Background Trinucleotide repeat expansion is the cause of at least 25 inherited neurological disorders, including Huntington's disease (HD), fragile X mental retardation, and myotonic dystrophy (DM1). An interesting feature of repeat expansion mutations is that they are genetically unstable, meaning that increased disease severity and decreased age-of-onset are observed as the mutation is transmitted from parent to offspring. Previous studies on spinocerebellar ataxia 7 and DM1 have identified the cis-acting DNA element CTCF to be implicated in repeat expansion. CTCF is a regulatory factor implicated in genomic imprinting, chromatin remodelling, and DNA conformation change. Mutation or CpG methylation of CTCF binding sites promotes triplet repeat instability both in germ line and somatic tissue.

Aim As binding sites for CTCF are associated with many highly unstable repeat loci, CTCF may also be involved in regulating genetic instability in HD.

Methods We have in silico identified putative CTCF binding sites in the HTT locus. Confirmation of these CTCF binding sites has been achieved by electrophoretic mobility shift assays. Chromatin immunoprecipitation was performed with a CTCF antibody followed by deep sequencing (ChIP-Seq) in two HD patient fibroblasts and two wild-type control cell lines.

Results Using electrophoretic mobility shift assay's we have identified several CTCF binding sites in the HTT locus of which at least three CTCF binding sites are proximal to the CAG repeat. Analysis of the ChIP-Seq data showed 30 CTCF sites on the genome with differential CTCF binding between HD and control fibroblast cell lines. No differences in CTCF binding within the HTT locus were found between the HD and control cell lines.

Conclusions No differential binding of CTCF to the HTT locus in fibroblasts that could suggest that CTCF can act as a modulator in genetic repeat instability in HD. Genome wide analysis and ChIP-Seq in brain tissue will determine if CTCF could be involved in HD pathogenesis.