Speaker: Sharu Paul Sharma, Department of Genetics, Development and Cell Biology graduate student in Thomas Peterson Lab

Title: “Functional and Structural Impacts of Ac/Ds Transposon System in Maize”

Abstract: Barbara McClintock discovered the maize Activator (Ac) and Dissociation (Ds) transposable elements while studying the phenomenon of chromosome breakage in the 1940s. Transposons have since been shown to play a significant role in genomic evolution. DNA elements such as Ac can cause structural rearrangements in the genome when multiple elements are present in proximity. I present the functional and structural impacts of Ac-induced rearrangements on the maize genome and the improvement of methods we use to detect these rearrangements.

DNA isolation, PCR amplification, and Agarose Gel Electrophoresis are the basic techniques used in molecular biology research labs. Even these basic techniques become tedious and costly when working with large population sizes. I describe modifications to these techniques to make them quicker, including the approaches we used to detect transposon-induced genome rearrangements. We use maize pericarp color 1 (p1) and pericarp color 2 (p2) genes to study various structural rearrangements. We found the molecular structures of six inversion cases between p1 and p2 genes induced by Alternative Transpositions of Ac and fractured Ac (fAc) transposable elements. Our results indicate that these inversions place the p2 gene promoter near a p1 gene enhancer which leads to activation of p2 expression in kernel pericarp.

Complex Chromosomal Rearrangements (CCRs) lead to formation of complex alleles in both animals and plants such as the Fibrinogen locus in humans or the sh2‑R allele of the maize shrunken‑2 locus and are also important in several human diseases. The underlying mechanisms of formation of alleles with complex structures remain understudied. Using our Ac/fAc transposon system in maize, we uncovered transposition-based mechanism for formation of CCRs. Through five cases in which multiple sequential transposition events occurred in the p1/p2 region, we show that transposon-induced duplications and rearrangements such as deletions, inversions and Composite Insertions can accumulate and form complex alleles in a relatively short time. These complex alleles have varied p1 enhancer copy numbers allowing us to study factors affecting enhancer function. We explored enhancer promoter interaction, and the relationship of enhancer copy number and location to its influence on target promoter.

In conclusion, my thesis presents improved methods and furthers the understanding of the capacity of DNA elements to cause functional and structural changes in the genome. This study expands our knowledge of enhancer function and the role played by DNA elements in genome evolution.

Zoom link: https://iastate.zoom.us/j/97094809970?pwd=dDQ4a09rWUJQS3h3MnRxLytkY0Zpdz09

July 15, 2022, Ph.D. Defense Seminar flyer: Sharu Paul Sharma