Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA

• Published in: Nucleic acids research Vol. 47; no. 18; pp. 9741 - 9760
• Main Authors: Yerlici, V Talya, Lu, Michael W, Hoge, Carla R, Miller, Richard V, Neme, Rafik, Khurana, Jaspreet S, Bracht, John R, Landweber, Laura F
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 10.10.2019
• Subjects: Cytoplasm - genetics; DNA Transposable Elements - genetics; DNA, Circular - genetics; DNA, Protozoan - genetics; Eukaryotic Cells; Gene Rearrangement - genetics; Genome, Protozoan - genetics; Genomics; High-Throughput Nucleotide Sequencing; Oxytricha - genetics; Recombination, Genetic
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkz725

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.