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Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome

5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene expression in metazoans and plants. Iron-(II)/α-ketoglutarate-dependent dioxygenases can oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Although these oxidized fo...

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Autores principales: Yakovlev, Igor A., Gackowski, Daniel, Abakir, Abdulkadir, Viejo, Marcos, Ruzov, Alexey, Olinski, Ryszard, Starczak, Marta, Fossdal, Carl Gunnar, Krutovsky, Konstantin V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6917789/
https://www.ncbi.nlm.nih.gov/pubmed/31848418
http://dx.doi.org/10.1038/s41598-019-55826-z
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author Yakovlev, Igor A.
Gackowski, Daniel
Abakir, Abdulkadir
Viejo, Marcos
Ruzov, Alexey
Olinski, Ryszard
Starczak, Marta
Fossdal, Carl Gunnar
Krutovsky, Konstantin V.
author_facet Yakovlev, Igor A.
Gackowski, Daniel
Abakir, Abdulkadir
Viejo, Marcos
Ruzov, Alexey
Olinski, Ryszard
Starczak, Marta
Fossdal, Carl Gunnar
Krutovsky, Konstantin V.
author_sort Yakovlev, Igor A.
collection PubMed
description 5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene expression in metazoans and plants. Iron-(II)/α-ketoglutarate-dependent dioxygenases can oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Although these oxidized forms of 5mC may serve as demethylation intermediates or contribute to transcriptional regulation in animals and fungi, experimental evidence for their presence in plant genomes is ambiguous. Here, employing reversed-phase HPLC coupled with sensitive mass spectrometry, we demonstrated that, unlike 5caC, both 5hmC and 5fC are detectable in non-negligible quantities in the DNA of a conifer, Norway spruce. Remarkably, whereas 5hmC content of spruce DNA is approximately 100-fold lower relative to human colorectal carcinoma cells, the levels of both - 5fC and a thymine base modification, 5-hydroxymethyluracil, are comparable in these systems. We confirmed the presence of modified DNA bases by immunohistochemistry in Norway spruce buds based on peroxidase-conjugated antibodies and tyramide signal amplification. Our results reveal the presence of specific range of noncanonical DNA bases in conifer genomes implying potential roles for these modifications in plant development and homeostasis.
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spelling pubmed-69177892019-12-19 Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome Yakovlev, Igor A. Gackowski, Daniel Abakir, Abdulkadir Viejo, Marcos Ruzov, Alexey Olinski, Ryszard Starczak, Marta Fossdal, Carl Gunnar Krutovsky, Konstantin V. Sci Rep Article 5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene expression in metazoans and plants. Iron-(II)/α-ketoglutarate-dependent dioxygenases can oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Although these oxidized forms of 5mC may serve as demethylation intermediates or contribute to transcriptional regulation in animals and fungi, experimental evidence for their presence in plant genomes is ambiguous. Here, employing reversed-phase HPLC coupled with sensitive mass spectrometry, we demonstrated that, unlike 5caC, both 5hmC and 5fC are detectable in non-negligible quantities in the DNA of a conifer, Norway spruce. Remarkably, whereas 5hmC content of spruce DNA is approximately 100-fold lower relative to human colorectal carcinoma cells, the levels of both - 5fC and a thymine base modification, 5-hydroxymethyluracil, are comparable in these systems. We confirmed the presence of modified DNA bases by immunohistochemistry in Norway spruce buds based on peroxidase-conjugated antibodies and tyramide signal amplification. Our results reveal the presence of specific range of noncanonical DNA bases in conifer genomes implying potential roles for these modifications in plant development and homeostasis. Nature Publishing Group UK 2019-12-17 /pmc/articles/PMC6917789/ /pubmed/31848418 http://dx.doi.org/10.1038/s41598-019-55826-z Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Yakovlev, Igor A.
Gackowski, Daniel
Abakir, Abdulkadir
Viejo, Marcos
Ruzov, Alexey
Olinski, Ryszard
Starczak, Marta
Fossdal, Carl Gunnar
Krutovsky, Konstantin V.
Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome
title Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome
title_full Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome
title_fullStr Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome
title_full_unstemmed Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome
title_short Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome
title_sort mass spectrometry reveals the presence of specific set of epigenetic dna modifications in the norway spruce genome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6917789/
https://www.ncbi.nlm.nih.gov/pubmed/31848418
http://dx.doi.org/10.1038/s41598-019-55826-z
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