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Nucleic Acids Res. 2019 Oct 10;47(18):9741-9760. doi: 10.1093/nar/gkz725.

Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA.

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Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
Department of Biology, American University, Washington, DC 20016, USA.


Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.

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