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Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells
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CRISPR/Cas9-induced gene conversion between ATAD3 paralogs.

Shira Yanovsky-Dagan1, Ayala Frumkin1, James R Lupski2,3,4

  • 1Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel.

HGG Advances
|February 24, 2022
PubMed
Summary

CRISPR gene editing unexpectedly caused gene conversion between ATAD3A and ATAD3B paralogs. This highlights the need for careful clone evaluation when targeting genes with similar paralogs, especially for potential gene therapies.

Keywords:
ATAD3ACRISPR/Cas9break-induced replication (BIR)double-strand break repair (DSBR)gene editinghalf crossoversparalogspseudogenes

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Area of Science:

  • Genomics and Molecular Biology
  • Gene Editing Technologies
  • Human Genetics

Background:

  • Paralogs and pseudogenes are common in the human genome and can lead to non-allelic homologous recombination (NAHR) and gene conversion.
  • The ATAD3 locus, with its tandem paralogs, is susceptible to NAHR-mediated deletions and duplications, often linked to neurological disorders.

Purpose of the Study:

  • To generate biallelic loss-of-function variants in the ATAD3A gene using CRISPR/Cas9 genome editing.
  • To investigate the complex recombination repair mechanisms at the ATAD3 locus.

Main Methods:

  • CRISPR/Cas9 genome editing was employed to target the ATAD3A gene.
  • Analysis of generated clones to identify and characterize genetic alterations.

Main Results:

  • Unexpectedly, two clones exhibited gene conversion, where the targeted ATAD3A sequence was replaced by a sequence from its paralog, ATAD3B.
  • This demonstrates the potential for unintended sequence replacement when targeting genes with highly similar paralogs.

Conclusions:

  • CRISPR/Cas9 targeting of genes with paralogs requires meticulous evaluation of resultant clones due to complex recombination events like gene conversion.
  • Endogenous gene conversion may offer a therapeutic strategy for repairing missense variants in genes possessing paralogs or pseudogenes.