Circular DNA are common structural variants in healthy human tissue and blood

Henrik Devitt Møller ¹ Marghoob Mohiyuddin ² Iñigo Prada-Luengo ¹ M. Reza Sailani ³ Jens Frey Halling ¹ Peter Plomgaard ^4,5 Lasse Maretty ¹ Anders Johannes Hansen ⁶ Michael P. Snyder ³ Henriette Pilegaard ¹ Hugo Y.K. Lam ² Birgitte Regenberg ¹

¹Department of Biology, University of Copenhagen, Denmark
²Sequencing Solutions, Roche, USA
³Department of Genetics, Stanford University, USA
⁴Department of Clinical Biochemistry, Rigshospitalet, Denmark
⁵The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Denmark
⁶The Natural History Museum of Denmark, University of Copenhagen, Denmark

The human genome is generally organized into stable chromosomes, but somatic cells can accumulate genomic structural variations as they age. A much overlooked mutation is circular DNA that is primarily known from tumor cells. However, it must be expected that kb circular DNAs also exist in normal cells as a result of deletions. To examine this, we purified and sequenced circular DNAs from muscle and blood samples from 16 healthy men (age +60), detecting ~180,000 unique circular DNA types from 16 million nuclei. Half of these structures carried genes or gene fragments and the majority were smaller than 25 kb. Transcription from circular DNAs suggests that circular DNAs reside in nuclei and recurrence of certain circular DNAs in several individuals implies DNA circularization hotspots. Gene-rich chromosomes contribute to more circular DNAs per megabase and the most transcribed protein-coding gene in muscle, TTN (titin), provides the most circular DNAs per gene. Thus, somatic genomes are rich in chromosome-derived circular DNAs that may influence phenotypes through altered gene copy numbers and transcription of full-length or truncated genes.