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Haplotype-Resolved Chromatin Conformation Data Reveals Relationship Between Transposable Elements and Chromosomal
Luke K Genutis1, Patrick Villanueva1, Rita M Graze2
1Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90046, USA.
Genome Biology and Evolution
|November 26, 2025
Summary
Transposable elements (TEs) disrupt homologous chromosome pairing in Drosophila melanogaster and mouse cells. This suggests TEs impact genomic stability and could influence disease progression by altering chromosomal structure.
Area of Science:
- Genetics
- Genomics
- Molecular Biology
Background:
- Genomic instability can lead to chromosomal structural changes, observed in diseases and species hybrids.
- Repetitive elements, including transposable elements (TEs), are implicated in disease progression, but their role in chromosomal structure is unclear.
- Diminished control of repetitive elements is a known phenomenon in compromised genomic contexts.
Purpose of the Study:
- To investigate the hypothesis that transposable elements (TEs) affect chromosomal structure.
- To examine the association between TEs and homologous chromosome pairing in a Drosophila melanogaster hybrid cell line.
- To determine if the observed association between TEs and chromosome pairing is conserved across species.
Main Methods:
- Utilized an intraspecific hybrid Drosophila melanogaster cell line (PnM).
- Analyzed the degree of homologous chromosome pairing in genomic regions with and without TEs.
- Compared findings in Drosophila with data from mouse models to assess conservation.
Main Results:
- The presence of TEs, specifically LINE and LTR elements (e.g., Baggins1, Gypsy), significantly reduced homologous chromosome pairing in Drosophila melanogaster.
- Chromosomal pairing was markedly lower in genomic windows containing TEs compared to those without TEs.
- Similar effects of TEs on chromosome pairing were observed in mouse, indicating a conserved association.
Conclusions:
- Transposable elements (TEs) can negatively impact homologous chromosome pairing.
- The association between TEs and altered chromosome pairing is conserved across species, suggesting a fundamental role in genome regulation.
- TEs may contribute to chromosomal structural changes and influence phenotypes by disrupting chromosome pairing.
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