Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• Chromatin organization is crucial for gene regulation.
• Transposable elements constitute a significant portion of mammalian genomes.
• Analyzing individual transposon activity is challenging due to their repetitive nature.

Purpose of the Study:

• To develop novel methods for analyzing transposable element (TE) interactions.
• To understand the role of TEs in chromatin folding and gene regulation.

Main Methods:

• Developed 4Tran, a PCR and Capture-based chromosome conformation capture (3C) technique.
• Utilized 4Tran to capture interactions from multiple copies of endogenous retroviruses (ERVs).
• Applied 4Tran-PCR for selective read mapping and Capture-4Tran for identifying interaction endpoints.

Main Results:

• 4Tran enables the identification of interaction profiles for individual ERV families and specific integration events.
• Demonstrated that transposons participate in long-range intra-chromosomal interactions within chromosomal compartments and TADs.
• Capture-4Tran successfully identified specific transposable element insertions interacting with potential target genes.

Conclusions:

• 4Tran offers novel insights into transposon contributions to chromosome architecture.
• Identified target genes potentially regulated by transposable elements.
• Advanced the understanding of TE impact on genome organization and gene expression.