The Fire Ant Social Chromosome Exerts a Major Influence on Genome Regulation

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Supergenes are crucial for maintaining linked coadapted alleles underlying complex traits.
• The regulatory mechanisms by which supergenes influence genome regulation remain largely unknown.
• A specific supergene in fire ants (Solenopsis invicta) governs social polymorphism across multiple castes.

Purpose of the Study:

• To investigate the genome-wide effects of a supergene on gene regulation.
• To understand how supergene variations impact chromatin accessibility and enhancer activity.
• To elucidate the interplay between supergene structure, transposable elements, and gene expression.

Main Methods:

• ATAC-seq to assess chromatin accessibility variations based on supergene genotype.
• STARR-seq to characterize enhancer activity across different supergene haplotypes.
• Integration of gene co-expression data, transposable element mapping, and copy number variant (CNV) analysis.

Main Results:

• The supergene significantly impacts chromatin structure, gene transcription, and regulatory element activity.
• A bias towards open chromatin and increased gene expression was observed with the derived supergene haplotype.
• Intact transposable elements (TEs) in proximity to the supergene are particularly associated with altered gene expression.
• Copy number variants (CNVs) and regulatory element divergence appear to have co-evolved to modulate supergene-encoded factor expression.

Conclusions:

• Supergene structure exerts widespread influence on genome regulation and gene expression.
• Transcription factors encoded within the supergene may contribute to its trans-regulatory effects.
• The findings provide insights into how genome architecture, like supergenes, shapes regulatory landscapes and organismal traits.