Circulating cell-free DNA is predominantly composed of retrotransposable elements and non-telomeric satellite DNA

[Display omitted] •The distribution of circulating cell-free DNA coverage over the respective reference genome is highly non-uniform.•Retrotransposable elements and non-telomeric satellite DNA are consistently overrepresented in human plasma and bovine serum.•Telomeric satellite DNA is underrepresented.•DNA from retrotransposable elements and non-telomeric satellite DNA is potentially actively secreted from cells, most likely via exosomes.•Sepsis patients have elevated fractions of DNA from retrotransposable elements. Circulating cell-free DNAs (cfDNAs) are DNA fragments which can be isolated from mammalian blood serum or plasma. In order to gain deeper insight into their origin(s), we have characterized the composition of human and cattle cfDNA via large-scale analyses of high-throughput sequencing data. We observed significant differences between the composition of cfDNA in serum/plasma and the corresponding DNA sequence composition of the human genome. Retrotransposable elements and non-telomeric satellite DNA were particularly overrepresented in the cfDNA population, while telomeric satellite DNA was underrepresented. This was consistently observed for human plasma, bovine serum and for the supernatant of human cancer cell cultures. Our results suggest that reverse transcription of retrotransposable elements and secondary-structure formation during the replication of satellite DNA are contributing to the composition of the cfDNA molecules in the mammalian blood stream. We believe that our work is an important step towards the understanding of the biogenesis of cfDNAs and thus may also facilitate the future exploitation of their diagnostic potential.