title: Stable DNA methylation boundaries and expanded trinucleotide repeats: role of DNA insertions.
abstract: The human genome segment upstream of the FMR1 (fragile X mental retardation 1) gene (Xq27.3) contains several genetic signals, among them is a DNA methylation boundary that is located 65-70 CpGs upstream of the CGG repeat. In fragile X syndrome (FXS), the boundary is lost, and the promoter is inactivated by methylation spreading. Here we document boundary stability in spite of critical expansions of the CGG trinucleotide repeat in male or female premutation carriers and in high functioning males (HFMs). HFMs carry a full CGG repeat expansion but exhibit an unmethylated promoter and lack the FXS phenotype. The boundary is also stable in Turner (45, X) females. A CTCF-binding site is located slightly upstream of the methylation boundary and carries a unique G-to-A polymorphism (single nucleotide polymorphism), which occurs 3.6 times more frequently in genomes with CGG expansions. The increased frequency of this single nucleotide polymorphism might have functional significance. In CGG expansions, the CTCF region does not harbor additional mutations. In FXS individuals and often in cells transgenomic for EBV (Epstein Barr Virus) DNA or for the telomerase gene, the large number of normally methylated CpGs in the far-upstream region of the boundary is decreased about 4-fold. A methylation boundary is also present in the human genome segment upstream of the HTT (huntingtin) promoter (4p16.3) and is stable both in normal and Huntington disease chromosomes. Hence, the vicinity of an expanded repeat does not per se compromise methylation boundaries. Methylation boundaries exert an important function as promoter safeguards.
authors.affiliation: Institute for Clinical and Molecular Virology, Erlangen University Medical School, D-91054 Erlangen, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Naumann
authors.affiliation: Institute for Human Genetics, Erlangen University Medical School, D-91054 Erlangen, Germany.
authors.forename: Cornelia
authors.initials: C
authors.lastname: Kraus
authors.affiliation: Department of Clinical Genetics, Erasmus University Medical School, 3000 DR Rotterdam, The Netherlands.
authors.forename: André
authors.initials: A
authors.lastname: Hoogeveen
authors.affiliation: Department of Biostatistics and Statistics, University of California, Los Angeles, CA 90095, USA.
authors.forename: Christina M
authors.initials: CM
authors.lastname: Ramirez
authors.affiliation: Institute for Clinical and Molecular Virology, Erlangen University Medical School, D-91054 Erlangen, Germany; Institute of Genetics, University of Cologne, D-50674 Cologne, Germany. Electronic address: walter.doerfler@viro.med.uni-erlangen.de.
authors.forename: Walter
authors.initials: W
authors.lastname: Doerfler
mesh_terms: D001665:Binding Sites; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D051860:Fragile X Messenger Ribonucleoprotein 1 / Q000235:genetics; D005600:Fragile X Syndrome / Q000235:genetics*; D006801:Humans; D000071058:Huntingtin Protein; D008297:Male; D009419:Nerve Tissue Proteins / Q000235:genetics; D011401:Promoter Regions, Genetic; D019680:Trinucleotide Repeat Expansion; D014424:Turner Syndrome / Q000235:genetics
chemical_list: D051860:Fragile X Messenger Ribonucleoprotein 1; D000071058:Huntingtin Protein; D009419:Nerve Tissue Proteins; C497683:FMR1 protein, human; C086055:HTT protein, human
keywords: FMR1 and HTT promoters and DNA methylation boundaries; loss of boundary in fragile X syndrome (FXS); loss of far-upstream methylation upon foreign DNA insertions; safeguard against de novo methylation; stable boundaries even in trinucleotide repeat expansions