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

Тип публикации: статья из журнала

Год издания: 2019

Идентификатор DOI: 10.1038/s41598-019-55826-z

Аннотация: 5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene expression in metazoans and plants. Iron-(11)/alpha-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 noncanonica I DNA bases in conifer genomes implying potential roles for these modifications in plant development and homeostasis.

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Издание

Журнал: SCIENTIFIC REPORTS

Выпуск журнала: Vol. 9

Номера страниц: 19314

ISSN журнала: 20452322

Место издания: LONDON

Издатель: NATURE PUBLISHING GROUP

Авторы

  • Yakovlev Igor A. (Norwegian Inst Bioecon Res, Pb 115, NO-1431 As, Norway)
  • Gackowski Daniel (Nicolaus Copernicus Univ, Coll Med, Dept Clin Biochem, Ul Karlowicza 24, PO-85092 Bydgoszcz, Poland)
  • Abakir Abdulkadir (Univ Nottingham, Ctr Biomol Sci, Sch Med,Div Canc & Stem Cells, Wolfson Ctr Stem Cells Tissue Engn & Modelling ST, Univ Pk, Nottingham NG7 2RD, England)
  • Viejo Marcos (Norwegian Inst Bioecon Res, Pb 115, NO-1431 As, Norway)
  • Ruzov Alexey (Univ Nottingham, Ctr Biomol Sci, Sch Med,Div Canc & Stem Cells, Wolfson Ctr Stem Cells Tissue Engn & Modelling ST, Univ Pk, Nottingham NG7 2RD, England)
  • Olinski Ryszard (Nicolaus Copernicus Univ, Coll Med, Dept Clin Biochem, Ul Karlowicza 24, PO-85092 Bydgoszcz, Poland)
  • Starczak Marta (Nicolaus Copernicus Univ, Coll Med, Dept Clin Biochem, Ul Karlowicza 24, PO-85092 Bydgoszcz, Poland)
  • Fossdal Carl Gunnar (Norwegian Inst Bioecon Res, Pb 115, NO-1431 As, Norway)
  • Krutovsky Konstantin (Georg August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany; Russian Acad Sci, NI Vavilov Inst Gen Genet, Lab Populat Genet, Gubkina Str 3, Moscow 119991, Russia; Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Genome Res & Educ Ctr, Lab Forest Genom, Akad Gorodok 50a-2, Krasnoyarsk 660036, Russia; Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USAArticle)

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