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

Area of Science:

• Genomics
• Molecular Biology
• Neuroscience

Background:

• Microexons (≤30 nucleotides) are conserved, regulated cassette exons.
• They play critical roles in nervous system development, function, behavior, and cognition.
• Standard RNA-seq aligners often miss microexons, hindering their study.

Purpose of the Study:

• To present MicroExonator, a novel pipeline for reproducible de novo discovery and quantification of microexons.
• To provide the most comprehensive survey of microexons in mice across development.
• To investigate the function and cell-type specificity of microexons.

Main Methods:

• Processed 289 RNA-seq datasets from 18 mouse tissues across 9 developmental stages.
• Utilized MicroExonator for de novo microexon discovery and quantification.
• Applied unsupervised clustering and single-cell RNA-seq analysis.

Main Results:

• Detected 2984 microexons, with 332 differentially spliced during embryonic brain development.
• Identified 29 novel microexons not in existing databases.
• Clustering revealed segregation of brain tissues by developmental time.
• Suggested microexon function in axon growth and synapse formation.
• Reported differential microexon inclusion between neuronal subpopulations in the visual cortex.

Conclusions:

• MicroExonator facilitates microexon investigation in large transcriptome datasets.
• The study discovered previously uncharacterized microexons.
• Provided a comprehensive microexon inclusion catalog during mouse development.