ArticleNature communications2015
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos.
Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 96 citations in OpenAlex.
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- DNA Methylation Dynamics in Development and Disease: Insights from Zebrafish Models.Biomedicines · 2026Review
- Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo.Cell reports · 2025Article
- H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition.PLoS biology · 2025Article
- tet2 and tet3 regulate cell fate specification and differentiation events during retinal development.bioRxiv : the preprint server for biology · 2024Article
- DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.GigaScience · 2024Article
- Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species.Nucleic acids research · 2023Article
- Review
- Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress.BMC genomics · 2022Article
- Epigenomic analysis reveals prevalent contribution of transposable elements toGenome research · 2022Article
- Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models.International journal of molecular sciences · 2022Review
- Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish.Genome biology · 2021Article
- AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis.Genomics, proteomics & bioinformatics · 2021Article
- A comprehensive epigenome atlas reveals DNA methylation regulating skeletal muscle development.Nucleic acids research · 2021Article
- Developmental remodelling of non-CG methylation at satellite DNA repeats.Nucleic acids research · 2020Article
- Establishment and function of chromatin modification at enhancers.Open biology · 2020Article
- MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.Genome biology · 2020Article
- Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation.Nucleic acids research · 2020Article
- Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility.Genome biology · 2020Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.