A new type of tandem repeats in the Mus musculus genome – GC-rich megasatellites

Third-generation sequencing technologies have overcome existing technical challenges in sequencing repetitive regions of eukaryotic genomes and achieved complete T2T assemblies of a number of model genomes, including the mouse Mus musculus. This technological breakthrough has opened up opportunities for studying the structural and functional organization of complex genomes. We were able to verify previously identified tandem repeats in the mouse genome and discover new regions of periodicity, which we termed GC-rich megasatellites. This article describes the megasatellites found on mouse chromosome 6. There are only two of them, but each has its own characteristics. These extended tandem repeats in intergenic regions, with an average GC-content of 56 %, contain tracks of micro- and minisatellites, which cover more than a third of each copy. The average lengths of the variable-length patterns in the two described megasatellites are 4320 and 2440 nucleotide pairs, with copy numbers of 83 and 71, respectively. A characteristic feature of both tandem repeats is the presence of extended conserved regions interspersed with islands of variability – micro- and minisatellite tracks. In the first megasatellite, the islands of variability are formed by the tracks (ACCCC)n, (AAACG)n, (AAAC)n, (GTCT)n, (GT)n, (CTTC)n, (GAGAAG)n, and (TCC)n. The second megasatellite has three islands of variability with homopurine-homopyrimidine tracks (CT)n, (CA)n, and (CT)n. The first megasatellite contains the coding sequence of a proline-rich protein at the 3'- end of each copy. The copies were found to be heterogeneous in GC content: specifically, 10 % of the pattern's length at the 5'- end and 20 % at the 3'-end are more than 65 % GC, while the inner 70 % of the pattern's length is approximately 50 % GC. The second megasatellite is more GC-rich overall than the first. However, copies of the second region are more uniform in length, GC-composition, and oligonucleotide track coverage.