Full-length transcript atlas of the developing human cortex

Abstract

Alternative splicing enables multiple RNA isoforms to be produced from a single mRNA precursor. Alternative splicing dramatically increases transcriptomic and proteomic diversity from the coding genome and is an important mechanism in the control of gene expression in the central nervous system. Long-read sequencing approaches can be used to generate full-length transcript sequences and fully characterise isoform diversity. We used Oxford Nanopore transcriptome sequencing to profile transcript diversity across human brain development and ageing. Sequencing libraries were prepared from high-quality RNA extracted from human cortex tissue dissected from foetal, neonatal, and adult donors (n=47 donors aged 6 weeks post-conception to 83 years old) and sequenced on PromethION Flow Cells. Sequencing data was processed using a novel analysis pipeline developed by our group for isoform visualisation and quantification. We compared both cDNA (whole and targeted) and direct RNA sequencing approaches and transcript annotations were integrated with cell-type-specific nanopore DNA methylation data generated on the same samples.

We identify widespread transcript diversity and usage in the developing cortex, including for genes associated with neuropsychiatric phenotypes such as autism and schizophrenia. We identify developmental changes and sex differences in alternative splicing, with differential transcript expression and usage between human foetal and adult cortex. We highlight many examples of alternative splicing colocalising with developmentally dynamic regions of differential DNA methylation. Our transcript and methylation annotations are available as a resource to the research community via browsable tracks and database.

Biography

Rosie works as a Postdoctoral Research Fellow in the Complex Disease Epigenetics Group at the University of Exeter. Her current research focusses on using long-read and single-cell sequencing technologies to advance genomics research into neurological development, disease, and disorders.