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Updated: Jul 6, 2026
11:52
Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
Published on: April 23, 2016
Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
Keiko Akagi1, Jingfeng Li, Robert M Stephens
1Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA.
Genome Research
|April 3, 2008
Summary
Recent endogenous retrotransposons, primarily L1 elements, drive significant genomic variation in mouse strains. These mobile genetic elements alter gene structure and expression, contributing to natural genetic diversity.
Area of Science:
- Genomics
- Molecular Biology
- Genetics
Background:
- Inbred mouse strains are crucial models for human diseases and genetic diversity research.
- Understanding molecular differences between mouse strains is essential but largely unknown.
- Mammalian genome assemblies provide a framework for identifying structural variations.
Purpose of the Study:
- To identify genomic variants between inbred mouse strains at single nucleotide resolution.
- To analyze the contribution of endogenous retrotransposons to genetic variation.
- To investigate the impact of these variants on gene structure and expression.
Main Methods:
- Alignment of 26 million sequence traces from four laboratory mouse strains to the C57BL/6J reference genome.
- Discovery and analysis of over 10,000 intermediate-length genomic variants (100 nucleotides to 10 kilobases).
- Identification of endogenous retrotransposons, particularly L1 elements, as the source of variants.
Main Results:
- Over 10,000 intermediate-length genomic variants were identified between mouse strains and the reference genome.
- Approximately 85% of these variants resulted from recent endogenous retrotransposon mobilization, predominantly L1 elements.
- Polymorphic L1 retrotransposons were found to alter the structure and expression of numerous genes, including Drosha, Parp8, Scn1a, and Arhgap15.
- L1 polymorphisms showed nonrandom distribution, being excluded from the X chromosome and cell cycle genes, but enriched in receptor genes.
Conclusions:
- Recent endogenous L1 retrotransposition has extensively diversified mouse genomic structures and transcripts.
- This retrotransposition significantly distinguishes different mouse lineages.
- Endogenous L1 retrotransposition drives a substantial portion of natural genetic variation in mice.
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