LTR retrotransposons are a group of endogenous mobile genetic elements widely distributed in eukaryotic genomes, significantly contributing to their evolution and functioning. The retrotransposon RNA genome (gRNA), similar to viral, is a specific instruction that serves as a template for protein synthesis, as well as a DNA copy that can integrate into the host genome. Studies show that not only the sequence of RNA genomes but also their structure plays an important role during replication.

Researchers from IBCH PAS under the supervision of Dr. Katarzyna Pachulska-Wieczorek (MSc. Eng. Angelika Andrzejewska-Romanowska, Dr. Julita Gumna, MSc. Eng. Ewa Tykwińska) used the SHAPE-MaP strategy to determine the secondary structure of the entire RNA genome of the Ty3 retrotransposon in vivo and in extracellular conditions. Until now, the only model of the retrotransposon gRNA in vivo was the one developed for the Ty1 element, also by the team of Dr. Katarzyna Pachulska-Wieczorek (Andrzejewska et al., 2021, NAR). The new work indicates a number of dependent and independent of the cell environment structural changes of Ty3 gRNA, characterizes the structural context of functional sequences, and proposes a new model of genome dimerization, similar to the evolutionarily related HIV-1 virus. In addition, the work presents the first and comprehensive comparison of the structure of the RNA genomes of three main representatives of retroelements – Ty1, Ty3, and HIV-1.