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Related Concept Videos

Nucleotide Excision Repair01:08

Nucleotide Excision Repair

Overview
Overview of DNA Repair02:25

Overview of DNA Repair

In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
Chemically...
Nucleotide Excision Repair01:08

Nucleotide Excision Repair

Overview
Overview of DNA Repair02:25

Overview of DNA Repair

In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
Chemically...
Nucleotide Excision Repair01:38

Nucleotide Excision Repair

DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...

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A mutational scar-based genome-wide map of DNA double-strand break repair.

Nature communications·2026
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TONSL suppresses polymerase theta-dependent tandem duplications through chromatin-guided repair.

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MUSICiAn: genome-wide identification of genes involved in DNA repair via control-free mutational spectra analysis.

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Related Experiment Video

Updated: May 11, 2026

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI
13:06

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI

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MUSICiAn: Genome-wide Identification of Genes Involved in DNA Repair via Control-Free Mutational Spectra Analysis.

Colm Seale1,2, Marco Barazas3, Robin van Schendel3

  • 1Pattern Recognition & Bioinformatics, Department of Intelligent Systems, EEMCS Faculty, Delft University of Technology, Delft, The Netherlands.

Biorxiv : the Preprint Server for Biology
|February 20, 2025
PubMed
Summary

MUSICiAn identifies novel DNA double-strand break (DSB) repair factors by analyzing mutational signatures without traditional controls. This method highlights the spliceosome

Keywords:
DNA damage responseDNA repaircompositional data analysiscontrol-freemutational spectraoutlier detection

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding DNA double-strand break (DSB) repair is critical for developing targeted anti-cancer therapies.
  • The roles of many genes in DSB repair remain unclear, hindering therapeutic development.
  • Perturbations in specific genes can alter mutation patterns after DSB repair, suggesting screening approaches.

Purpose of the Study:

  • To develop a method for genome-wide screening of DSB repair factors.
  • To identify novel genes involved in DSB repair by analyzing mutational spectra.
  • To overcome challenges in designing controls for genome-wide perturbation screens.

Main Methods:

  • Developed MUSICiAn (Mutational Signature Catalogue Analysis), a compositional data analysis method.
  • MUSICiAn ranks gene perturbation-specific mutational spectra by measuring deviations from central tendencies.
  • The method analyzes mutational outcomes from CRISPR-Cas9 induced DSBs across a genome-wide dataset.

Main Results:

  • MUSICiAn effectively estimated pseudo-controls for existing datasets, screening 476 genes.
  • Applied to a genome-wide dataset of 18,406 gene perturbations, MUSICiAn recovered known DSB repair genes.
  • The spliceosome was highlighted as a significant, previously underappreciated player in DSB repair.

Conclusions:

  • MUSICiAn provides a robust framework for identifying DSB repair factors without traditional controls.
  • The method successfully identified novel candidates for further investigation in DSB repair pathways.
  • This approach advances the understanding of DNA repair mechanisms relevant to cancer therapy.