Nucleosome positioning is not only related to genomic DNA compaction but also to other biological functions. After the chromatin is digested by micrococcal nuclease, nucleosomal (nucleosome-bound) DNA fragments can be sequenced and mapped on the genomic DNA sequence. Due to the development of modern DNA sequencing technology, genome-wide nucleosome mapping has been performed in a wide range of eukaryotic species. Comparative analyses of the nucleosome positions have revealed that the nucleosome is more frequently formed in exonic than intronic regions, and that most of transcription start and translation (or transcription) end sites are located in nucleosome linker DNA regions, indicating that nucleosome positioning influences transcription initiation, transcription termination, and gene splicing. In addition, nucleosomal DNA contains guanine and cytosine (G + C)-rich sequences and a high level of cytosine methylation. Thus, the nucleosome positioning system has been conserved during eukaryotic evolution. 1. Introduction Eukaryotic genomic DNA is packaged with histone proteins to form chromatin [1, 2]. The most fundamental repeating unit of chromatin is the nucleosome, which consists of an octamer of histones (2 copies of each histone protein: H2A, H2B, H3, and H4) and the genomic DNA wrapped around the octamer [3, 4]. Modification (e.g., acetylation, methylation, and phosphorylation) of the nucleosomal core histones influences chromatin structure and biological functions [5–7]. The modified nucleosome should be formed at the genomic position or in the genomic region. In this paper, I will focus on nucleosome positioning (not histone modification), because nucleosome positioning is not only related to compacting the genomic DNA but also to gene regulation [8–17]. Due to the development of DNA sequencing technology and genomic tiling array technology, genome-wide nucleosome mapping has been performed in a wide range of eukaryotic species, including the budding ascomycetous yeast, Saccharomyces cerevisiae [19]; the nematode, Caenorhabditis elegans [20]; the fruit fly, Drosophila melanogaster [21]; humans, Homo sapiens [22]; the malaria parasite, Plasmodium falciparum [23]; the filamentous ascomycete, Aspergillus fumigatus [24]; the fission ascomycetous yeast, Schizosaccharomyces pombe [25]; the plant, Arabidopsis thaliana [26]; several ascomycetous yeasts [27]; the mouse, Mus musculus [28]; the basidiomycete, Mixia osmundae [29]; the amoebozoa, Dictyostelium discoideum [30]. 2. Nucleosome Positioning and DNA Sequence Preference The DNA sequence plays an
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