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Exonic splicing code and protein binding sites for calcium.

Reuben J Pengelly1, Dara Bakhtiar1, Ivana Borovská2

  • 1University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK.

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|April 27, 2022
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Summary
This summary is machine-generated.

Exonic sequences binding calcium ions (Ca2+) show higher exon inclusion levels, influencing RNA splicing and evolution. This suggests Ca2+ coordination sites are retained in mature transcripts, aiding exon expansion.

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genetics

Background:

  • Exonic splicing enhancers (ESEs) and silencers (ESSs) are crucial for RNA splicing, influenced by protein binding.
  • Previous studies linked ESE/ESS evolution to metal binding, specifically the Irving-Williams (I-W) series.
  • The role of specific metal ions, like Ca2+, in shaping splicing codes is not well understood.

Purpose of the Study:

  • To investigate the splicing activities of exonic sequences encoding Ca2+-binding sites.
  • To determine if Ca2+ coordination residues influence exon inclusion levels.
  • To explore the evolutionary implications of Ca2+-binding sites in RNA splicing.

Main Methods:

  • Analysis of predicted exon inclusion levels for EF-hand motifs and other Ca2+-binding residues.
  • Comparison of splicing patterns between canonical and noncanonical EF-hands.
  • Utilizing splicing assays and crosslinking/immunoprecipitation data.
  • Identification of trans-acting factors binding to specific motifs.

Main Results:

  • Exonic sequences with Ca2+-binding sites, particularly EF-hand motifs, exhibit higher predicted exon inclusion levels.
  • A specific hierarchy (1>12>3∼5>9) was observed for Ca2+-coordinating residues in canonical EF-hands.
  • Exon splits were preferentially located in the N-terminal halves and around codon 12 of EF-hand loops.
  • Candidate trans-acting factors binding GA-rich motifs encoding negatively charged amino acids were identified.

Conclusions:

  • Codons for Ca2+-coordinating residues have a high capacity for retention in mature transcripts.
  • This retention facilitates exon-level expansion during eukaryotic evolution.
  • Ca2+ binding sites play a significant role in the evolution of RNA splicing codes.