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Generating CRISPR/Cas9 Mediated Monoallelic Deletions to Study Enhancer Function in Mouse Embryonic Stem Cells
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Sequence-based characterization of structural variation in the mouse genome.

Binnaz Yalcin1, Kim Wong, Avigail Agam

  • 1The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.

Nature
|September 17, 2011
PubMed
Summary
This summary is machine-generated.

Structural variants (SVs) are common in mouse genomes, with retrotransposon insertions being a major cause. Despite their abundance, SVs infrequently impact gene expression or phenotype, though some disrupt gene function, particularly in immunology.

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Area of Science:

  • Genomics
  • Mammalian Genetics
  • Molecular Biology

Background:

  • Structural variations (SVs) are prevalent in mammalian genomes and implicated in disease.
  • The abundance, origins, and functional impact of SVs on phenotypic variation are not fully understood.

Purpose of the Study:

  • To comprehensively identify and characterize structural variants in inbred mouse strains.
  • To investigate the causes and functional consequences of structural variants.

Main Methods:

  • Combined experimental and automated analyses to identify SVs across thirteen classical and four wild-derived inbred mouse strains.
  • Mapped SV breakpoints to base pair resolution.
  • Analyzed the impact of SVs on gene expression and phenotypic variation.

Main Results:

  • Identified 711,920 SVs at 281,243 sites in mouse genomes.
  • The majority of SVs are small (<1 kb), with 98% being deletions or insertions.
  • Retrotransposon insertions account for over half of the identified SVs.
  • SVs are less likely than other sequence variants to affect gene expression or quantitative traits.
  • Identified 24 SVs disrupting coding exons, with one-third affecting immunological genes.

Conclusions:

  • Structural variants are abundant in mouse genomes, primarily driven by retrotransposon activity.
  • Despite their prevalence, SVs have a limited impact on gene expression and phenotype compared to other variants.
  • Rare, large-effect SVs can significantly disrupt gene function, particularly impacting immunological pathways.