The DNA of eukaryotic cells is packaged into chromatin by histone proteins, which play a central role in regulating access to genetic information. The nucleosome core is the basic structural unit of chromatin: it is composed of an octamer of the four major core histones (two molecules each of H2A, H2B, H3, and H4), around which are wrapped ∼1.75 negative superhelical turns of DNA, a total of 145-147bp. Nucleosome cores are regularly spaced along the DNA in vivo, separated by linker DNA. Nucleosomes are compact structures capable of blocking access to the DNA that they contain. For example, they may prevent the binding of transcription factors to their cognate sites. It is therefore very important to obtain quantitative information on the positions of nucleosomes with respect to regulatory regions in vivo. The advent of high-throughput sequencing methods has revolutionized this field. We describe the use and advantages of paired-end sequencing to map nucleosomal DNA obtained by micrococcal nuclease digestion of budding yeast nuclei. This approach provides high-quality genome-wide nucleosome occupancy and position maps.
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