Evidence map›Paper›PMID 26227972›Full record

ArticleNucleic acids research2015

Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes.

Abdullah H Sahyoun, Martin Hölzer, Frank Jühling, Christian Höner zu Siederdissen, Marwa Al-Arab, Kifah Tout, Manja Marz, Martin Middendorf, Peter F Stadler, Matthias Bernt

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
1.5field-weighted citation impact, top 18% of its field
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

16 citing papers in PubMed, 29 citations in OpenAlex.

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  11. SMORE: Synteny Modulator of Repetitive Elements.Life (Basel, Switzerland) · 2017
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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

10 authors at 5 institutions in 5 countries.

Abdullah H SahyounBioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany Bioinformatics Unit and Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany sahyoun@ie-freiburg.mpg.de.
Martin HölzerRNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany.
Frank JühlingBioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.
Christian Höner zu SiederdissenBioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
Marwa Al-ArabBioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon.
Kifah ToutDoctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon.
Manja MarzRNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany Michael Stifel Center Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
Martin MiddendorfParallel Computing and Complex Systems Group, Department of Computer Science, Leipzig University, Augustusplatz 10, D-04109 Leipzig, Germany.
Peter F StadlerBioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria Max-Planck-Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany Fraunhofer Institut für Zelltherapie und Immunologie Perlickstraße 1, D-04103 Leipzig, Germany Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA.
Matthias BerntParallel Computing and Complex Systems Group, Department of Computer Science, Leipzig University, Augustusplatz 10, D-04109 Leipzig, Germany bernt@informatik.uni-leipzig.de.
Leipzig University · DEErnst Abbe University of Applied Sciences Jena · DEFraunhofer Institute for Cell Therapy and Immunology · DEFriedrich Schiller University Jena · DELebanese University · LB

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Remolding of tRNAs is a well-documented process in mitochondrial genomes that changes the identity of a tRNA. It involves a duplication of a tRNA gene, a mutation that changes the anticodon and the loss of the ancestral tRNA gene. The net effect is a functional tRNA that is more closely related to tRNAs of a different alloacceptor family than to tRNAs with the same anticodon in related species. Beyond being of interest for understanding mitochondrial tRNA function and evolution, tRNA remolding events can lead to artifacts in the annotation of mitogenomes and thus in studies of mitogenomic evolution. Therefore, it is important to identify and catalog these events. Here we describe novel methods to detect tRNA remolding in large-scale data sets and apply them to survey tRNA remolding throughout animal evolution. We identify several novel remolding events in addition to the ones previously mentioned in the literature. A detailed analysis of these remoldings showed that many of them are derived from ancestral events.

Indexed as

Evolution, MolecularGenome, MitochondrialAnimalsAnticodonCodonCrustaceaMutationPoriferaRNA, TransferRNA, Transfer, LeuSequence AlignmentAnticodonCodonRNA, TransferRNA, Transfer, Leu

Identifiers

PMID26227972
PMCPMC4783518
OpenAlexW1896350454

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

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.