ArticleGenome biology2016
Enhancers reside in a unique epigenetic environment during early zebrafish development.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed.
- Article
- Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks.Genome biology · 2025Article
- H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition.PLoS biology · 2025Article
- Article
- Comprehensive pan-cancer analysis reveals NTN1 as an immune infiltrate risk factor and its potential prognostic value in SKCM.Scientific reports · 2025Article
- Comprehensive pan-cancer analysis reveals CCDC58 as a carcinogenic factor related to immune infiltration.Apoptosis : an international journal on programmed cell death · 2024Article
- Enhancer-promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation.Nature genetics · 2024Article
- Upregulation of FAM50A promotes cancer development.Medical oncology (Northwood, London, England) · 2023Article
- Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models.International journal of molecular sciences · 2022Review
- Methylome inheritance and enhancer dememorization reset an epigenetic gate safeguarding embryonic programs.Science advances · 2021Article
- The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo.Nature communications · 2021Article
- Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain.Frontiers in cell and developmental biology · 2021Article
- Article
- Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation.PLoS genetics · 2020Article
- Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development.Cell reports · 2018Article
- TALE factors use two distinct functional modes to control an essential zebrafish gene expression program.eLife · 2018Article
- Enhancer DNA methylation in acute myeloid leukemia and myelodysplastic syndromes.Cellular and molecular life sciences : CMLS · 2018Review
- Bloody Zebrafish: Novel Methods in Normal and Malignant Hematopoiesis.Frontiers in cell and developmental biology · 2018Article
- Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio).PloS one · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEnhancers, not promoters, are the most dynamic in their DNA methylation status throughout development and differentiation. Generally speaking, enhancers that are primed to or actually drive gene expression are characterized by relatively low levels of DNA methylation (hypo-methylation), while inactive enhancers display hyper-methylation of the underlying DNA. The direct functional significance of the DNA methylation state of enhancers is, however, unclear for most loci.
resultsIn contrast to conventional epigenetic interactions at enhancers, we find that DNA methylation status and enhancer activity during early zebrafish development display very unusual correlation characteristics: hypo-methylation is a unique feature of primed enhancers whereas active enhancers are generally hyper-methylated. The hypo-methylated enhancers that we identify (hypo-enhancers) are enriched close to important transcription factors that act later in development. Interestingly, hypo-enhancers are de-methylated shortly before the midblastula transition and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers do become active at later developmental stages and that they are physically associated with the transcriptional start site of target genes, irrespective of target gene activity.
conclusionsWe demonstrate that early development in zebrafish embodies a time window characterized by non-canonical DNA methylation-enhancer relationships, including global DNA hypo-methylation of inactive enhancers and DNA hyper-methylation of active enhancers.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.