Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA
| Autor: | Laura F. Landweber, John R. Bracht, Michael W Lu, Jaspreet S. Khurana, V Talya Yerlici, Hoge C, Rafik Neme, Richard Miller |
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| Rok vydání: | 2019 |
| Předmět: |
Transposable element
Cytoplasm Computational biology Extrachromosomal circular DNA Oxytricha Genome law.invention 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine law Genetics Polymerase chain reaction 030304 developmental biology Gene Rearrangement Recombination Genetic 0303 health sciences biology Inverse polymerase chain reaction High-Throughput Nucleotide Sequencing Genomics DNA Protozoan biology.organism_classification Eukaryotic Cells chemistry DNA Transposable Elements Nucleic acid DNA Circular Genome Protozoan 030217 neurology & neurosurgery DNA |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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