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Control of gene output by intron RNA structure.

Leonard Schärfen1,2, Pernille Bech1, Paulina Podszywałow-Bartnicka1

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Intron RNA structure significantly impacts gene expression by modulating pre-mRNA splicing. Modifying intron base pairing can improve splicing efficiency and fine-tune gene output.

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MPRARNA StructureSplicingStructure Prediction

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Pre-mRNA splicing removes introns, a crucial step in eukaryotic gene expression.
  • Intronic mutations can cause genetic diseases, but the role of intron sequence beyond splice sites is unclear.
  • RNA structure within introns may influence splicing efficiency and gene output.

Purpose of the Study:

  • To systematically investigate how intron RNA structure formation modulates gene output.
  • To determine the impact of base pairing at every position across a natural intron on splicing.
  • To explore the potential for designing intron alterations to improve splicing efficiency.

Main Methods:

  • Generation of intron variant libraries to test base pairing impacts.
  • Massively parallel reporter assay (MPRA) to measure splicing modulation.
  • Thermodynamic structure prediction and machine learning models to explain gene output.

Main Results:

  • Base pairing involving splice sites significantly modulates splicing across orders of magnitude.
  • An upstream intron region's sensitivity to structure suggests steric hindrance.
  • Machine learning models accurately predict gene output based on RNA structure.
  • Designed intron sequence alterations improved inefficient splicing of human β-globin IVS1.

Conclusions:

  • Intron RNA structure is a critical regulator of gene expression.
  • Modulating intron base pairing offers a strategy to fine-tune gene output and correct splicing defects.
  • Intronic mutations altering RNA structure are rapidly selected during evolution.