ArticleGenome research2018
Evolutionary expansion of DNA hypomethylation in the mammalian germline genome.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 25 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.
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Who cites it
25 citing papers in PubMed, 45 citations in OpenAlex.
- Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Determinants of de novo mutations in extended pedigrees of 43 dog breeds.Genome biology · 2025Article
- rDNA Copy Number Variation and Methylation in Human and Mouse Sperm.International journal of molecular sciences · 2025Article
- Unraveling the DNA methylation landscape in dog blood across breeds.BMC genomics · 2024Article
- Age-related and species-specific methylation changes in the protein-coding marmoset sperm epigenome.Aging cell · 2024Article
- High prevalence of PRDM9-independent recombination hotspots in placental mammals.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Iterative oxidation by TET1 is required for reprogramming of imprinting control regions and patterning of mouse sperm hypomethylated regions.Developmental cell · 2024Article
- Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats.Molecular biology and evolution · 2024Article
- DNA methylation networks underlying mammalian traits.Science (New York, N.Y.) · 2023Article
- Global effects of identity and aging on the human sperm methylome.Clinical epigenetics · 2023Article
- Review
- Predicting male fertility from the sperm methylome: application to 120 bulls with hundreds of artificial insemination records.Clinical epigenetics · 2022Article
- A comparative methylome analysis reveals conservation and divergence of DNA methylation patterns and functions in vertebrates.BMC biology · 2022Article
- Species-Specific Paternal Age Effects and Sperm Methylation Levels of Developmentally Important Genes.Cells · 2022Article
- The epigenome of male germ cells and the programming of phenotypes in cattle.Animal frontiers : the review magazine of animal agriculture · 2021Article
- An Analysis of Methylome Evolution in Primates.Molecular biology and evolution · 2021Article
- Comparative Analyses of Sperm DNA Methylomes Among Three Commercial Pig Breeds Reveal Vital Hypomethylated Regions Associated With Spermatogenesis and Embryonic Development.Frontiers in genetics · 2021Article
- Gestational arsenic exposure induces site-specific DNA hypomethylation in active retrotransposon subfamilies in offspring sperm in mice.Epigenetics & chromatin · 2020Article
- Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo.Nature communications · 2020Article
- Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns.BMC biology · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
Abstract
DNA methylation in the germline is among the most important factors influencing the evolution of mammalian genomes. Yet little is known about its evolutionary rate or the fraction of the methylome that has undergone change. We compared whole-genome, single-CpG DNA methylation profiles in sperm of seven species-human, chimpanzee, gorilla, rhesus macaque, mouse, rat, and dog-to investigate epigenomic evolution. We developed a phylo-epigenetic model for DNA methylation that accommodates the correlation of states at neighboring sites and allows for inference of ancestral states. Applying this model to the sperm methylomes, we uncovered an overall evolutionary expansion of the hypomethylated fraction of the genome, driven both by the birth of new hypomethylated regions and by extensive widening of hypomethylated intervals in ancestral species. This expansion shows strong lineage-specific aspects, most notably that hypomethylated intervals around transcription start sites have evolved to be considerably wider in primates and dog than in rodents, whereas rodents show evidence of a greater trend toward birth of new hypomethylated regions. Lineage-specific hypomethylated regions are enriched near sets of genes with common developmental functions and significant overlap across lineages. Rodent-specific and primate-specific hypomethylated regions are enriched for binding sites of similar transcription factors, suggesting that the plasticity accommodated by certain regulatory factors is conserved, despite substantial change in the specific sites of regulation. Overall our results reveal substantial global epigenomic change in mammalian sperm methylomes and point to a divergence in
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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.