Identification of short tandemly repeated sequences in extrachromosomal circular DNAs from Drosophila melanogaster embryos

Abstract

A sequence (scl) belonging to the recently identified dodeca satellite family was found to be a major family of extrachromosomal circular DNA molecules from Drosophila melanogaster embryos. The basic unit consists of the 11-bp repeat 5' ACTGGTCCCGT 3', is 63% G + C rich, and shares some similarity with the Escherichia coli chi sequence. This family accounts for only about 0.06% of the genome but very likely for a higher proportion of the circular DNA molecules. It is organized in the genome into at least five main clusters contained in DNA fragments larger than 20 kb and several minor clusters. These clusters are located in the heterochromatic pericentromeric regions. Two other families of simple repeated sequences, the 1.686 g/cm3 (5' AATAACATAG 3') and the 1.705 g/cm3 (5' AAGAG 3') satellite DNAs, were also found in circular DNAs, while another family, the 1.672 g/cm3 (5' AATAT 3'), was not detected. The representation of the simple repeated sequences in circular molecules is not correlated to their genomic representation. Among the seven families of sequences identified to date in extrachromosomal circular DNAs from embryos, the dodeca satellite, the 240-bp repeat of the rDNA intergenic spacer, and the 1.688 and 1.705 g/cm3 satellite DNAs are the most represented families, while the 5S genes, the histone genes, and the 1.686 g/cm3 satellite DNA are present in a lower amount.