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Beyond RNA-binding domains: determinants of protein-RNA binding.

Inbal Zigdon1, Miri Carmi1, Sagie Brodsky1

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Intrinsically disordered regions (IDRs) in RNA-binding proteins (RBPs) are crucial for RNA binding, often more so than predicted RNA-binding domains (RBDs). This study reveals complex RBP-RNA interactions in vivo.

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RNA binding domains (RBDs)RNA binding proteins (RBPs)S. cerevisiaeintrinsically disordered regions (IDRs)mRNA binding proteins (mRBPs)

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • RNA-binding proteins (RBPs) utilize RNA-binding domains (RBDs) and intrinsically disordered regions (IDRs) for RNA interaction.
  • The in vivo contribution of IDRs versus RBDs to RBP-RNA binding patterns remains incompletely understood.
  • Previous studies highlighted potential roles for disordered linkers and repeats in RNA binding.

Purpose of the Study:

  • To investigate the in vivo transcriptome-wide binding patterns of multiple RBPs in budding yeast.
  • To elucidate the specific roles of predicted RBDs and IDRs in mediating RBP-RNA interactions.
  • To differentiate the contributions of RBDs and IDRs to RNA binding affinity and specificity.

Main Methods:

  • Upscaled RNA-tagging techniques to map transcriptome-wide RBP binding sites.
  • Performed extensive sequence mutagenesis on selected RBPs to identify binding determinants.
  • Analyzed binding patterns in vivo to assess the functional significance of RBDs and IDRs.

Main Results:

  • The majority of tested predicted RBDs were not essential for mRNA binding individually.
  • Several IDRs, lacking predicted RNA-binding potential, were found to be critical for binding affinity and specificity.
  • Mapping revealed transcriptome-wide binding for 16 RBPs, with functional dissection in eight.

Conclusions:

  • In vivo RBP-RNA interactions are complex and encoded in a distributed manner.
  • IDRs play a significant, often underestimated, role in determining RBP binding affinity and specificity.
  • Findings offer new insights into the functional mechanisms of less-studied RBPs.