G-Quadruplexes in the Archaea Domain
The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-09-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/10/9/1349 |
| _version_ | 1797553052250537984 |
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| author | Václav Brázda Yu Luo Martin Bartas Patrik Kaura Otilia Porubiaková Jiří Šťastný Petr Pečinka Daniela Verga Violette Da Cunha Tomio S. Takahashi Patrick Forterre Hannu Myllykallio Miroslav Fojta Jean-Louis Mergny |
| author_facet | Václav Brázda Yu Luo Martin Bartas Patrik Kaura Otilia Porubiaková Jiří Šťastný Petr Pečinka Daniela Verga Violette Da Cunha Tomio S. Takahashi Patrick Forterre Hannu Myllykallio Miroslav Fojta Jean-Louis Mergny |
| author_sort | Václav Brázda |
| collection | DOAJ |
| description | The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in <i>Hadesarchaea archeon</i> (strikingly, more than 50% of the <i>Hadesarchaea archaeon</i> isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the <i>Parvarchaeota</i> phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea. |
| first_indexed | 2024-03-10T16:09:54Z |
| format | Article |
| id | doaj.art-a96d853c875849e9b8b00020f3d9ea06 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T16:09:54Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-a96d853c875849e9b8b00020f3d9ea062023-11-20T14:33:49ZengMDPI AGBiomolecules2218-273X2020-09-01109134910.3390/biom10091349G-Quadruplexes in the Archaea DomainVáclav Brázda0Yu Luo1Martin Bartas2Patrik Kaura3Otilia Porubiaková4Jiří Šťastný5Petr Pečinka6Daniela Verga7Violette Da Cunha8Tomio S. Takahashi9Patrick Forterre10Hannu Myllykallio11Miroslav Fojta12Jean-Louis Mergny13Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech RepublicInstitut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, FranceDepartment of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech RepublicFaculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech RepublicInstitute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech RepublicFaculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech RepublicDepartment of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech RepublicInstitut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, FranceInstitut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, FranceInstitut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, FranceInstitut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, FranceLaboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, FranceInstitute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech RepublicInstitute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech RepublicThe importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in <i>Hadesarchaea archeon</i> (strikingly, more than 50% of the <i>Hadesarchaea archaeon</i> isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the <i>Parvarchaeota</i> phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.https://www.mdpi.com/2218-273X/10/9/1349G4-forming motifgenome analysisArchaeaunusual nucleic acid structuressequence prediction |
| spellingShingle | Václav Brázda Yu Luo Martin Bartas Patrik Kaura Otilia Porubiaková Jiří Šťastný Petr Pečinka Daniela Verga Violette Da Cunha Tomio S. Takahashi Patrick Forterre Hannu Myllykallio Miroslav Fojta Jean-Louis Mergny G-Quadruplexes in the Archaea Domain Biomolecules G4-forming motif genome analysis Archaea unusual nucleic acid structures sequence prediction |
| title | G-Quadruplexes in the Archaea Domain |
| title_full | G-Quadruplexes in the Archaea Domain |
| title_fullStr | G-Quadruplexes in the Archaea Domain |
| title_full_unstemmed | G-Quadruplexes in the Archaea Domain |
| title_short | G-Quadruplexes in the Archaea Domain |
| title_sort | g quadruplexes in the archaea domain |
| topic | G4-forming motif genome analysis Archaea unusual nucleic acid structures sequence prediction |
| url | https://www.mdpi.com/2218-273X/10/9/1349 |
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