisms involved in AS include the use of alternative first (AF) and last (AL) exons, exon skipping (SE), alternative 50 (A50) and A30 splice sites, mutually exclusive exons (MX), and intron retention (IR) (Wang et al, 2008). These phenomena are common, influencing the transcription of >95% of human genes (Pan et al, 2009). Because alternatively spliced transcripts from a single gene can produce proteins with different functions (Eksi et al, 2013; Yang et al, 2016), there is increasing interest in their role in human disease (Wang and Cooper, 2007).

Methods

Results

Discussion

Conclusion