Haplotype-Resolved Chromatin Conformation Data Reveals Relationship Between Transposable Elements and Chromosomal Pairing

Chromosomal structural changes happen when genomic stability is compromised, such as in disease or in species hybrids. In these contexts, diminished control of repetitive elements has been reported, but the reasons for this are not yet well understood. There are causal associations between repetitive elements and phenotypes such as disease progression, leading us to the hypothesis that chromosomal structure may be affected by transposable elements (TEs). In an intraspecific hybrid Drosophila melanogaster cell line (PnM), the degree of pairing among trans homologous chromosomes was affected by the presence of nearby TEs, in particular, LINE and LTR elements, such as Baggins1 or Gypsy. Chromosomal pairing was significantly lower in windows containing TEs than in windows without any TEs. Pairing was also affected by TEs in mouse, which suggests a possible general association between TEs and pairing that is highly conserved.