Complex chromosomal rearrangements induced by transposons in maize

Area of Science:

• Genetics
• Molecular Biology
• Genomics

Background:

• Eukaryotic genomes are complex, with gene expression influenced by regulatory elements and chromatin structure.
• Transposable elements (TEs) are known drivers of genome evolution, but their precise mechanisms in altering genome structure and gene expression require further investigation.
• Previous research indicated that Activator and related TEs can induce genome rearrangements via Reversed Ends Transposition in plants.

Purpose of the Study:

• To investigate how transposable elements, specifically Activator, contribute to the formation of complex alleles through duplications and rearrangements.
• To determine the impact of TE-induced structural variations on gene expression, using the maize p1 gene enhancer and p2 gene as a model system.
• To identify and characterize instances of rapid, sequential transposition events and their consequences on genetic variation.

Main Methods:

• Screening for ectopic p2 gene expression in maize pericarp tissue as an indicator of p1 enhancer activity.
• Analyzing cases with multiple sequential transposition events to quantify changes in p1 enhancer copy number and proximity to p2.
• Correlating the loss of p2 expression with the excision of p1 enhancers.
• Employing targeted Chromosome Conformation Capture (3C) to assess physical interactions between the p1 enhancer and p2 promoter.

Main Results:

• Identified 5 cases exhibiting multiple sequential transposition events, leading to increased copy numbers of the p1 enhancer.
• Demonstrated active p2 gene expression in all 5 cases due to the presence of multiple p1 enhancer copies near the p2 gene.
• Confirmed the regulatory role of p1 enhancers, as loss of p2 expression was linked to transposition-induced enhancer excision.
• Provided evidence for physical interaction between the p1 enhancer and p2 promoter using Chromosome Conformation Capture.

Conclusions:

• Activator transposable elements can rapidly induce duplications and rearrangements, leading to the formation of complex alleles.
• TE-mediated genome rearrangements can significantly alter gene expression by changing the distance and interaction between regulatory elements and genes.
• These findings highlight the substantial role of transposon-induced structural variations in generating genetic diversity and driving genomic evolution.