DNA Tetraplexes and Nucleosome Positioning Sequences
All eukaryotic organisms package their genomes into a nucleoprotein complex known as chromatin, whose major constituents are the DNA and proteins known as histones. The non-covalent association of histones with DNA results in considerable compaction and allows the organisation of the genome into the cell nucleus. The elementary repeating units of chromatin are called nucleosomes. The nucleosome consists of two subunits each of the histone proteins H2A, H2B, H3, and H4, one subunit of histone H1-type proteins, and a definite number of DNA base-pairs. The nucleosome is arranged as follows: an octameric core of histones, two each of H2A, H2B, H3, and H4, is encompassed by 146 base-pairs of DNA, which winds almost two left-handed superhelical turns around it. This unit is called the nucleosome core particle. The remaining DNA, whose length is both tissue and species specific, is referred to as linker DNA. It joins adjacent nucleosome core particles and is associated with histones of the H1-type. Nucleosomes can be randomly or precisely positioned on a DNA molecule. However, the genomes of higher eukaryots are immense and amount to extensive helical structure polymorphism, which precludes a total random positioning of nucleosomes in vivo. A major determinant for nucleosome positioning is the DNA sequence. The thesis describes the generation and characterisation of sequences that are superior in formation of nucleosome core particles as well as sequences that readily desist formation of nucleosome core particles.
One of the first steps in the activation process of a gene is the rearrangement or disruption of chromatin structure, which otherwise might prevent the binding of transcription factors to the promoter. The thesis describes how the formation of a novel DNA structure, activates the c-myc oncogene. The structure is a DNA tetraplex and its sequence features are not unique to the c-myc promoter, but occur frequently in the promoter regions of eukaryotic genes.