Rapid Detection of Transposon-Induced Genome Rearrangements

2022

Genetics

Self Cite

Eukaryotic genomes are large and complex, and gene expression can be affected by multiple regulatory elements and their positions within the dynamic chromatin architecture. Transposable elements are known to play important roles in genome evolution, yet questions remain as to how transposable elements alter genome structure and affect gene expression. Previous studies have shown that genome rearrangements can be induced by Reversed Ends Transposition involving termini of Activator and related transposable elements in maize and other plants. Here, we show that complex alleles can be formed by the rapid and progressive accumulation of Activator-induced duplications and rearrangements. The p1 gene enhancer in maize can induce ectopic expression of the nearby p2 gene in pericarp tissue when placed near it via different structural rearrangements. By screening for p2 expression, we identified and studied 5 cases in which multiple sequential transposition events occurred and increased the p1 enhancer copy number. We see active p2 expression due to multiple copies of the p1 enhancer present near p2 in all 5 cases. The p1 enhancer effects are confirmed by the observation that loss of p2 expression is correlated with transposition-induced excision of the p1 enhancers. We also performed a targeted Chromosome Conformation Capture experiment to test the physical interaction between the p1 enhancer and p2 promoter region. Together, our results show that transposon-induced rearrangements can accumulate rapidly and progressively increase genetic variation important for genomic evolution.

Section: Methodsmentioning

confidence: 99%

Complex chromosomal rearrangements induced by transposons in maize

2022

Genetics

Self Cite

“…1988) techniques were used to locate these breakpoints adjacent to Ac and fAc , respectively. For visualizing PCR products, a high-efficiency agarose gel electrophoresis method was used (Sharma and Peterson 2021). PCR amplicons were sequenced by the Iowa State University DNA Sequencing Facility.…”

Section: Methodsmentioning

confidence: 99%

Complex chromosomal rearrangements induced by transposons in maize

2022

Preprint

Self Cite

Eukaryotic genomes are large and complex, and gene expression can be affected by multiple regulatory elements and their positions within the dynamic chromatin architecture. Transposable Elements (TEs) are known to play important roles in genome evolution, yet questions remain as to how TEs alter genome structure and affect gene expression. Previous studies have shown that genome rearrangements can be induced by Reversed Ends Transposition (RET) involving termini of Activator (Ac) and related TEs in maize and other plants. Here, we show that complex alleles can be formed by the rapid and progressive accumulation of Ac-induced duplications and rearrangements. The p1 gene enhancer in maize can induce ectopic expression of the nearby p2 gene in pericarp tissue when placed near it via different structural rearrangements. By screening for p2 expression, we identified and studied five cases in which multiple sequential transposition events occurred and increased the p1 enhancer copy number. We see active p2 expression due to multiple copies of the p1 enhancer present near p2 in all five cases. The p1 enhancer effects are confirmed by the observation that loss of p2 expression is correlated with transposition-induced excision of the p1 enhancers. We also performed a targeted Chromosome Conformation Capture (3C) experiment to test the physical interaction between the p1 enhancer and p2 promoter region. Together, our results show that transposon-induced rearrangements can accumulate rapidly, and progressively increase genetic variation important for genomic evolution.

Transposon-induced inversions activate gene expression in Maize pericarp

Zuo

2021

Preprint

Chromosomal inversions can have considerable biological and agronomic impacts including disrupted gene function, change in gene expression and inhibited recombination. Here we describe the molecular structure and functional impact of six inversions caused by Alternative Transpositions between p1 and p2 genes responsible for floral pigmentation in maize. In maize line p1-wwB54, the p2 gene is expressed in anther and silk but not in pericarp, making the kernels white. We identified inversions in this region caused by transposition of Ac and fractured Ac (fAc) transposable elements. These inversions change the position of a p1 enhancer and activate the expression of p2 in the kernel pericarp, resulting in red kernel color. We hypothesize that these inversions place the p2 gene promoter near a p1 gene enhancer, thereby activating p2 expression in kernel pericarp.