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Star-PAP RNA Binding Landscape Reveals Novel Role of Star-PAP in mRNA Metabolism That Requires RBM10-RNA Association

Ganesh R Koshre1,2, Feba Shaji1,3, Neeraja K Mohanan1,2

  • 1Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India.

International Journal of Molecular Sciences
|September 28, 2021
PubMed

Insights

Star-PAP (a poly(A) polymerase) binds mRNAs genome-wide, impacting their stability. Its coregulator RBM10 is crucial for Star-PAP

Area of Science:

  • Molecular Biology
  • RNA Metabolism
  • Gene Regulation

Background:

  • Star-PAP is a non-canonical poly(A) polymerase with poorly understood mRNA target specificity.
  • The genome-wide binding landscape and precise mechanism of Star-PAP mRNA recognition remain unclear.

Purpose of the Study:

  • To map the cellular Star-PAP binding landscape using HITS-CLIP.
  • To elucidate the mechanism of global Star-PAP mRNA association and its role in mRNA metabolism.
  • To investigate the role of the coregulator RBM10 in Star-PAP-mediated mRNA regulation.

Main Methods:

  • High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) to map Star-PAP binding sites.
  • Star-PAP depletion experiments to assess transcriptome-wide association.
  • Knockdown of RBM10 to evaluate its effect on Star-PAP association and mRNA processing.
  • Analysis of mRNA stability and processing in response to Star-PAP and RBM10 modulation.

Main Results:

  • Star-PAP associates with mRNAs across the transcriptome, with binding diminished upon Star-PAP depletion.
  • Star-PAP predominantly binds to 3'-UTRs but also enriches in coding region exons (CDS) of 42% of target mRNAs, destabilizing them.
  • Star-PAP depletion leads to downregulation of UTR-associated transcripts and upregulation of CDS-associated mRNAs.
  • RBM10 knockdown globally reduces Star-PAP association with target mRNAs, affecting 3'-end processing and mRNA stability/turnover.

Conclusions:

  • This study establishes a global profile of Star-PAP mRNA association.
  • Star-PAP plays a novel role in mRNA metabolism, influencing both processing and stability, with distinct effects depending on binding location (UTR vs. CDS).
  • RBM10 is essential for Star-PAP's global mRNA association and its regulatory functions, highlighting a critical RBM10-mRNA interaction pathway.
Keywords:
3′-end processingHITS-CLIPRBM10RNA-turnoverStar-PAPmRNA metabolismpolyadenylation

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