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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

Identification of H3K27me3 peaks. a) Number of identified H3K27me3 peaks. b) Example of developmental increase in H3K27me3 peak size. Gray boxes correspond to MACS2 peaks. c) Boxplots (outliers not shown) representing size distributions of H3K27me3 peaks at three developmental stages. The statistical significance of differences in size distributions was assessed by a Kruskal–Wallis test and Dunn's multiple comparison test, (P < 0.05).
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f0010: Identification of H3K27me3 peaks. a) Number of identified H3K27me3 peaks. b) Example of developmental increase in H3K27me3 peak size. Gray boxes correspond to MACS2 peaks. c) Boxplots (outliers not shown) representing size distributions of H3K27me3 peaks at three developmental stages. The statistical significance of differences in size distributions was assessed by a Kruskal–Wallis test and Dunn's multiple comparison test, (P < 0.05).

Mentions: Sites of genomic enrichment (peaks) were called using the MACS algorithm (v2.1.0, https://github.com/taoliu/MACS/) [16] with default settings (callpeak) except for <-g 1.5e9 > and < –broad >. The <-g > option specifies the size of the zebrafish genome whereas the <–broad > option activates broad peak calling i.e. it clusters neighboring enriched regions into a broad region with a defined cut-off. This option is appropriate to use when expecting larger peak sizes which is often the case with H3K27me3 peaks [1], [2], [3], [4], [5], [6], [7]. The analysis resulted in the following number of peaks: N (dome) = 31,988, N (24 hpf) = 11,431, N (48 hpf) = 6436 (Fig. 2a). The peak files for H3K27me3 (dome) and H3K27me3 (48 hpf) are deposited in GEO (GSE70847) whereas the peak file for H3K27me3 (24 hpf) (GEO entry: GSE35050) is provided as Supplementary Table 1. We observe a significant (Kruskal–Wallis test, Dunn's multiple comparison test, P < 0.05) greater size distributions of H3K27me3 (24 hpf) and H3K27me3 (48 hpf) peaks when compared to H3K27me3 (dome) peaks (Fig. 2b, c) consistent with a previous report that demonstrated a developmental increase in H3K27me3 signal during Xenopus tropicalis embryogenesis [6].


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)

Identification of H3K27me3 peaks. a) Number of identified H3K27me3 peaks. b) Example of developmental increase in H3K27me3 peak size. Gray boxes correspond to MACS2 peaks. c) Boxplots (outliers not shown) representing size distributions of H3K27me3 peaks at three developmental stages. The statistical significance of differences in size distributions was assessed by a Kruskal–Wallis test and Dunn's multiple comparison test, (P < 0.05).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0010: Identification of H3K27me3 peaks. a) Number of identified H3K27me3 peaks. b) Example of developmental increase in H3K27me3 peak size. Gray boxes correspond to MACS2 peaks. c) Boxplots (outliers not shown) representing size distributions of H3K27me3 peaks at three developmental stages. The statistical significance of differences in size distributions was assessed by a Kruskal–Wallis test and Dunn's multiple comparison test, (P < 0.05).
Mentions: Sites of genomic enrichment (peaks) were called using the MACS algorithm (v2.1.0, https://github.com/taoliu/MACS/) [16] with default settings (callpeak) except for <-g 1.5e9 > and < –broad >. The <-g > option specifies the size of the zebrafish genome whereas the <–broad > option activates broad peak calling i.e. it clusters neighboring enriched regions into a broad region with a defined cut-off. This option is appropriate to use when expecting larger peak sizes which is often the case with H3K27me3 peaks [1], [2], [3], [4], [5], [6], [7]. The analysis resulted in the following number of peaks: N (dome) = 31,988, N (24 hpf) = 11,431, N (48 hpf) = 6436 (Fig. 2a). The peak files for H3K27me3 (dome) and H3K27me3 (48 hpf) are deposited in GEO (GSE70847) whereas the peak file for H3K27me3 (24 hpf) (GEO entry: GSE35050) is provided as Supplementary Table 1. We observe a significant (Kruskal–Wallis test, Dunn's multiple comparison test, P < 0.05) greater size distributions of H3K27me3 (24 hpf) and H3K27me3 (48 hpf) peaks when compared to H3K27me3 (dome) peaks (Fig. 2b, c) consistent with a previous report that demonstrated a developmental increase in H3K27me3 signal during Xenopus tropicalis embryogenesis [6].

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