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Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome.

Robin-Lee Troskie1, Yohaann Jafrani1, Tim R Mercer2

  • 1Mater Research Institute-University of Queensland, TRI Building, QLD, 4102, Woolloongabba, Australia.

Genome Biology
|May 11, 2021
PubMed
Summary
This summary is machine-generated.

Pseudogenes, once thought functionless, are actively transcribed and can even code for proteins. Deleting a single pseudogene impacts hundreds of other genes, revealing their complex role in human biology.

Keywords:
CRISPRLong-readPacBioPseudogenelncRNA

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Pseudogenes are typically considered non-functional evolutionary remnants of genes.
  • Their potential roles in cellular processes are largely unexplored.
  • Previous studies often overlooked their transcriptional activity and functional relevance.

Purpose of the Study:

  • To identify and characterize novel transcribed pseudogenes in human tissues and cancer cell lines.
  • To investigate the protein-coding potential of pseudogene transcripts.
  • To assess the biological impact of noncoding pseudogenes on gene regulation.

Main Methods:

  • Deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines.
  • Identification and analysis of novel transcribed pseudogenes.
  • CRISPR-Cas9 gene editing to delete a specific pseudogene (PDCL3P4).
  • Analysis of gene expression changes post-pseudogene deletion.

Main Results:

  • Hundreds of novel transcribed pseudogenes were identified with tissue-specific expression patterns.
  • Some pseudogene transcripts possess intact open reading frames and are translated, representing unannotated protein-coding genes.
  • CRISPR-Cas9 deletion of the pseudogene PDCL3P4 resulted in perturbation of hundreds of genes.
  • This indicates a significant biological impact of noncoding pseudogenes.

Conclusions:

  • Pseudogenes represent a dynamic and complex component of the human transcriptional landscape.
  • Contrary to previous assumptions, pseudogenes can be transcribed, translated, and functionally relevant.
  • Further research into pseudogene functions is crucial for a comprehensive understanding of genome biology and disease.