Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell...

Area of Science:

• Neuroscience
• Genomics
• Molecular Biology

Background:

• Alternative splicing (AS) generates diverse gene isoforms crucial for distinct neuron types.
• Existing research on RNA-binding proteins (RBPs) and AS is limited to a few neuron types, necessitating comprehensive modeling.

Purpose of the Study:

• To create a holistic map of the neuron type-specific AS regulatory landscape.
• To identify RBPs and splicing modules that define neuronal identity and diversity.

Main Methods:

• Network reverse engineering applied to single-cell transcriptomes from 133 mouse neocortical cell types.
• Inferred regulons of 350 RBPs and their cell type-specific activities.
• In vitro validation of RBP function using an ESC differentiation system.

Main Results:

• Successfully mapped the AS regulatory landscape and inferred 350 RBP regulons with cell type-specific activities.
• Identified Elavl2 as a key RBP regulating MGE-specific splicing in GABAergic interneurons.
• Discovered exon and regulator modules specific to long- and short-projection neurons across various neuronal classes.

Conclusions:

• The study provides a valuable resource for understanding splicing regulatory programs that drive neuronal molecular diversity.
• Neuronal identity is shaped by AS regulatory programs, some of which are independent of gene expression classifications.
• This work advances the understanding of how alternative splicing contributes to the complexity of the nervous system.