Nucleotide sequences recognized and bound by DNA-binding proteins (DBPs) are critical to control and maintain gene expression, replication, chromosome segregation, cell division, and nucleoid structure in bacterial cells. Therefore, determination of the binding sequences of DBPs is important not only to study DBP recognition mechanisms, but also to understand the fundamentals of cell homeostasis. While ChIP-seq analysis appears to be an effective way to determine DBP-binding sites on the genome, the resolution is sometimes not sufficient to identify the sites precisely. Here, we introduce a simple and effective method named Genome footprinting with high-throughput sequencing (GeF-seq) to determine binding sites of DBPs at single base-pair resolution. GeF-seq detects binding sites of DBPs as sharp peaks and thus makes it possible to identify the recognition sequence in each "binding peak" more easily and accurately than using ChIP-seq.
Keywords: Consensus sequence; DNA-binding proteins; DNaseI footprinting; GeF-seq; Genome footprinting; High resolution ChIP-seq.