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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.

Author information

1
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
2
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
3
Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
4
Department of Biology, American University, Washington, DC 20016, USA.

Abstract

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.

PMID:
31504770
PMCID:
PMC6765146
DOI:
10.1093/nar/gkz725
[Indexed for MEDLINE]
Free PMC Article

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