Summary of Section 7
Packaging of DNA serves to protect against damage, to compact the DNA helix into a suitable size within the cell, and to act as both a platform for and an intrinsic part of the structural and regulatory machinery involved in DNA metabolism.
DNA compaction in prokaryotes achieved through a combination of supercoiling and interactions with proteins that aid DNA bending.
Compaction of the eubacterial chromosome is facilitated by positively charged polyamines, which neutralize repulsive forces between neighbouring regions of the negatively charged DNA backbone, and by small, positively charged DNA binding proteins, which bend the DNA.
Eukaryotic DNA is condensed through interactions with histone proteins to form nucleosomes, structures that introduce negative supercoils into the helix and play critical roles in DNA metabolism.
Four core histones, each containing a characteristic histone fold structure, form an octamer made from two H3, two H4 and two heterodimers of H2A/B. DNA wraps twice around this core to form the nucleosome. Histone H1 serves to compact this structure further, through interactions with linker DNA.
The tails of histone proteins can be modified by methylation, acetylation and phosphorylation, modifications that can alter specific interactions with other proteins and affect the ability to pack nucleosomes together into more compact structures.
The DNA within the eukaryotic nucleus is packaged into a series of different structures, from nucleosomes to higher-order fibres. The degree of compaction is influenced by the degree of histone octamer acetylation and this compaction is also intimately related to the regulation of processes that occur within the chromatin milieu. Regions that are transcriptionally silent are highly compacted and specific histone modifications occur within these regions.
Chromatin compactness and histone modification can be analysed using nucleases and immunoprecipitation assays.