7 DNA packaging and chromatin
Until now, we have discussed DNA primarily as a double helix, but in its natural state within the cell it is found packaged as a complex mixture with many different proteins and other components. You have already seen examples of proteins with specific roles to play, such as topoisomerases and the proteins with various DNA binding domains, but in this section we will turn our attention to the proteins that serve to pack and organise the DNA into what we call chromatin.
The packaging of the long DNA chains in chromatin essentially plays three critical roles within the cell.
Protection. The intrinsic chemical properties of DNA and its reactions with reactive agents generated within the cell or from exposure to the environment make it extremely vulnerable to both chemical and physical damage, as you saw in Section 5. This DNA damage could be deleterious or even lethal to the cell, through the loss or mutation of genetic information encoded by the ordered base pairs. Whilst several specialist DNA repair systems exist to repair much of this damage, part of the front-line protection against damage is provided by packaging chromosomal DNA into chromatin. The packaging components, which are found in great abundance within the cell, serve to protect the chemically vulnerable sites in the DNA backbone and bases, as well as shielding the long strands of DNA from physical forces that could cause it to break.
Compaction. If you glance back to Table 1, you can see that the amounts of DNA that cells contain are large. Packaging serves to compact the extremely long strands of DNA into a size that will fit within the living cell. In the case of the E. coli bacterial chromosome, this compaction is over 1000-fold, condensing the single 4.6 Mb (4 600 000 bp) chromosome, with an extended length of 1 mm, into a structure between 0.5 and 1 μm in length. Even greater compaction is required in eukaryotic cells. For example, an average human chromosome, with a naked DNA length of over 10 cm, is compacted down over 10 000-fold to less then 10 μm. In order to compact and package DNA to such levels, the DNA helix itself also undergoes changes, with the ATP-dependent formation of supercoils through the action of specialist enzymes such as DNA topoisomerases (discussed in Section 3.2).
DNA metabolism. The DNA within both prokaryotic and eukaryotic cells is, of course, the storage facility for the cell's genetic information and chromosomes serve as platforms for key cell processes and systems. These include transcription, which must occur within the context of chromatin, and DNA storage and segregation, in which specialist chromatin components play central roles. DNA metabolism is itself a dynamic process and chromatin plays central roles in processes such as transcription; so it is not surprising that chromatin components themselves are very dynamic, changing with the cell cycle and, in multicellular organisms, differing between cell lineages.
In this section, we will focus on the components of chromatin of prokaryotic and eukaryotic cells and how these contribute to the three roles outlined above. The various roles of chromatin components and their contribution to the chromosomal environment in gene transcription.