The Zinc Finger Protein CTCF Binds to the APBβ Domain of the Amyloid β-Protein Precursor Promoter

Abstract

The promoter of the amyloid ␤-protein precursor (APP) gene directs high levels of cell type-specific transcription with 94 base pairs 5 to the main transcriptional start site. An essential activator domain in this proximal APP promoter is a nuclear factor binding site designated as APB␤. The recognition domain for the APB␤ binding factor is located between position ؊93 and ؊82 relative to the main transcriptional start site.The nuclear factor that binds to the APB␤ site was partially purified by multiple steps of ion exchange and hydroxyapatite chromatography. Based on UV crosslinking results, a protein with an apparent molecular mass of 140 kDa was selected as the putative APB␤ binding protein. After the final purification step consisting of preparative SDS-polyacrylamide gel electrophoresis, partial peptide sequences were obtained that completely matched the transcriptional factor CTCF. This protein is a known regulator of c-myc and lysozyme gene expression, and it binds to a variety of diverse DNA sequences.The binding of CTCF to the APB␤ domain was further established by competition with CTCF binding oligonucleotides in mobility shift electrophoresis. The identity was also confirmed by the observation that the APB␤ binding factor is recognized by antibodies against Cand N-terminal sequences of CTCF. In addition, oligonucleotide competition during in vitro transcription affirmed that CTCF acts as a transcriptional activator in the APP gene promoter.

Epigenetic dysregulation by nickel through repressive chromatin domain disruption

“…As a CTCF-binding sequence, we used a DNA fragment containing the well-characterized CTCF-binding site at the APP locus (Fig. S9A) (35). When incubated with BEAS-2B nuclear extracts, retardation in the migration of the wildtype probe due to the formation of a protein/DNA complex was observed (Fig.…”

YB-1 and CTCF Differentially Regulate the 5-HTT Polymorphic Intron 2 Enhancer Which Predisposes to a Variety of Neurological Disorders

“…CTCF, in addition to transcriptional silencing or activating in a context-dependent manner, organizes epigenetically controlled chromatin insulators that regulate imprinted genes in soma (Klenova et al, 1993;Filippova et al, 1996;Ohlsson et al, 2001;Klenova et al, 2002). CTCF has been implicated previously in the deregulation of other neuronal-specific genes (Vostrov and Quitschke, 1997;Burton et al, 2002;Vostrov et al, 2002). Our data and model for regulation of the VNTR provides insights into the molecular mechanisms associated with development of neurological disorders in which the 5-HTT gene is implicated.…”

CTCF terminal segments are unstructured

“…The same protein can act as a repressor, 1 activator, 2 or insulator 3 when bound to different DNA sites. The genome-wide distribution of CTCF occupancy also suggests variation in function.…”