Evidence map›Paper›PMID 31504770›Full record

ArticleNucleic acids research2019

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

V Talya Yerlici, Michael W Lu, Carla R Hoge, Richard V Miller, Rafik Neme, Jaspreet S Khurana, John R Bracht, Laura F Landweber

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
31citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

31 citing papers in PubMed, 1 synthesis or guideline pooled it.

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  5. A PIWI protein-dependent DNA N6-adenine methylation pathway inbioRxiv : the preprint server for biology · 2026
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

V Talya YerliciDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Michael W LuDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Carla R HogeDepartment of Biological Sciences, Columbia University, New York, NY 10027, USA.
Richard V MillerDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Rafik NemeDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Jaspreet S KhuranaDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
John R BrachtDepartment of Biology, American University, Washington, DC 20016, USA.
Laura F LandweberDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Funding

Understanding Complex Genome Editing and RNA Biology in OxytrichaR35GM122555 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI LAURA F LANDWEBER · 2017 to 2026
$7.9M
UNDERSTANDING COMPLEX GENE EDITING SYSTEMS IN PROTISTSR01GM059708 · NIGMS · PRINCETON UNIVERSITY · PI LANDWEBER, LAURA F · 1999 to 2016
$4.4M
NIGMS NIH HHS R01 GM059708NIGMS NIH HHS R35 GM122555
6 · The paper itself

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.

Indexed as

Recombination, GeneticCytoplasmDNA, CircularDNA, ProtozoanDNA Transposable ElementsEukaryotic CellsGene RearrangementGenome, ProtozoanHigh-Throughput Nucleotide SequencingOxytrichaDNA, CircularDNA, ProtozoanDNA Transposable Elements

Identifiers

PMID31504770
PMCPMC6765146

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.