Chromosomal DNA Compaction and its Implications in Replication and Transcription

Metaphase chromosomes in cells undergoing mitosis are visible under the light microscope. Their formation requires some 10⁴- to 10⁵-fold condensation of uninterrupted linear duplex DNA which has a 2-nm diameter. Such compaction is accomplished in a highly complex and stepwise fashion. Because DNA is a polyelectrolyte with two negative charges per nucleotide, charge neutralization and shielding is required before the polymer can be folded in an ordered, condensed structure. In addition to metal ions and polyamines, the major source of the positive charge in chromatin is the family of highly basic small proteins, called histones, which are rich in the basic amino acid residues lysine and arginine needed to neutralize the charge of the phosphate backbone of DNA. The prokaryotes also have basic proteins (such as HU protein in E. coli) which induce DNA condensation. However, chromatin compaction in eukaryotes is carried out in stages. The simplest folded unit of DNA is the 10-nm nucleosome, consisting of a core histone octamer containing two molecules each of histone H2A, H2B, H3, and H4 around which nearly two turns of the DNA is wrapped. The nucleosome cores are connected by a stretch of linear DNA (linker) of variable length which is covered by histone H1 or H5. The polymeric chain nucleosomes are then folded in a 30-nm fiber whose structure is stabilized by the interaction among histones and a number of other proteins collectively called nonhistone chromosomal proteins (NHC), including high mobility group (HMG), which are not particularly basic. Eventually, the fibers are condensed into highly compacted metaphase chromosomes. The nature of the interactions present in interphase and metaphase chromosomes is not clear.

However, the implications of this compaction are profound. It is absolutely essential to condense the mammalian genome, which in an extended linear form more than 1 m long, to a volume which can be accommodated in the nuclear volume of 10–30 femtoliters. At the same time, the genes will be buried in condensed chromatin, and yet their specific sequences need to be exposed for various processes of information transfer. Thus, for both transcription and replication, the chromatin has to be decondensed. This was evident in early in vitro studies which showed that both these processes are severely inhibited when DNA is complexed with histones.