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CTCF cis-regulates trinucleotide repeat instability in an epigenetic manner: a novel basis for mutational hot spot determination.

Libby RT, Hagerman KA, Pineda VV, Lau R, Cho DH, Baccam SL, Axford MM, Cleary JD, Moore JM, Sopher BL, Tapscott SJ, Filippova GN, Pearson CE, La Spada AR - PLoS Genet. (2008)

Bottom Line: At least 25 inherited disorders in humans result from microsatellite repeat expansion.We found that CTCF binding-site mutation promotes triplet repeat instability both in the germ line and in somatic tissues, and that CpG methylation of CTCF binding sites can further destabilize triplet repeat expansions.As CTCF binding sites are associated with a number of highly unstable repeat loci, our findings suggest a novel basis for demarcation and regulation of mutational hot spots and implicate CTCF in the modulation of genetic repeat instability.

View Article: PubMed Central - PubMed

Affiliation: Department of Laboratory Medicine, University of Washington Medical Center, Seattle, WA, USA.

ABSTRACT
At least 25 inherited disorders in humans result from microsatellite repeat expansion. Dramatic variation in repeat instability occurs at different disease loci and between different tissues; however, cis-elements and trans-factors regulating the instability process remain undefined. Genomic fragments from the human spinocerebellar ataxia type 7 (SCA7) locus, containing a highly unstable CAG tract, were previously introduced into mice to localize cis-acting "instability elements," and revealed that genomic context is required for repeat instability. The critical instability-inducing region contained binding sites for CTCF -- a regulatory factor implicated in genomic imprinting, chromatin remodeling, and DNA conformation change. To evaluate the role of CTCF in repeat instability, we derived transgenic mice carrying SCA7 genomic fragments with CTCF binding-site mutations. We found that CTCF binding-site mutation promotes triplet repeat instability both in the germ line and in somatic tissues, and that CpG methylation of CTCF binding sites can further destabilize triplet repeat expansions. As CTCF binding sites are associated with a number of highly unstable repeat loci, our findings suggest a novel basis for demarcation and regulation of mutational hot spots and implicate CTCF in the modulation of genetic repeat instability.

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Model for CTCF regulation of CAG repeat instability.Non-expanded CAG repeat is stable, as CTCF is bound to adjacent site. Upon repeat expansion, chromatin environment and DNA structure of repeat region is altered, permitting instability. Loss of CTCF binding at adjacent CTCF binding site, either by CpG methylation or CTCF binding site mutation, further promotes repeat instability.
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pgen-1000257-g005: Model for CTCF regulation of CAG repeat instability.Non-expanded CAG repeat is stable, as CTCF is bound to adjacent site. Upon repeat expansion, chromatin environment and DNA structure of repeat region is altered, permitting instability. Loss of CTCF binding at adjacent CTCF binding site, either by CpG methylation or CTCF binding site mutation, further promotes repeat instability.

Mentions: We have identified a CTCF binding site as the first cis-element regulating CAG tract instability at a disease locus. Furthermore, binding of the trans-factor CTCF to this cis-element influences CAG instability, and this interaction is epigenetically regulated. At the SCA7 locus and four other CAG/CTG repeat loci known to display pronounced anticipation, functional CTCF binding sites occur immediately adjacent to the repeats, and CTCF binding can affect DNA structure and chromatin packaging at such loci, and elsewhere [14], [23]–[26]. Although an interplay between GC-content, CpG islands, epigenetic modification, chromatin structure, repeat length, and unusual DNA conformation has long been postulated to underlie trinucleotide repeat instability [11], [27]–[29], the mechanistic basis of this process is ill-defined. CTCF insulator and genomic imprinting functions are subject to epigenetic regulation, as methylation status is a key determinant of CTCF action at certain “differentially methylated domains” and methylation changes at CTCF binding sites are linked to oncogenic transformation [16],[18]. At the SCA7 locus, methylation status of the CTCF-I binding site may be similarly important for its ability to tamp down repeat instability, as hypermethylation of the CTCF-I site was associated with a dramatic enhancement of somatic instability in the SCA7 genomic fragment transgenic mouse model. Thus, inability to bind CTCF at sites adjacent to CAG tracts, because of binding site mutation or CpG methylation in the case of the SCA7-CTCF-I site, can promote further expansion of disease-length CAG repeat alleles (Figure 5).


CTCF cis-regulates trinucleotide repeat instability in an epigenetic manner: a novel basis for mutational hot spot determination.

Libby RT, Hagerman KA, Pineda VV, Lau R, Cho DH, Baccam SL, Axford MM, Cleary JD, Moore JM, Sopher BL, Tapscott SJ, Filippova GN, Pearson CE, La Spada AR - PLoS Genet. (2008)

Model for CTCF regulation of CAG repeat instability.Non-expanded CAG repeat is stable, as CTCF is bound to adjacent site. Upon repeat expansion, chromatin environment and DNA structure of repeat region is altered, permitting instability. Loss of CTCF binding at adjacent CTCF binding site, either by CpG methylation or CTCF binding site mutation, further promotes repeat instability.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC2573955&req=5

pgen-1000257-g005: Model for CTCF regulation of CAG repeat instability.Non-expanded CAG repeat is stable, as CTCF is bound to adjacent site. Upon repeat expansion, chromatin environment and DNA structure of repeat region is altered, permitting instability. Loss of CTCF binding at adjacent CTCF binding site, either by CpG methylation or CTCF binding site mutation, further promotes repeat instability.
Mentions: We have identified a CTCF binding site as the first cis-element regulating CAG tract instability at a disease locus. Furthermore, binding of the trans-factor CTCF to this cis-element influences CAG instability, and this interaction is epigenetically regulated. At the SCA7 locus and four other CAG/CTG repeat loci known to display pronounced anticipation, functional CTCF binding sites occur immediately adjacent to the repeats, and CTCF binding can affect DNA structure and chromatin packaging at such loci, and elsewhere [14], [23]–[26]. Although an interplay between GC-content, CpG islands, epigenetic modification, chromatin structure, repeat length, and unusual DNA conformation has long been postulated to underlie trinucleotide repeat instability [11], [27]–[29], the mechanistic basis of this process is ill-defined. CTCF insulator and genomic imprinting functions are subject to epigenetic regulation, as methylation status is a key determinant of CTCF action at certain “differentially methylated domains” and methylation changes at CTCF binding sites are linked to oncogenic transformation [16],[18]. At the SCA7 locus, methylation status of the CTCF-I binding site may be similarly important for its ability to tamp down repeat instability, as hypermethylation of the CTCF-I site was associated with a dramatic enhancement of somatic instability in the SCA7 genomic fragment transgenic mouse model. Thus, inability to bind CTCF at sites adjacent to CAG tracts, because of binding site mutation or CpG methylation in the case of the SCA7-CTCF-I site, can promote further expansion of disease-length CAG repeat alleles (Figure 5).

Bottom Line: At least 25 inherited disorders in humans result from microsatellite repeat expansion.We found that CTCF binding-site mutation promotes triplet repeat instability both in the germ line and in somatic tissues, and that CpG methylation of CTCF binding sites can further destabilize triplet repeat expansions.As CTCF binding sites are associated with a number of highly unstable repeat loci, our findings suggest a novel basis for demarcation and regulation of mutational hot spots and implicate CTCF in the modulation of genetic repeat instability.

View Article: PubMed Central - PubMed

Affiliation: Department of Laboratory Medicine, University of Washington Medical Center, Seattle, WA, USA.

ABSTRACT
At least 25 inherited disorders in humans result from microsatellite repeat expansion. Dramatic variation in repeat instability occurs at different disease loci and between different tissues; however, cis-elements and trans-factors regulating the instability process remain undefined. Genomic fragments from the human spinocerebellar ataxia type 7 (SCA7) locus, containing a highly unstable CAG tract, were previously introduced into mice to localize cis-acting "instability elements," and revealed that genomic context is required for repeat instability. The critical instability-inducing region contained binding sites for CTCF -- a regulatory factor implicated in genomic imprinting, chromatin remodeling, and DNA conformation change. To evaluate the role of CTCF in repeat instability, we derived transgenic mice carrying SCA7 genomic fragments with CTCF binding-site mutations. We found that CTCF binding-site mutation promotes triplet repeat instability both in the germ line and in somatic tissues, and that CpG methylation of CTCF binding sites can further destabilize triplet repeat expansions. As CTCF binding sites are associated with a number of highly unstable repeat loci, our findings suggest a novel basis for demarcation and regulation of mutational hot spots and implicate CTCF in the modulation of genetic repeat instability.

Show MeSH
Related in: MedlinePlus