A Distinct DNA-Methylation Boundary in the 5′- Upstream Sequence of the FMR1 Promoter Binds Nuclear Proteins and Is Lost in Fragile X Syndrome
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We have discovered a distinct DNA-methylation boundary at a site between 650 and 800 nucleotides upstream of the CGG repeat in the first exon of the human FMR1 gene. This boundary, identified by bisulfite sequencing, is present in all human cell lines and cell types, irrespective of age, gender, and developmental stage. The same boundary is found also in different mouse tissues, although sequence homology between human and mouse in this region is only 46.7%. This boundary sequence, in both the unmethylated and the CpG-methylated modes, binds specifically to nuclear proteins from human cells. We interpret this boundary as carrying a specific chromatin structure that delineates a hypermethylated area in the genome from the unmethylated FMR1 promoter and protecting it from the spreading of DNA methylation. In individuals with the fragile X syndrome (FRAXA), the methylation boundary is lost; methylation has penetrated into the FMR1 promoter and inactivated the FMR1 gene. In one FRAXA genome, the upstream terminus of the methylation boundary region exhibits decreased methylation as compared to that of healthy individuals. This finding suggests changes in nucleotide sequence and chromatin structure in the boundary region of this FRAXA individual. In the completely de novo methylated FMR1 promoter, there are isolated unmethylated CpG dinucleotides that are, however, not found when the FMR1 promoter and upstream sequences are methylated in vitro with the bacterial M-SssI DNA methyltransferase. They may arise during de novo methylation only in DNA that is organized in chromatin and be due to the binding of specific proteins.
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In fragile X syndrome, cytosines up to about 1 kb upstream of the CGG repeats, including the FMR1 promoter, are methylated.
“In FXS, cytosines located approximately up to 1-kb upstream of the CGG repeat sequences, including the FMR1 promoter, are methylated (14,15).”
From Fragile X syndrome: causes, diagnosis, mechanisms, and therapeutics (2012) · cites this paper as [15]
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Fragile X syndrome: causes, diagnosis, mechanisms, and therapeutics
Bagni, C., Tassone, F., Neri, G., & Hagerman, R. (2012) · Journal of Clinical Investigation · doi:10.1172/jci63141 · Cited by 321 · see citing works
- Authors
- Naumann, A., Hochstein, N., Weber, S., Fanning, E., & Doerfler, W.
- Affiliations
- Friedrich-Alexander-Universität Erlangen-Nürnberg (DE)
- Vanderbilt University (US)
- University of Cologne (DE)
- Corresponding author
- Doerfler, Walter
- ORCID
- Doerfler, Walter
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2009-11
- Volume
- 85
- Issue
- 5
- Pages
- 606-616
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC2775827
- OpenAlex
- W2089579982
- Cited by
- 107
- References
- 44
- Citations by year
- 2026: 2 · 2024: 6 · 2023: 6 · 2022: 5 · 2021: 6 · 2020: 4 · 2019: 4 · 2018: 9 · 2017: 5 · 2016: 10 · 2015: 5 · 2014: 8 · 2013: 11 · 2012: 7
- FWCI
- 4.87
- Type
- journal article
- Language
- en
- Update notices
- erratum (2010-01-08)
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- FRAXA Research Foundation
- National Institute of General Medical Sciences (GM-52948, R01GM052948)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- 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
- Keywords
- FMR1 gene, fragile X syndrome, DNA methylation, promoter, CGG repeat, nuclear protein binding, chromatin structure, CpG methylation, de novo methylation, gene silencing
- MeSH terms
- Adult, Animals, Base Sequence, Cell Line, Cells, Cultured, DNA, Female, Fibroblasts, Fragile X Syndrome, Humans, Male, Molecular Sequence Data, Nuclear Proteins, Promoter Regions, Genetic, Protein Binding, Sulfites, Genome, Human, Genome, Sequence Analysis, DNA, CpG Islands, DNA Methylation, 5' Untranslated Regions, HCT116 Cells, Mice, Fragile X Messenger Ribonucleoprotein 1, Fragile X Mental Retardation Protein
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