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| Status |
Public on Feb 13, 2015 |
| Title |
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MRE-seq) |
| Organism |
Danio rerio |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis.
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| |
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| Overall design |
MRE profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.
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| |
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| Contributor(s) |
Lee H, Johnson SL, Wang T |
| Citation(s) |
25697895 |
| Submission date |
Nov 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hyung Joo Lee |
| Organization name |
Washington University School of Medicine
|
| Department |
Department of Genetics
|
| Lab |
Ting Wang
|
| Street address |
4515 McKinley Avenue
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
|
| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE52706 |
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos |
|
| Relations |
| BioProject |
PRJNA229866 |
| SRA |
SRP033302 |
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