Variation-Based Binding Affinity Analysis of the Human CTCF Transcription Factor

Abstract

Unlike other transcription factors, CTCF recognizes a longer core motif region and possesses multiple Zinc finger domains for reading additional sequences around the motif. CTCF's role in providing anchor sites for cohesin rings, which create DNA loops, is highlighted as crucial for gene expression regulation. We utilized the human ChIPSummitDB database, containing extensive data on CTCF binding sites, to conduct the study. We collected and analyzed ChIP-seq experiments, developing pipelines to automatically analyze raw sequencing data and identify variations in CTCF binding sites. The study reveals that specific bases in the CTCF motif, particularly the 2nd and 7th positions, exhibit higher frequencies of reference alleles due to their high binding affinity.