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Global analysis of cytosine and adenine DNA modifications across the tree of life.

Published version
Peer-reviewed

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Authors

Varma, Sreejith Jayasree  ORCID logo  https://orcid.org/0000-0002-1669-2254
Calvani, Enrica 
Grüning, Nana-Maria 
Messner, Christoph B 

Abstract

Interpreting the function and metabolism of enzymatic DNA modifications requires both position-specific and global quantities. Sequencing-based techniques that deliver the former have become broadly accessible, but analytical methods for the global quantification of DNA modifications have thus far been applied mostly to individual problems. We established a mass spectrometric method for the sensitive and accurate quantification of multiple enzymatic DNA modifications. Then, we isolated DNA from 124 archean, bacterial, fungal, plant, and mammalian species, and several tissues and created a resource of global DNA modification quantities. Our dataset provides insights into the general nature of enzymatic DNA modifications, reveals unique biological cases, and provides complementary quantitative information to normalize and assess the accuracy of sequencing-based detection of DNA modifications. We report that only three of the studied DNA modifications, methylcytosine (5mdC), methyladenine (N6mdA) and hydroxymethylcytosine (5hmdC), were detected above a picomolar detection limit across species, and dominated in higher eukaryotes (5mdC), in bacteria (N6mdA), or the vertebrate central nervous systems (5hmdC). All three modifications were detected simultaneously in only one of the tested species, Raphanus sativus. In contrast, these modifications were either absent or detected only at trace quantities, across all yeasts and insect genomes studied. Further, we reveal interesting biological cases. For instance, in Allium cepa, Helianthus annuus, or Andropogon gerardi, more than 35% of cytosines were methylated. Additionally, next to the mammlian CNS, 5hmdC was also detected in plants like Lepidium sativum and was found on 8% of cytosines in the Garra barreimiae brain samples. Thus, identifying unexpected levels of DNA modifications in several wild species, our resource underscores the need to address biological diversity for studying DNA modifications.

Description

Keywords

Research Article, Biochemistry and Chemical Biology, dna epigenetic modification, liquid chromatography, mass spectrometry, D. melanogaster, E. coli, Human, Mouse, S. cerevisiae

Journal Title

Elife

Conference Name

Journal ISSN

2050-084X
2050-084X

Volume Title

Publisher

eLife Sciences Publications, Ltd
Sponsorship
Cancer Research UK (FC001134)
Medical Research Council (FC001134)
Wellcome Trust (FC001134)
Federal Ministry of Education and Research (BMBF) (031L0220)
Wellcome Trust (200829/Z/16/Z)
Wellcome Trust (101503/Z/13/Z)