Cited by 104Epigenetics and DNA MethylationGenomics and Chromatin DynamicsGenetic Syndromes and Imprinting

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Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms

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Turner, J. D., Pelascini, L. P. L., Macedo, J. A., Muller, C. P.·2008·Nucleic Acids Research

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Abstract

The transcription start sites (TSS) and promoters of many genes are located in upstream CpG islands. Methylation within such islands is known for both imprinted and oncogenes, although poorly studied for other genes, especially those with complex CpG islands containing multiple first exons and promoters. The glucocorticoid receptor (GR) CpG island contains seven alternative first exons and their promoters. Here we show for the five GR promoters activated in PBMCs that methylation patterns are highly variable between individuals. The majority of positions were methylated at levels >25% in at least one donor affecting each promoter and TSS. We also examined the evolutionarily conserved transcription factor binding sites (TFBS) using an improved in silico phylogenetic footprinting technique. The majority of these contain methylatable CpG sites, suggesting that methylation may orchestrates alternative first exon usage, silencing and controlling tissue-specific expression. The heterogeneity observed may reflect epigenetic mechanisms of GR fine tuning, programmed by early life environment and events. With 78% of evolutionarily conserved alternative first exons falling into such complex CpG islands, their internal structure and epigenetic modifications are bound to be biologically important, and may be a common transcriptional control mechanism used throughout many phyla.

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Authors: Turner, J. D., Pelascini, L. P. L., Macedo, J. A., & Muller, C. P.
Affiliations: Laboratoire National de Santé (LU)
Corresponding author: Muller, C. P.
ORCID: Turner, J. D.
Macedo, J. A.
Muller, C. P.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2008-11-12
Volume: 36
Issue: 22
Pages: 7207-7218
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkn897
PMC: PMC2602793
OpenAlex: W2169090691
Cited by: 104
References: 56
Citations by year: 2026: 1 · 2025: 1 · 2024: 1 · 2023: 1 · 2022: 5 · 2021: 2 · 2020: 2 · 2018: 6 · 2017: 2 · 2016: 5 · 2015: 12 · 2014: 13 · 2013: 10 · 2012: 19
FWCI: 3.29
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/2.0/uk/ (vor, 2883 d)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
Funders: Deutsche Forschungsgemeinschaft (GRK 1389/1)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
Keywords: glucocorticoid receptor, alternative first exons, promoter methylation, CpG islands, transcription start sites, transcription factor binding sites, phylogenetic footprinting, tissue-specific gene expression, epigenetic regulation, peripheral blood mononuclear cells
MeSH terms: Adult, Aged, Animals, Binding Sites, Cattle, Female, Humans, Male, Middle Aged, Phylogeny, Promoter Regions, Genetic, Receptors, Glucocorticoid, Transcription Factors, CpG Islands, DNA Methylation, Genomics, Transcription Initiation Site, Epigenesis, Genetic, Mice, Rats

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Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms

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