Isoform-level profiling of m⁶A epitranscriptomic signatures in human brain

Area of Science:

• Neuroscience
• Molecular Biology
• Genomics

Background:

• N6-methyladenosine (m⁶A) is a prevalent RNA modification in the human brain, linked to neurological disorders.
• Understanding m⁶A at the RNA isoform level is essential for deciphering brain function and disease mechanisms.
• A comprehensive atlas of brain m⁶A sites across isoforms is currently lacking.

Purpose of the Study:

• To create the first isoform-level atlas of m⁶A modification sites in the human brain.
• To investigate the brain region-specific patterns of m⁶A modifications.
• To explore the relationship between m⁶A modifications, RNA isoforms, and neuronal cell types.

Main Methods:

• Utilized Oxford Nanopore direct RNA sequencing (DRS) on postmortem human brain tissues.
• Analyzed samples from three distinct brain regions: prefrontal cortex, caudate nucleus, and cerebellum.
• Simultaneously profiled the transcriptome and epitranscriptome at the isoform level.

Main Results:

• Identified over 57,000 m⁶A sites within approximately 15,000 RNA isoforms.
• Revealed distinct isoform- and brain region-specific patterns of m⁶A modifications.
• The prefrontal cortex showed unique m⁶A profiles, enriched in excitatory neurons, with a high proportion of novel sites. A subset of hypermodified isoforms was consistently associated with excitatory neurons across all regions.

Conclusions:

• Direct RNA sequencing enables high-resolution profiling of RNA modifications at the isoform level.
• The study provides critical insights into the epitranscriptomic landscape of the human brain.
• Findings highlight the importance of m⁶A modifications in brain region specificity, with implications for neural development and disease pathogenesis.