Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex
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...
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doaj-b37bc8bc847a48e989d55aad7b7c696b2020-11-24T22:43:12ZengMDPI AGGenes2073-44252015-12-0171110.3390/genes7010001genes7010001Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulexDovilė Strepetkaitė0Gediminas Alzbutas1Eimantas Astromskas2Arūnas Lagunavičius3Rasa Sabaliauskaitė4Kęstutis Arbačiauskas5Juozas Lazutka6Department of Botany and Genetics, Vilnius University, 21 Čiurlionis Str., LT-03101 Vilnius, LithuaniaThermo Fisher Scientific Baltics, Graičiūno g. 8, LT-02241 Vilnius, LithuaniaThermo Fisher Scientific Baltics, Graičiūno g. 8, LT-02241 Vilnius, LithuaniaThermo Fisher Scientific Baltics, Graičiūno g. 8, LT-02241 Vilnius, LithuaniaThermo Fisher Scientific Baltics, Graičiūno g. 8, LT-02241 Vilnius, LithuaniaNature Research Centre, Akademijos str. 2, LT-08412 Vilnius, LithuaniaDepartment of Botany and Genetics, Vilnius University, 21 Čiurlionis Str., LT-03101 Vilnius, LithuaniaThe 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.http://www.mdpi.com/2073-4425/7/1/1Daphnia pulex5-methyl-cytosine5-hydroxymethyl-cytosinewhole genome sequencingepigenetic modificationsCox4Cand2Ephx1 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Dovilė Strepetkaitė Gediminas Alzbutas Eimantas Astromskas Arūnas Lagunavičius Rasa Sabaliauskaitė Kęstutis Arbačiauskas Juozas Lazutka |
spellingShingle |
Dovilė Strepetkaitė Gediminas Alzbutas Eimantas Astromskas Arūnas Lagunavičius Rasa Sabaliauskaitė Kęstutis Arbačiauskas Juozas Lazutka Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex Genes Daphnia pulex 5-methyl-cytosine 5-hydroxymethyl-cytosine whole genome sequencing epigenetic modifications Cox4 Cand2 Ephx1 |
author_facet |
Dovilė Strepetkaitė Gediminas Alzbutas Eimantas Astromskas Arūnas Lagunavičius Rasa Sabaliauskaitė Kęstutis Arbačiauskas Juozas Lazutka |
author_sort |
Dovilė Strepetkaitė |
title |
Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex |
title_short |
Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex |
title_full |
Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex |
title_fullStr |
Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex |
title_full_unstemmed |
Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex |
title_sort |
analysis of dna methylation and hydroxymethylation in the genome of crustacean daphnia pulex |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2015-12-01 |
description |
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. |
topic |
Daphnia pulex 5-methyl-cytosine 5-hydroxymethyl-cytosine whole genome sequencing epigenetic modifications Cox4 Cand2 Ephx1 |
url |
http://www.mdpi.com/2073-4425/7/1/1 |
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