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Related Experiment Video

Updated: Nov 1, 2025

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
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Comprehensive Detection of Pseudogenes Transcribed by Readthrough.

Rui Pinto1, Daniel Sobral1, Ana Rita Grosso2

  • 1UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal.

Methods in Molecular Biology (Clifton, N.J.)
|June 24, 2021
PubMed
Summary

Researchers developed a computational pipeline to detect pseudogene expression caused by transcription readthrough. This method identifies how readthrough events can impact gene regulation and biological functions, particularly in renal cancer.

Keywords:
BioinformaticsPseudogeneRNA chimeraRNA-seqTranscription readthroughTranscriptome

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Transcription termination is crucial for producing functional messenger RNA (mRNA) and proteins.
  • Transcription machinery can bypass termination signals, leading to transcription readthrough and expression of silenced pseudogenes.
  • Readthrough transcribed pseudogenes, due to sequence similarity with parental genes, can influence protein-coding genes and biological functions.

Purpose of the Study:

  • To develop a computational pipeline for detecting readthrough transcribed pseudogenes using expression profiles.
  • To investigate the role of pseudogene expression in biological functions and gene regulation.
  • To analyze readthrough events in renal cancer biopsies.

Main Methods:

  • Utilized existing bioinformatic tools to create a computational pipeline.
  • Integrated strand-specific transcriptome data and epigenetic profiles to enhance detection accuracy.
  • Applied the pipeline to analyze renal cancer patient data.

Main Results:

  • The pipeline successfully detected readthrough transcribed pseudogenes from expression profiles.
  • Combining transcriptome and epigenetic data improved the identification and corroboration of readthrough events.
  • Observed pseudogenes being transcribed as part of unspliced transcripts or processed RNA chimeras in renal cancer.

Conclusions:

  • The developed pipeline offers a robust method for scrutinizing transcriptome profiles to detect diverse readthrough events.
  • This approach facilitates the study of pseudogene expression and its potential impact on gene regulation and disease.
  • The findings highlight the significance of transcription readthrough in gene expression and cellular function.