Genomic footprinting of budding yeast replication origins during the cell cycle

Abstract

Publisher Summary This chapter discusses the genomic footprinting of budding yeast replication origins during the cell cycle. Nucleotide resolution genomic footprinting can be a powerful tool for the monitoring of protein-DNA interactions in vivo or in a cell extract. The technique involves the use of an enzymatic or chemical agent as a probe to induce modifications in the DNA as the first step. The presence of a protein bound to the DNA can alter the specificity of the probe, either reducing the level of modification (implying protection) or increasing the level of modification (resulting in hypersensitive sites). These alterations can include chemical or enzymatic cleavage of DNA or chemical modifications of the DNA. A number of genomic footprinting procedures have been described; however, the use of this technique has often been limited by problems encountered in the detection of signals derived from sequences that represent only a small fraction of the total DNA, such as single-copy sequences in the eukaryotic genome.