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Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos.

de la Calle Mustienes E, Gómez-Skarmeta JL, Bogdanović O - Genom Data (2015)

Bottom Line: DNA methylation and histone modifications are epigenetic marks implicated in the complex regulation of vertebrate embryogenesis.We observe a strong antagonism between the two epigenetic marks present in CpG islands and their compatibility throughout the bulk of the genome, as previously reported in mammalian ESC lines (Brinkman et al., 2012).Next generation sequencing data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession numbers GSE35050 and GSE70847.

View Article: PubMed Central - PubMed

Affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain.

ABSTRACT
DNA methylation and histone modifications are epigenetic marks implicated in the complex regulation of vertebrate embryogenesis. The cross-talk between DNA methylation and Polycomb-dependent H3K27me3 histone mark has been reported in a number of organisms [1], [2], [3], [4], [5], [6], [7] and both marks are known to be required for proper developmental progression. Here we provide genome-wide DNA methylation (MethylCap-seq) and H3K27me3 (ChIP-seq) maps for three stages (dome, 24 hpf and 48 hpf) of zebrafish (Danio rerio) embryogenesis, as well as all analytical and methodological details associated with the generation of this dataset. We observe a strong antagonism between the two epigenetic marks present in CpG islands and their compatibility throughout the bulk of the genome, as previously reported in mammalian ESC lines (Brinkman et al., 2012). Next generation sequencing data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession numbers GSE35050 and GSE70847.

No MeSH data available.


Related in: MedlinePlus

Genomic profiles of DNA methylation (mC) and H3K27me3 expressed as mean read density in a) H3K27me3 (24 hpf) peaks and b) CpG islands. c) An example of the DNA methylation/H3K27me3 antagonism in the wnt10b/wnt1 locus.
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f0015: Genomic profiles of DNA methylation (mC) and H3K27me3 expressed as mean read density in a) H3K27me3 (24 hpf) peaks and b) CpG islands. c) An example of the DNA methylation/H3K27me3 antagonism in the wnt10b/wnt1 locus.

Mentions: To explore the genomic relationships of DNA methylation and H3K27me3, we superimposed the DNA methylation signal (mapped reads in BED format) from dome, 24 hpf and 48 hpf embryos over H3K27me3 peaks using seqMINER (v1.3.3) [17] with default settings (5 kb upstream/downstream extension, 200 bp read extension, wiggle step = 50 bp, percentile threshold = 75%) (Fig. 3a). DNA methylation and H3K27me3 signals are generally compatible within H3K27me3 24 hpf peaks and similar genomic profiles were detected for H3K27me3 (dome) and H3K27me3 (48 hpf) peaks (Supplementary Fig. 1a-c). Next, we wanted to investigate the relationships between DNA methylation and H3K27me3 in CpG islands, major regulatory elements associated with vertebrate promoters [18]. To that end, we used a dataset that corresponds to CpG islands (also called non-methylated islands or NMIs) identified in 24 hpf zebrafish embryos through CxxC Bio-CAP profiling (GEO entry: GSE43512, sample: GSM1064697) [18]. Average profiles of DNA methylation and H3K27me3 over these regulatory elements identified a strong antagonism between DNA methylation and H3K27me3 at all the examined stages (Fig. 3b, c).


Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos.

de la Calle Mustienes E, Gómez-Skarmeta JL, Bogdanović O - Genom Data (2015)

Genomic profiles of DNA methylation (mC) and H3K27me3 expressed as mean read density in a) H3K27me3 (24 hpf) peaks and b) CpG islands. c) An example of the DNA methylation/H3K27me3 antagonism in the wnt10b/wnt1 locus.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664660&req=5

f0015: Genomic profiles of DNA methylation (mC) and H3K27me3 expressed as mean read density in a) H3K27me3 (24 hpf) peaks and b) CpG islands. c) An example of the DNA methylation/H3K27me3 antagonism in the wnt10b/wnt1 locus.
Mentions: To explore the genomic relationships of DNA methylation and H3K27me3, we superimposed the DNA methylation signal (mapped reads in BED format) from dome, 24 hpf and 48 hpf embryos over H3K27me3 peaks using seqMINER (v1.3.3) [17] with default settings (5 kb upstream/downstream extension, 200 bp read extension, wiggle step = 50 bp, percentile threshold = 75%) (Fig. 3a). DNA methylation and H3K27me3 signals are generally compatible within H3K27me3 24 hpf peaks and similar genomic profiles were detected for H3K27me3 (dome) and H3K27me3 (48 hpf) peaks (Supplementary Fig. 1a-c). Next, we wanted to investigate the relationships between DNA methylation and H3K27me3 in CpG islands, major regulatory elements associated with vertebrate promoters [18]. To that end, we used a dataset that corresponds to CpG islands (also called non-methylated islands or NMIs) identified in 24 hpf zebrafish embryos through CxxC Bio-CAP profiling (GEO entry: GSE43512, sample: GSM1064697) [18]. Average profiles of DNA methylation and H3K27me3 over these regulatory elements identified a strong antagonism between DNA methylation and H3K27me3 at all the examined stages (Fig. 3b, c).

Bottom Line: DNA methylation and histone modifications are epigenetic marks implicated in the complex regulation of vertebrate embryogenesis.We observe a strong antagonism between the two epigenetic marks present in CpG islands and their compatibility throughout the bulk of the genome, as previously reported in mammalian ESC lines (Brinkman et al., 2012).Next generation sequencing data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession numbers GSE35050 and GSE70847.

View Article: PubMed Central - PubMed

Affiliation: Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville 41013, Spain.

ABSTRACT
DNA methylation and histone modifications are epigenetic marks implicated in the complex regulation of vertebrate embryogenesis. The cross-talk between DNA methylation and Polycomb-dependent H3K27me3 histone mark has been reported in a number of organisms [1], [2], [3], [4], [5], [6], [7] and both marks are known to be required for proper developmental progression. Here we provide genome-wide DNA methylation (MethylCap-seq) and H3K27me3 (ChIP-seq) maps for three stages (dome, 24 hpf and 48 hpf) of zebrafish (Danio rerio) embryogenesis, as well as all analytical and methodological details associated with the generation of this dataset. We observe a strong antagonism between the two epigenetic marks present in CpG islands and their compatibility throughout the bulk of the genome, as previously reported in mammalian ESC lines (Brinkman et al., 2012). Next generation sequencing data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession numbers GSE35050 and GSE70847.

No MeSH data available.


Related in: MedlinePlus