Comprehensive profiling of L1 retrotransposons in mouse

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• LINE-1 (L1) elements are active retrotransposons in mammals.
• L1 dysregulation is linked to cancer, aging, infertility, and neurological diseases.
• Accurate mapping of endogenous L1 insertions is crucial for understanding their role in disease.

Purpose of the Study:

• To adapt and validate a novel method, nanoTIPseq, for efficient and comprehensive mapping of mouse L1 insertions.
• To identify both annotated and previously undiscovered L1 insertions in mouse genomes.
• To demonstrate the utility of nanoTIPseq for single-cell analysis of L1 retrotransposition in vivo.

Main Methods:

• Developed nanoTIPseq, a modified transposon insertion profiling technique.
• Combined nanoTIPseq with nanopore sequencing for selective enrichment of young mouse L1s.
• Applied nanoTIPseq to C57BL/6 genomic DNA and individual mouse breast cancer cells.

Main Results:

• nanoTIPseq identified >95% of annotated L1s from C57BL/6 DNA with high efficiency (200,000 reads).
• Discovered 82 novel, unannotated L1 insertions in a single mouse genome, often missed by short-read methods.
• Successfully detected cell-specific L1 insertions in individual mouse breast cancer cells.

Conclusions:

• nanoTIPseq is a powerful tool for comprehensive L1 insertion profiling in mouse genomes.
• The method enables the discovery of novel L1 elements and analysis of retrotransposition at the single-cell level.
• nanoTIPseq facilitates in vivo studies of L1 activity in disease models.