Active LTR Retrotransposons Shaping the Dynamic Evolution of Maize Genomes

Presentation Type

Poster

Faculty Advisor

Chunguang Du

Access Type

Event

Start Date

26-4-2024 2:15 PM

End Date

26-4-2024 3:15 PM

Description

Long terminal repeats (LTR) retrotransposons are transposable elements which can copy and insert themselves into other loci within a genome. These transposable elements are similar to retroviruses in that they rely on reverse transcriptase to “copy and paste” themselves elsewhere in the host genome. From their own RNA transcript, they are able to use reverse transcriptase to make another DNA copy of themselves. However, in the decades after the discovery of reverse transcriptase and LTR retrotransposons, it became known that non-genic DNA could have other functions. LTR retrotransposons are sources of mutation, inserting themselves into and mutating genes within their host organism. Moreover, LTR retrotransposons are also prone to mutation themselves, quickly becoming inactive, and ultimately incapable of transposition. The vast majority of these LTR retrotransposons are completely inactive. While these inactive retrotransposons can be useful for gleaning information about an organism’s evolutionary history, the rare active LTR retrotransposons are of more interest. In this study, we created a tool for filtering out the inactive LTR retrotransposons and locating potentially active ones by adding extra functionalities, to the freely available tool “LTR Detector” for locating LTR’s. In an initial filter, LTR Detector found over three million potential LTR retrotransposons across thirty publicly available maize lines. After incorporating restrictions for size, an intact primer binding site, a polypurine tract, and coding sequences for reverse transcriptase, RNase and integrase, we narrowed down that large pool of candidates to just 27 potentially active LTR retrotransposons.

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Additional Authors: Laura Lepore, Istiaque Chowdhury

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Apr 26th, 2:15 PM Apr 26th, 3:15 PM

Active LTR Retrotransposons Shaping the Dynamic Evolution of Maize Genomes

Long terminal repeats (LTR) retrotransposons are transposable elements which can copy and insert themselves into other loci within a genome. These transposable elements are similar to retroviruses in that they rely on reverse transcriptase to “copy and paste” themselves elsewhere in the host genome. From their own RNA transcript, they are able to use reverse transcriptase to make another DNA copy of themselves. However, in the decades after the discovery of reverse transcriptase and LTR retrotransposons, it became known that non-genic DNA could have other functions. LTR retrotransposons are sources of mutation, inserting themselves into and mutating genes within their host organism. Moreover, LTR retrotransposons are also prone to mutation themselves, quickly becoming inactive, and ultimately incapable of transposition. The vast majority of these LTR retrotransposons are completely inactive. While these inactive retrotransposons can be useful for gleaning information about an organism’s evolutionary history, the rare active LTR retrotransposons are of more interest. In this study, we created a tool for filtering out the inactive LTR retrotransposons and locating potentially active ones by adding extra functionalities, to the freely available tool “LTR Detector” for locating LTR’s. In an initial filter, LTR Detector found over three million potential LTR retrotransposons across thirty publicly available maize lines. After incorporating restrictions for size, an intact primer binding site, a polypurine tract, and coding sequences for reverse transcriptase, RNase and integrase, we narrowed down that large pool of candidates to just 27 potentially active LTR retrotransposons.