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Human introns contain conserved tissue-specific cryptic poison exons.

Sergey Margasyuk1, Antonina Kuznetsova1, Lev Zavileyskiy1

  • 1Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, 121205, Moscow, Russia.

NAR Genomics and Bioinformatics
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Summary

Human introns contain hidden cryptic exons that can be expressed, especially in rare conditions or cancer. These cryptic poison exons are often missed in standard RNA sequencing, highlighting gaps in current gene annotation.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Gene Expression

Background:

  • Alternative splicing generates numerous transcripts from single genes, but exon catalogs are incomplete.
  • Human introns harbor conserved elements with unknown functions, potentially including regulatory or coding sequences.
  • Cryptic exons, expressed under specific conditions, may contribute to transcriptomic diversity.

Purpose of the Study:

  • To investigate whether conserved intronic elements in human protein-coding genes represent cryptic exons.
  • To determine the functional impact and expression patterns of identified cryptic exons.
  • To validate the expression of cryptic exons using experimental methods.

Main Methods:

  • Analysis of RNA-seq data from the Genotype-Tissue Expression (GTEx) dataset to identify potential cryptic exons.
  • Comparison of cryptic exon characteristics (evolutionary conservation, read coverage) with annotated exons.
  • RNA sequencing of A549 cells treated with cycloheximide to inhibit nonsense-mediated decay (NMD).
  • Quantitative polymerase chain reaction (qPCR) to confirm the expression of selected cryptic exons.

Main Results:

  • A set of cryptic exons was identified in human introns, exhibiting characteristics similar to annotated exons.
  • Many identified cryptic exons function as poison exons, leading to NMD isoforms upon inclusion.
  • Evidence suggests tissue-specific and cancer-specific expression and regulation of these cryptic exons.
  • Experimental validation confirmed the expression of seven out of eight tested cryptic exons, particularly after NMD inhibition.

Conclusions:

  • Human protein-coding gene introns contain cryptic poison exons within conserved regions.
  • These cryptic exons are often unannotated due to limited representation in standard RNA-seq libraries.
  • Their expression in specific conditions and potential role in NMD highlight their significance in gene regulation and disease.