Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during...

Area of Science:

• Plant genomics
• Epigenetics
• Polyploid evolution

Background:

• Bread wheat (Triticum aestivum) is an allohexaploid with a large, complex genome hindering understanding of regulatory element roles.
• Investigating chromatin structure and gene expression in wheat is challenging due to its polyploid nature.

Purpose of the Study:

• To generate open chromatin interaction maps for hexaploid wheat and its diploid/tetraploid relatives.
• To understand how open chromatin interactions and structural variations contribute to gene expression and evolution in wheat.

Main Methods:

• Utilized open chromatin enrichment and network Hi-C (OCEAN-C) to map genome-wide chromatin interactions.
• Analyzed chromatin accessibility, histone modifications, transcription factor binding motifs, and gene expression patterns.

Main Results:

• Identified chromatin loops anchored in open chromatin regions, with hubs of open chromatin interactions (HOCIs) significantly enriched for transcription factor motifs.
• Genes linked by HOCIs exhibit higher expression and lower variance, suggesting coordinated co-expression.
• Discovered structural variations contribute to chromatin interaction divergence and topology changes between wheat species, impacting gene expression.

Conclusions:

• Open chromatin interactions play a crucial role in regulating gene expression in wheat.
• This study provides novel insights into the function of open chromatin interactions in the evolution of polyploid wheat species.