Exploring DNA methylation patterns in copper exposed Folsomia candida and Enchytraeus crypticus

J.W. Noordhoek, Jasper Koning, Janine Mariën, J. Kamstra, M.J.B. Amorim, C.A.M. van Gestel, N.M. van Straalen, T.F.M. Roelofs

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Accumulating evidence shows that epigenetics-mediated phenotypic plasticity plays a role in an organism’s ability to deal with environmental stress. However, to date, the role of epigenetic modifications in response to stress is hardly investigated in soil invertebrates. The main objective of this proof of principle study was to explore whether total cytosine and locus-specific CpG methylation are present in two important ecotoxicological model organisms, the springtail Folsomia candida and the potworm Enchytraeus crypticus, and if so, whether methylation patterns might change with increased toxicant exposure. LC-MS/MS analyses and bisulfite sequencing were performed to identify the CpG methylation state of the organisms. We show here, for the first time, a total level of 1.4% 5-methyl cytosine methylation in the genome of E. crypticus, and an absence of both total cytosine and locus-specific CpG methylation in F. candida. In E. crypticus, methylation of CpG sites was observed in the coding sequence (CDS) of the housekeeping gene Elongation Factor 1α, while the CDS of the stress inducible Heat Shock Protein 70 gene almost lacked methylation. This confirms previous observations that DNA methylation differs between housekeeping and stress-inducible genes in invertebrates. DNA methylation patterns in E. crypticus were not affected by exposure to copper (II) sulfate pentahydrate (CuSO4·5H2O) mixed in with LUFA 2.2 soil at sublethal effect concentrations that decreased reproduction by 10%, 20% and 50%. Although, differences in CpG methylation patterns between specific loci suggest a functional role for DNA methylation in E. crypticus, genome-wide bisulfite sequencing is needed to verify whether environmental stress affects this epigenetic hallmark.
LanguageEnglish
Pages52-57
JournalPedobiologia
Volume66
Issue numberJanuary
DOIs
StatePublished - Jan 2018

Fingerprint

Enchytraeus
Folsomia candida
methylation
DNA methylation
copper
DNA
cytosine
epigenetics
bisulfites
copper sulfate
loci
organisms
environmental stress
soil invertebrates
gene
genome
sublethal effects
invertebrate
Collembola
phenotypic plasticity

Keywords

  • DNA methylation
  • copper
  • Folsomia candida
  • Enchytraeus crypticus
  • invertebrate
  • LC-MS

Cite this

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title = "Exploring DNA methylation patterns in copper exposed Folsomia candida and Enchytraeus crypticus",
abstract = "Accumulating evidence shows that epigenetics-mediated phenotypic plasticity plays a role in an organism’s ability to deal with environmental stress. However, to date, the role of epigenetic modifications in response to stress is hardly investigated in soil invertebrates. The main objective of this proof of principle study was to explore whether total cytosine and locus-specific CpG methylation are present in two important ecotoxicological model organisms, the springtail Folsomia candida and the potworm Enchytraeus crypticus, and if so, whether methylation patterns might change with increased toxicant exposure. LC-MS/MS analyses and bisulfite sequencing were performed to identify the CpG methylation state of the organisms. We show here, for the first time, a total level of 1.4{\%} 5-methyl cytosine methylation in the genome of E. crypticus, and an absence of both total cytosine and locus-specific CpG methylation in F. candida. In E. crypticus, methylation of CpG sites was observed in the coding sequence (CDS) of the housekeeping gene Elongation Factor 1α, while the CDS of the stress inducible Heat Shock Protein 70 gene almost lacked methylation. This confirms previous observations that DNA methylation differs between housekeeping and stress-inducible genes in invertebrates. DNA methylation patterns in E. crypticus were not affected by exposure to copper (II) sulfate pentahydrate (CuSO4·5H2O) mixed in with LUFA 2.2 soil at sublethal effect concentrations that decreased reproduction by 10{\%}, 20{\%} and 50{\%}. Although, differences in CpG methylation patterns between specific loci suggest a functional role for DNA methylation in E. crypticus, genome-wide bisulfite sequencing is needed to verify whether environmental stress affects this epigenetic hallmark.",
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author = "J.W. Noordhoek and Jasper Koning and Janine Mari{\"e}n and J. Kamstra and M.J.B. Amorim and {van Gestel}, C.A.M. and {van Straalen}, N.M. and T.F.M. Roelofs",
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Exploring DNA methylation patterns in copper exposed Folsomia candida and Enchytraeus crypticus. / Noordhoek, J.W.; Koning, Jasper; Mariën, Janine ; Kamstra, J.; Amorim, M.J.B.; van Gestel, C.A.M.; van Straalen, N.M.; Roelofs, T.F.M.

In: Pedobiologia, Vol. 66, No. January, 01.2018, p. 52-57.

Research output: Contribution to JournalArticleAcademicpeer-review

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AU - Mariën,Janine

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AU - Amorim,M.J.B.

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KW - copper

KW - Folsomia candida

KW - Enchytraeus crypticus

KW - invertebrate

KW - LC-MS

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DO - 10.1016/j.pedobi.2017.10.001

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JF - Pedobiologia

SN - 0031-4056

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