A collaborative research group led by Sayuri Tsukahara and Tetsuji Kakutani from the University of Tokyo has revealed how retrotransposons—genetic components capable of “jumping” within chromosomes and known to play a significant role in evolution—preferentially insert themselves into centromeres. Their findings have been published in the journal Nature.
The centromere is the narrowest portion of a chromosome, similar to how a waist divides the upper and lower parts of the body. It plays a crucial role in passing on genetic information during cell division and has remained consistent among eukaryotes, which are cells that have a nucleus surrounded by a membrane. Despite the considerable variations in DNA sequences both within and between species—known as the “centromere paradox”—researchers have established that retrotransposons inserting at centromeres contribute to this variation and the acceleration of evolution. However, the precise mechanisms behind these insertions were previously unknown. To address this, the researchers examined how retrotransposons Tal1 and EVD insert into the plant Arabidopsis lyrata, also known as lyrate rockcress.
“It has long been understood that a significant portion of eukaryotic genomes consists of transposons that are predominantly found near the centromere,” explains Tsukahara, the lead author. “However, we lacked knowledge concerning the factors influencing their distribution and their function within the centromere. Investigating how retrotransposons integrate could shed light on the evolutionary processes that shaped eukaryotic genomes.”
Until recently, there were no reliable centromere reference data for Arabidopsis or many other organisms. However, with recent improvements in DNA sequencing technology, researchers were finally able to gather this reference data, paving the way for this study. They also used an innovative technique developed by several co-authors of this work that efficiently identifies retrotransposon insertions (TEd-seq). By combining these two advancements, the researchers were better able to “read” and accurately map insertion locations to the centromere region in the reference data.
“The results from TEd-seq surprised us,” recalls Tsukahara. “Tal1 showed a strong bias toward integrating into the centromere, with almost no insertions occurring in the chromosomal arms. Conversely, EVD preferred integrating into the chromosomal arms, despite being closely related to Tal1.
Additionally, the researchers discovered that these integration preferences could be reversed by replacing a specific part of the two retrotransposons—the c-terminal integrase region. Tsukahara notes the potential for further investigation, suggesting that nature holds many more secrets yet to be uncovered.
“We were truly impressed by the intricate mechanisms involved in retrotransposon integration. We are eager to delve deeper into the specific processes that lead to Tal1‘s unique integration at the centromere. For instance, we aim to identify the molecules that interact with Tal1 and explore whether there is a preference in passing Tal1 containing centromeres to the next generation. This could significantly enhance our understanding of the effects of retrotransposon insertions within centromeres.”
