Tau gene promoter rs242557 and allele-specific protein binding

Abstract

AbstractThe H1 haplotype clade of the tau gene (MAPT) is associated with increased risk of the sporadic disorders, progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD) and to a lesser extent, Parkinson’s disease (PD). The H1c sub-haplotype drives this association in PSP and CBD, and is also weakly associated with Alzheimer’s disease (AD), suggesting involvement in common pathogenic pathway(s). The rs242557 single-nucleotide polymorphism (SNP) that defines H1c resides in a highly conserved repressor domain in the MAPT promoter. Previously, in cellular reporter assays, we showed significant rs242557 allele-specific differences in transcriptional repression, with the H1c-specific rs242557/A allele contributing a significantly higher MAPT promoter activity compared to the non-H1c rs242557/G allele. With evidence of allele-specific differences in protein binding to this repressor domain, we set out to identify those proteins that bind to this region. Electrophoretic mobility shift assay (EMSA) analysis strongly suggested allele-specific differences in protein affinities. In order to identify nuclear proteins that differentially bind to this repressor domain, we carried out a promoter-trap assay and analysed the bound proteins by SDS-PAGE and HPLC ESI-QTOF mass spectrometry. We identified 37 proteins and used bioinformatic tools such as STRING and Reactome to analyse and stratify the results. These included U2AF65, hnRNPU, PTBP1, hnRNPD0, U5 snRNP 116, ALY, HMGB2, H1 and actin and provide the basis for further studies of the role of the MAPT repressor domain and the binding proteins in regulating MAPT gene transcription and splicing.