Nucleosome positioning, nucleosome spacing and the nucleosome code.
Nucleosome positioning has been the subject of intense study for many years. The properties of micrococcal nuclease, the enzyme central to these studies, are discussed. The various methods used to determine nucleosome positions in vitro and in vivo are reviewed critically. These include the traditional low resolution method of indirect end-labelling, high resolution methods such as primer extension, monomer extension and nucleosome sequencing, and the high throughput methods for genome-wide analysis (microarray hybridisation and parallel sequencing). It is established that low resolution mapping yields an averaged chromatin structure, whereas high resolution mapping reveals the weighted superposition of all the chromatin states in a cell population. Mapping studies suggest that yeast DNA contains information specifying the positions of nucleosomes and that this code is made use of by the cell. It is proposed that the positioning code facilitates nucleosome spacing by encoding information for multiple alternative overlapping nucleosomal arrays. Such a code might facilitate the shunting of nucleosomes from one array to another by ATP-dependent chromatin remodelling machines.
Clark
David J
DJ
Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Building 6A, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892, USA. clarkda@mail.nih.gov
D001483:Base Sequence; D042002:Chromatin Assembly and Disassembly / Q000235:genetics / Q000502:physiology*; D002874:Chromosome Mapping; D004271:DNA, Fungal / Q000378:metabolism; D016681:Genome, Fungal / Q000235:genetics; D008836:Micrococcal Nuclease / Q000378:metabolism; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA
D004271:DNA, Fungal; D009707:Nucleosomes; D008836:Micrococcal Nuclease