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Open AccessCommunication
Genes 2016, 7(1), 1; doi:10.3390/genes7010001

Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex

1
Department of Botany and Genetics, Vilnius University, 21 Čiurlionis Str., LT-03101 Vilnius, Lithuania
2
Thermo Fisher Scientific Baltics, Graičiūno g. 8, LT-02241 Vilnius, Lithuania
3
Nature Research Centre, Akademijos str. 2, LT-08412 Vilnius, Lithuania
*
Author to whom correspondence should be addressed.
Academic Editors: Paul Richardson and J. Peter W. Young
Received: 1 September 2015 / Revised: 7 December 2015 / Accepted: 22 December 2015 / Published: 31 December 2015
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Abstract

The aim of our study was to analyze the presence of 5-methyl-cytosine (5-mC) and 5-hydroxymethyl-cytosine (5-hmC) in the genome of crustacean Daphnia pulex. First, the presence of 5-mC and 5-hmC in genomic DNA was demonstrated by using antibodies specific to either 5-mC or 5-hmC. Then, analysis of 5-mC and 5-hmC using pairs of restriction enzymes with different sensitivity to methylation and hydroxymethylation confirmed the presence of both modifications in selected regions of three genes (Cox4, Cand2 and Ephx1). To get a detailed picture of 5-hmC distribution over the D. pulex genome, we performed 5-hmC enrichment and sequenced the enriched fraction using next generation sequencing and non-enriched library (input) as a control. Comparison of input and enriched libraries showed that 5-hmC in exons is twice as frequent as in introns. Functional analysis indicated that 5-hmC abundance is associated with genes that are involved in the adenylate cyclase-activating G-protein-coupled receptor signaling pathway, molting cycles, morphogenesis and cell fate determination. Genes that lack 5-hmC tend to be involved in the regulation of the transforming growth factor beta receptor signaling pathway and in many mRNA-related processes. Our results suggest that epigenetic modifications are present in the genome of D. pulex and most likely are involved in the regulation of gene expression of this crustacean. View Full-Text
Keywords: Daphnia pulex; 5-methyl-cytosine; 5-hydroxymethyl-cytosine; whole genome sequencing; epigenetic modifications; Cox4; Cand2; Ephx1 Daphnia pulex; 5-methyl-cytosine; 5-hydroxymethyl-cytosine; whole genome sequencing; epigenetic modifications; Cox4; Cand2; Ephx1
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Strepetkaitė, D.; Alzbutas, G.; Astromskas, E.; Lagunavičius, A.; Sabaliauskaitė, R.; Arbačiauskas, K.; Lazutka, J. Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex. Genes 2016, 7, 1.

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