iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function

Area of Science:

• Molecular Biology
• Neuroscience
• Genetics

Background:

• Scaffold attachment factor B1 (SAFB1) is an RNA-binding protein involved in transcription, DNA repair, and RNA processing.
• Understanding SAFB1's genome-wide RNA interactions is crucial for elucidating its cellular functions.

Purpose of the Study:

• To map SAFB1's RNA interactions genome-wide using iCLIP.
• To investigate SAFB1's role in gene expression regulation, alternative splicing, and neuronal function.

Main Methods:

• Individual-nucleotide-resolution crosslinking and immunoprecipitation (iCLIP) to map SAFB1-RNA interactions.
• RT-PCR and exon array analysis to assess gene expression and splicing changes upon SAFB1 knockdown.
• Minigene assays to confirm SAFB1's role in alternative splicing.

Main Results:

• SAFB1 preferentially binds exons, ncRNAs, and UTRs, recognizing a purine-rich GAAGA motif.
• SAFB1 knockdown altered the expression of coding and non-coding genes, including NCAM1 and ASTN2.
• SAFB1 regulates alternative splicing, particularly of downregulated exons correlated with its binding motif, and impacts dendritic spine density in neurons.

Conclusions:

• SAFB1 possesses uncharacterized RNA-binding properties that regulate isoform-specific gene expression.
• SAFB1 is a key regulator of neuronal processes, including splicing and synaptic function, with implications for neuropsychiatric diseases.