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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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Autores principales: Strepetkaitė, Dovilė, Alzbutas, Gediminas, Astromskas, Eimantas, Lagunavičius, Arūnas, Sabaliauskaitė, Rasa, Arbačiauskas, Kęstutis, Lazutka, Juozas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728381/
https://www.ncbi.nlm.nih.gov/pubmed/26729172
http://dx.doi.org/10.3390/genes7010001
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author Strepetkaitė, Dovilė
Alzbutas, Gediminas
Astromskas, Eimantas
Lagunavičius, Arūnas
Sabaliauskaitė, Rasa
Arbačiauskas, Kęstutis
Lazutka, Juozas
author_facet Strepetkaitė, Dovilė
Alzbutas, Gediminas
Astromskas, Eimantas
Lagunavičius, Arūnas
Sabaliauskaitė, Rasa
Arbačiauskas, Kęstutis
Lazutka, Juozas
author_sort Strepetkaitė, Dovilė
collection PubMed
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.
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spelling pubmed-47283812016-02-08 Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex Strepetkaitė, Dovilė Alzbutas, Gediminas Astromskas, Eimantas Lagunavičius, Arūnas Sabaliauskaitė, Rasa Arbačiauskas, Kęstutis Lazutka, Juozas Genes (Basel) Communication 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. MDPI 2015-12-31 /pmc/articles/PMC4728381/ /pubmed/26729172 http://dx.doi.org/10.3390/genes7010001 Text en © 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons by Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Communication
Strepetkaitė, Dovilė
Alzbutas, Gediminas
Astromskas, Eimantas
Lagunavičius, Arūnas
Sabaliauskaitė, Rasa
Arbačiauskas, Kęstutis
Lazutka, Juozas
Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex
title 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_short 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
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728381/
https://www.ncbi.nlm.nih.gov/pubmed/26729172
http://dx.doi.org/10.3390/genes7010001
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