London Calling 2023: Integrating the transcriptome and epitranscriptome of the human brain using direct RNA sequencing

The human brain is subject to complex regulation of gene expression, with high levels of splicing and RNA modification N6-methyladenosine (m6A). Investigating how these different biological mechanisms interact and contribute to the brain's function is critical for our understanding of brain development and disease. Long-read direct RNA sequencing (DRS) from Oxford Nanopore Technologies allows for simultaneous investigation of the human brain transcriptome and epitranscriptome. Here, we applied DRS to three brain regions and identified thousands of differentially expressed isoforms and 1,658 isoforms with differential m6A modification levels between brain regions. Highly methylated isoforms were associated with synaptic function, whereas lowly modified isoforms were associated with DNA binding. We also found a subpopulation of highly methylated long non-coding RNAs. Our results reveal new insights into brain region specificity and functioning, providing new avenues for further investigation into neurological development and disease.