Unveiling the Secrets Behind Swift Centromere Evolution

A collaborative research team led by Sayuri Tsukahara and Tetsuji Kakutani at the University of Tokyo has elucidated a mechanism by which retrotransposons, genetic components that can “hop” across chromosomes and are recognized as factors in evolution, preferentially insert into the centromere. The results were published in the journal Nature.

The centromere represents the narrowest section of the chromosome that divides it into a long and short arm, similar to how the waist separates the upper and lower parts of the body. Its function in conveying information during cell division has remained constant across eukaryotes, which are cells that possess membrane-bound nuclei. This occurs despite significant variations in DNA sequences both among and within species, a phenomenon referred to as the “centromere paradox.”

Scientists have been aware that the insertion of retrotransposons into the centromere contributes to this variation and hasty evolution. Nevertheless, the specifics of the insertion processes have remained unclear. To bridge this gap, the researchers examined the insertion processes of retrotransposons Tal1 and EVD in the plant Arabidopsis lyrata, also known as lyrate rockcress.

“It has long been acknowledged that a substantial portion of the eukaryotic genome is comprised of transposons concentrated near the centromere,” remarks Tsukahara, the lead author. “However, the factors influencing their distribution and their function within the centromere had not been identified. Studying the mechanisms of retrotransposon integration could illuminate how evolution has ‘shaped’ eukaryotic genomes.”

Until recently, reference data regarding centromeres for Arabidopsis and many other organisms were lacking. However, due to recent advancements in DNA sequencing technology, this reference information has finally been acquired, allowing for the current study. The researchers also utilized a technique previously established by some of the co-authors of this paper, designed to efficiently detect retrotransposon insertions (TEd-seq).

By combining these two technological advancements, the researchers were able to “read” the insertion locations and accurately map the findings onto the centromere region of the reference data.

“The results from TEd-seq surprised us,” Tsukahara mentions, “as retrotransposons Tal1 and EVD exhibited pronounced integration biases. Tal1 integrated primarily into the centromere, with nearly no insertions in the chromosomal arm region. In contrast, EVD integrated into the chromosomal arm, despite being closely related to Tal1.”

Additionally, the researchers discovered that these integration biases reversed when they exchanged a specific region (c-terminal integrase region) between the two retrotransposons. With this indication that nature holds many more secrets yet to be uncovered, Tsukahara shares plans for future research.

“We were astonished by the intricate integration mechanisms of retrotransposons. We aspire to delve deeper into the mechanisms of centromere-specific integration of retrotransposon Tal1. For instance, we aim to identify the factors that bind to Tal1 and examine whether there is a bias in the transmission of Tal1-contained centromeres to the progeny. This may help clarify the effect of retrotransposon insertions on the centromere.”