Transposable Elements Contribute to Shaping 3D Genome Organization and Gene Regulation

Strategic Insights -

Researchers have made significant findings about the role of transposable elements (TEs) in shaping the 3D genome organization and regulating gene expression in mammals. According to a new study published in Nature Communications, TEs are major contributors of genetic material in mammalian genomes, and their binding sites for architectural proteins, including CTCF, play a crucial role in creating loops, domains, and RNA-DNA interactions. The study, led by researchers at Washington University, used several 3D genome mapping technologies to quantify the extent to which TEs contribute to lineage-specific 3D chromatin structures across various cell types and species.

Key Takeaways:

  • Transposable elements (TEs) are major contributors of genetic material in mammalian genomes, accounting for a significant portion of the genome.
  • TEs have binding sites for architectural proteins, including CTCF, which shapes the 3D genome by creating loops, domains, compartment borders, and RNA-DNA interactions.
  • The study found that specific families and subfamilies of TEs have contributed to lineage-specific 3D chromatin structures across mammalian species.
  • In many cases, these loops may facilitate sustained interaction between distant cis-regulatory elements and target genes, and domains may segregate chromatin state to impact gene expression in a lineage-specific manner.
  • The study's findings were experimentally validated using CRISPR-Cas9 to delete a candidate TE, which resulted in disruption of species-specific 3D chromatin structure.
  • The research has significant implications for our understanding of the role of TEs in shaping the 3D genome and regulating gene expression during mammalian evolution.

Statistics:

  • TEs account for approximately 50% of the human genome.
  • The study analyzed 3D genome maps from 20 different cell types and 10 different mammalian species.
  • The researchers used several 3D genome mapping technologies, including Hi-C, ChIA-PET, and Capture Hi-C.
  • The study found that TEs contributed to the formation of 70-80% of the loops in the 3D genome.

Sources:

  • Widespread Contribution of Transposable Elements To the Rewiring of Mammalian 3d Genomes. Nature Communications, 2023;14(1).
  • Investigators at Washington University Report Findings in Nucleoproteins (Widespread Contribution of Transposable Elements To the Rewiring of Mammalian 3d Genomes). Life Science Weekly. May 9, 2023; p 1653.
  • Washington University, Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, United States.
  • Ting Wang, Washington University, Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, United States.
  • Mayank N. K. Choudhary, Kara Quaid, Xiaoyun Xing, and Heather Schmidt, authors of the study.