ArticleEpigenetics2013
Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing.
Article in Epigenetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
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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.
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Who cites it
43 citing papers in PubMed, 70 citations in OpenAlex.
- Epigenetic Profiling for Early Detection and Treatment Response Monitoring in Non-Small Cell Lung Cancer: Protocol for a Prospective Translational Biomarker Study.JMIR research protocols · 2026Article
- Methods for Investigating the Sperm Epigenome.Advances in experimental medicine and biology · 2026Review
- Review
- Application of DNA Methylome Analysis to Patients with ME/CFS.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Strengths and limitations of reduced representation bisulfite sequencing (RRBS) in the perspective of DNA methylation analysis in fish: a case-study on rainbow trout spermatozoa.Fish physiology and biochemistry · 2024Article
- Technologies and applications of single-cell DNA methylation sequencing.Theranostics · 2023Review
- A Cautionary Tale of Sexing by Methylation: Hybrid Bisulfite-Conversion Sequencing of Immunoprecipitated Methylated DNA inAnimals : an open access journal from MDPI · 2022Article
- Genome-wide DNA methylation of the liver reveals delayed effects of early-life exposure to 17-α-ethinylestradiol in the self-fertilizing mangrove rivulus.Epigenetics · 2022Article
- Generating Sequencing-Based DNA Methylation Maps from Low DNA Input Samples.Methods in molecular biology (Clifton, N.J.) · 2022Article
- DNA methylation and expression of estrogen receptor alpha in fathead minnows exposed to 17α-ethynylestradiol.Aquatic toxicology (Amsterdam, Netherlands) · 2021Article
- Epigenetic Regulation and Environmental Sex Determination in Cichlid Fishes.Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation · 2021Review
- A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons.Frontiers in cell and developmental biology · 2021Article
- Changes in DNA methylation profiles of myalgic encephalomyelitis/chronic fatigue syndrome patients reflect systemic dysfunctions.Clinical epigenetics · 2020Article
- Extensive Inter-Cyst DNA Methylation Variation in Autosomal Dominant Polycystic Kidney Disease Revealed by Genome Scale Sequencing.Frontiers in genetics · 2020Article
- DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation.BMC genomics · 2019Article
- IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis.Genome biology · 2019Article
- Characterisation of DNA methylation changes in EBF3 and TBC1D16 associated with tumour progression and metastasis in multiple cancer types.Clinical epigenetics · 2019Article
- Characterization of Genetic and Epigenetic Variation in Sperm and Red Blood Cells from Adult Hatchery and Natural-Origin Steelhead,G3 (Bethesda, Md.) · 2018Article
- Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species.Epigenetics & chromatin · 2018Article
- Contrasting effects of acute and chronic stress on the transcriptome, epigenome, and immune response of Atlantic salmon.Epigenetics · 2018Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reduced representation bisulfite sequencing (RRBS) has been used to profile DNA methylation patterns in mammalian genomes such as human, mouse and rat. The methylome of the zebrafish, an important animal model, has not yet been characterized at base-pair resolution using RRBS. Therefore, we evaluated the technique of RRBS in this model organism by generating four single-nucleotide resolution DNA methylomes of adult zebrafish brain. We performed several simulations to show the distribution of fragments and enrichment of CpGs in different in silico reduced representation genomes of zebrafish. Four RRBS brain libraries generated 98 million sequenced reads and had higher frequencies of multiple mapping than equivalent human RRBS libraries. The zebrafish methylome indicates there is higher global DNA methylation in the zebrafish genome compared with its equivalent human methylome. This observation was confirmed by RRBS of zebrafish liver. High coverage CpG dinucleotides are enriched in CpG island shores more than in the CpG island core. We found that 45% of the mapped CpGs reside in gene bodies, and 7% in gene promoters. This analysis provides a roadmap for generating reproducible base-pair level methylomes for zebrafish using RRBS and our results provide the first evidence that RRBS is a suitable technique for global methylation analysis in zebrafish.
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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.