Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain

Area of Science:

• Neuroscience
• Molecular Biology
• Genetics

Background:

• Fused in sarcoma (FUS) and TAR DNA-binding protein 43 (TDP-43) are RNA-binding proteins implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD).
• The precise overlap in RNA targets and regulatory functions between FUS and TDP-43 remains largely unknown.
• Understanding these shared or distinct roles is crucial for elucidating disease mechanisms.

Purpose of the Study:

• To investigate whether FUS and TDP-43 regulate the same RNA transcripts.
• To characterize the binding patterns and splicing roles of FUS in the mouse brain.
• To compare the RNA binding sites and exon regulation by FUS and TDP-43.

Main Methods:

• Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) was employed in mouse brain tissue.
• Analysis of FUS binding patterns on nascent RNA and pre-mRNAs.
• Comparative analysis of RNA binding sites and regulated exons between FUS and TDP-43.

Main Results:

• FUS binds nascent RNA along its entire length with a preference for GGU motifs and remains bound until splicing completion.
• FUS plays a role in alternative splicing, with increased binding observed in introns flanking repressed exons in FUS-deficient brains.
• No significant overlap was found in the RNA binding sites or regulated exons between FUS and TDP-43.
• Both FUS and TDP-43 were found to regulate genes involved in neuronal development.

Conclusions:

• FUS and TDP-43 exhibit distinct RNA binding preferences and regulate different sets of transcripts.
• FUS is actively involved in regulating alternative splicing of pre-mRNAs.
• Despite distinct targets, both proteins converge on regulating genes critical for neuronal development, suggesting a shared functional outcome in neurobiology.