ArticleBMC genomics2016
Gene and transposable element methylation in great tit (Parus major) brain and blood.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 70 citations in OpenAlex.
- Epigenetic signatures of migratory orientation in a songbird hybrid zone.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2026Article
- Cooperative care influences genome-wide levels of DNA methylation in nestling chestnut-crowned babblers.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2026Article
- Seasonal timing in a changing world: the epigenetic link between environment and reproduction across taxa.Environmental epigenetics · 2026Article
- Non-CG DNA methylation in animal genomes.Nature genetics · 2025Review
- Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics.Molecular ecology resources · 2025Article
- The CpG Landscape of Protein Coding DNA in Vertebrates.Evolutionary applications · 2025Article
- Manipulation of a social signal affects DNA methylation of a stress-related gene in a free-living bird.The Journal of experimental biology · 2024Article
- Genetic and epigenetic differentiation in response to genomic selection for avian lay date.Evolutionary applications · 2024Article
- Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring FBMC biology · 2024Article
- Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery.Genome biology and evolution · 2024Article
- The genome of a globally invasive passerine, the common myna, Acridotheres tristis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Epigenetic changes to gene pathways linked to male fertility in ex situ black-footed ferrets.Evolutionary applications · 2024Article
- From maternal glucocorticoid and thyroid hormones to epigenetic regulation of offspring gene expression: An experimental study in a wild bird species.Evolutionary applications · 2023Article
- Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects.Molecular biology and evolution · 2023Article
- Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines.iScience · 2023Article
- Infection by a helminth parasite is associated with changes in DNA methylation in the house sparrow.Ecology and evolution · 2022Article
- The effect of experimental lead pollution on DNA methylation in a wild bird population.Epigenetics · 2022Article
- Performance of methods to detect genetic variants from bisulphite sequencing data in a non-model species.Molecular ecology resources · 2022Article
- Epigenetics and the city: Non-parallel DNA methylation modifications across pairs of urban-forest Great tit populations.Evolutionary applications · 2022Article
- Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird.Molecular ecology · 2021Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStudies on vertebrate DNA methylomes have revealed a regulatory role of tissue specific DNA methylation in relation to gene expression. However, it is not well known how tissue-specific methylation varies between different functional and structural components of genes and genomes. Using whole-genome bisulfite sequencing data we here describe both CpG and non-CpG methylation profiles of whole blood and brain tissue in relation to gene features, CpG-islands (CGIs), transposable elements (TE), and their functional roles in an ecological model species, the great tit (Parus major).
resultsWe show that hypomethylation at the transcription start site (TSS) is enriched in genes with functional classes that relate directly to processes specific to each tissue type. We find that 6877 (~21 %) of the CGIs are differentially methylated between blood and brain, of which 1186 and 2055 are annotated to promoter and intragenic regions, respectively. We observe that CGI methylation in promoter regions is more conserved between tissues compared to CGI methylation in intra and inter-genic regions. Differentially methylated CGIs in promoter and intragenic regions are overrepresented in genomic loci linked to development, suggesting a distinct role for CGI methylation in regulating expression during development. Additionally, we find significant non-CpG methylation in brain but not in blood with a strong preference for methylation at CpA dinucleotide sites. Finally, CpG hypermethylation of TEs is significantly stronger in brain compared to blood, but does not correlate with TE activity. Surprisingly, TEs showed significant hypomethylation in non-CpG contexts which was negatively correlated with TE expression.
conclusionThe discovery that TSS methylation levels are directly linked to functional classes related to each tissue provides new insights in the regulatory role of DNA-methylation patterns. The dominant sequence motifs for brain non-CpG methylation, similar to those found in mammals, suggests that a conserved non-CpG regulatory mechanism was already present in the amniote ancestor. The negative correlation between brain non-CpG methylation and TE activity (not found for CpG methylation) suggests that non-CpG is the dominant regulatory form of methylation in TE silencing.
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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.