Evaluating splicing factor and kinase network crosstalk through global phosphoproteomics.

Area of Science:

• Molecular Biology
• Cell Signaling
• Genomics

Background:

• Splicing and kinase signaling are fundamental cellular processes.
• Existing research suggests potential interactions between splicing factors and kinase pathways.
• The precise impact of altered splicing factor expression on kinase signaling networks remains largely uncharacterized.

Purpose of the Study:

• To investigate the extent to which altering splicing factor expression impacts kinase signaling networks.
• To identify splice factor perturbations that lead to significant alterations in phosphorylation-encoding proteins.
• To elucidate the interplay between splicing and kinase signaling.

Main Methods:

• Utilized ENCODE RNA-sequencing data for a data-driven analysis.
• Integrated data on post-translational modifications with splice events.
• Performed knockdown experiments for U2AF1 and SRSF3, followed by global phosphoproteomics and transcriptomic analysis.

Main Results:

• Knockdown of U2AF1 and SRSF3 caused extensive changes in phosphorylation and kinase activities.
• U2AF1 knockdown affected JNK signaling and chromosome regulation, while SRSF3 knockdown impacted cell cycle and cytoskeletal signaling.
• Phosphorylated splicing regulators were enriched, suggesting feedback loops between splicing and signaling pathways.
• Phosphoproteomic data revealed significant protein regulation not evident from transcriptomic data alone.

Conclusions:

• Splicing factor perturbations profoundly alter kinase signaling networks.
• There is a deep interconnection between splicing and kinase signaling, impacting cell physiology.
• Phosphoproteomic profiling is essential for a comprehensive understanding of splice factor perturbations.