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Intrinsic Disorder in Human RNA-Binding Proteins.

Bi Zhao1, Akila Katuwawala1, Christopher J Oldfield2

  • 1Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA.

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|September 6, 2021
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Summary

RNA-binding proteins (RBPs) show varied intrinsic disorder levels depending on the RNA type they bind. Disorder is enriched in non-RNA-binding regions, suggesting roles beyond direct RNA interaction.

Keywords:
PTMdisordered proteinsintrinsic disorderprotein-DNA interactionsprotein-RNA interactions

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • RNA-binding proteins (RBPs) are crucial for gene regulation and are known to contain intrinsically disordered regions.
  • Previous studies indicated a general enrichment of disorder in RBPs compared to the human proteome.
  • No prior research comprehensively analyzed disorder distribution across RBPs binding to specific RNA types.

Purpose of the Study:

  • To investigate the prevalence and distribution of intrinsic disorder in RBPs that bind to six distinct RNA types: mRNA, tRNA, snRNA, ncRNA, rRNA, and irRNA.
  • To differentiate the disorder content between RNA-binding domains (RBDs) and non-RNA-binding-domain (non-RBD) regions within these proteins.
  • To explore the functional implications of intrinsic disorder in RBPs, particularly in non-RBD regions.

Main Methods:

  • Computational analysis of intrinsic disorder predictions for RBPs across different RNA-binding specificities.
  • Comparison of disorder levels in RBPs with the general human proteome.
  • Validation of disorder predictions using experimental data from DisProt and domain information from Pfam.

Main Results:

  • RBPs exhibit significantly higher intrinsic disorder than the human proteome overall.
  • Disorder enrichment varies by RNA type: significant in mRNA-, rRNA-, and snRNA-binding proteins; not enriched in ncRNA- and irRNA-binding proteins; depleted in tRNA-binding proteins.
  • Non-RBD regions show significant disorder enrichment, while RBDs have low disorder levels, indicating disorder is rarely used for direct RNA binding.
  • Disordered non-RBD regions may harbor post-translational modification sites and interact with DNA.

Conclusions:

  • The distribution of intrinsic disorder in RBPs is highly dependent on the specific type of RNA they interact with.
  • Intrinsic disorder in RBPs primarily resides in non-RNA-binding regions, suggesting roles in protein-protein interactions, signaling, and regulation.
  • Disorder in non-RBD regions may facilitate crucial cellular functions, including post-translational modifications and DNA interactions, expanding the functional repertoire of RBPs.