TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function

Area of Science:

• Genomics
• Evolutionary Biology
• Epigenetics

Background:

• Topological associating domains (TADs) are key genomic structures regulating gene expression.
• The evolutionary conservation and functional significance of TADs and their boundaries are not well understood.

Purpose of the Study:

• To investigate the evolutionary conservation of TAD organization across primate and rodent species.
• To characterize the genetic and epigenetic properties of conserved and species-specific TAD boundaries.
• To assess the functional impact of TAD boundary evolution on gene regulation and phenotypes.

Main Methods:

• Comparative analysis of Hi-C and ChIP-seq data across eight species (four primates, four rodents).
• Identification and annotation of ultraconserved and species-specific TAD boundaries.
• CRISPR-Cas9 gene editing in mouse models to study boundary function.
• Analysis of gene expression changes and phenotypic outcomes post-deletion.

Main Results:

• 14% of human TAD boundaries are ultraconserved across all eight species; 15% are human-specific.
• Ultraconserved TAD boundaries exhibit greater insulation, CTCF binding, and retrotransposon enrichment.
• Disruption of an ultraconserved boundary in mice caused tissue-specific expression changes and morphological defects.
• Deletion of a human-specific boundary near the AUTS2 gene led to its upregulation in neurons.

Conclusions:

• TAD boundary evolution is significant, with conserved boundaries playing a critical role in genome organization.
• Species-specific TAD boundaries contribute to species-unique gene regulation and phenotypic differences.
• The study provides valuable evolutionary annotations for TAD boundaries and demonstrates their functional importance.