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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

Sequencing output and mapping efficiency for MethylCap-seq and H3K27me3 ChIP-seq data expressed as N reads (× 106).
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f0005: Sequencing output and mapping efficiency for MethylCap-seq and H3K27me3 ChIP-seq data expressed as N reads (× 106).

Mentions: MethylCap-seq and ChIP-seq libraries were sequenced on a HiSeq 2000 Sequencing System (Illumina, CASAVA v1.8.2), generating an average of 18.6 million reads per sample (Fig. 1). The sequenced data were mapped to the zebrafish (danRer7/zv9) genome using Bowtie2 (v2.1.0) [11] with default settings (end-to-end alignment) resulting in an average mapping efficiency of 92% (Fig. 1). Mapped reads in SAM format were converted to BAM using Samtools (v0.1.19) < view >, < sort >, and < index > commands [12]. The aligned reads in BAM format were filtered for duplicates using Samtools (v0.1.19) < rmdup > (-r) command (Fig. 1). After duplicate removal, BAM files were converted to BED format using Bedtools (v2.18) < bamToBed > command [13]. The reads in BED format were summed in 10 bp intervals to create a WIG file using the sum_bed.pl script as previously described [14] and visualized in the UCSC genome browser [15].


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)

Sequencing output and mapping efficiency for MethylCap-seq and H3K27me3 ChIP-seq data expressed as N reads (× 106).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0005: Sequencing output and mapping efficiency for MethylCap-seq and H3K27me3 ChIP-seq data expressed as N reads (× 106).
Mentions: MethylCap-seq and ChIP-seq libraries were sequenced on a HiSeq 2000 Sequencing System (Illumina, CASAVA v1.8.2), generating an average of 18.6 million reads per sample (Fig. 1). The sequenced data were mapped to the zebrafish (danRer7/zv9) genome using Bowtie2 (v2.1.0) [11] with default settings (end-to-end alignment) resulting in an average mapping efficiency of 92% (Fig. 1). Mapped reads in SAM format were converted to BAM using Samtools (v0.1.19) < view >, < sort >, and < index > commands [12]. The aligned reads in BAM format were filtered for duplicates using Samtools (v0.1.19) < rmdup > (-r) command (Fig. 1). After duplicate removal, BAM files were converted to BED format using Bedtools (v2.18) < bamToBed > command [13]. The reads in BED format were summed in 10 bp intervals to create a WIG file using the sum_bed.pl script as previously described [14] and visualized in the UCSC genome browser [15].

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