There is a tremendous amount of room for variation on a single nucleosome, and this room for variation expands even further when we take into account nucleosomes that incorporate variants of histones. On the other hand, it is common knowledge that the modifications to the histones occur in synchronized groups. There have been found to be around 15 different sets of this kind in mammalian cells. However, it is not known how many different forms of chromatin are required for proper cellular function at this time.

The knowledge that certain combination of histones have a specific meaning for the cell in terms of how and when the DNA that is packaged in the nucleosomes is to be accessed or altered led to the conception of the idea of a "histone code." This code would allow the cell to access or modify the DNA in a specific way and at a specific time.

For instance, certain markings indicate that a section of chromatin has recently undergone replication, while others indicate that the DNA contained within that section of chromatin has been damaged and needs to be repaired. Both of these indications can be found on the same piece of chromatin. Still others point to the sequence of events that occur during gene expression. There are many regulatory proteins that feature small domains that bind to specific marks, one example of which is a trimethylated lysine 4 on histone H3. These domains can be found on a variety of regulatory proteins. The fact that these domains are often related to one another as modules within a single large protein or protein complex enables it to recognize a specific group of histone modifications. The final outcome is a reader complex that permits certain combinations of chromatin markings to attract additional proteins in order to carry out the appropriate biological activity at the appropriate time.

The marks that are left on nucleosomes by covalent modifications to histones are dynamic; this means that they are constantly being deleted and added at rates that vary depending on where they are located on the chromosome. Because they extend outward from the nucleosome core and are likely to be accessible even when chromatin is condensed, the histone tails seem to offer an especially suitable format for making marks that can be easily altered as a cell's needs change. This would seem to make them a particularly good choice for the purpose. despite the fact that there is still a great deal to discover regarding the importance of the numerous histone alterations.

Enzymes that can add to or remove from the modifications that are already present on histones that are located in nucleosomes are found in multisubunit complexes. They can first be brought to a particular region of chromatin by one of the DNA-binding proteins that are sequence specific (transcription regulators). The succeeding processes, however, may resemble a chain reaction once a modifying enzyme has "written" its signature on a few nucleosomes in the immediate vicinity. Within the context of this scenario, the "writer enzyme" works in conjunction with a "reader protein" that is a component of the same protein complex. After the nucleosome has been modified, it is read by a module within the reader protein, which identifies the mark and then forms a stable bond with the nucleosome. Because of this, the associated writer enzyme becomes active and moves closer to the nucleosome that is next to it. Across a series of read-write cycles, the reader protein is able to carry the writer enzyme through the DNA, which ultimately results in the mark being distributed step by step along the chromosome.

The actual process is significantly more involved than what you have just read about it. Readers and writers are both components of a protein complex that, in order to propagate, must have a greater number of readers and writers than there are markings on the nucleosome. As the reader moves along the nucleosome-packaged DNA, many of these reader-writer complexes contain an ATP-dependent chromatin remodeling protein. This occurs as the reader moves along the DNA. Long lengths of chromatin can be either decondensed or condensed by a collaborative effort involving the reader, the writer, and the remodeling protein.

An "eraser enzyme" such as a histone demethylase or histone deacetylase, for example, is introduced into the complex in a manner analogous to that described above in order to remove histone modifications from particular DNA sequences. These modifications, which occur as a result of the writer complex, are managed by DNA-binding proteins that are sequence-specific (transcription regulators). The findings of genetic searches for genes that promote or repress the spreading and stability of heterochromatin provide some insight into the complexities of the processes described above. These findings were observed as effects on position effect variation in Drosophila. As was said before, more than one hundred of these genes have been discovered so far, and it is quite likely that the bulk of them code for components of one or more reader-writer-remodeling protein complexes.

The process of the chromatin structure spreading that was explained earlier has the potential to create a problem. Given that each chromosome contains one continuous, extraordinarily long DNA molecule, what prevents a cacophony of confused cross-talk between adjacent chromatin areas of differing structure and function? The earliest studies on position effect variegation suggested a solution, which was as follows: certain DNA sequences establish chromatin domain boundaries and differentiate one domain from another. Several of these barrier sequences have recently been found and characterized with the assistance of genetic engineering techniques. These techniques allow specific sections of DNA to be removed from or added to chromosomes, which has led to the discovery and study of a number of these barrier sequences.

For instance, in cells that are supposed to grow into red blood cells, a region of silent, condensed chromatin that is bordering the active chromatin domain that contains the human globin locus is frequently separated from the active chromatin domain by a sequence that is known as HS4.

If this region is deleted, then condensed chromatin will invade the locus for the -globin gene. This chromatin spreads to variable degrees in different cells and, as a result, silences the genes that it covers. This phenomenon is analogous to the location effect variation observed in Drosophila. The consequences are disastrous: People who have such a loss are predisposed to a severe form of anemia, and their globin genes only express themselves to a moderate degree.

In studies of genetic engineering that are designed to insert a gene into the genome of a mammalian organism, it is common practice to add the HS4 sequence to both ends of a gene that is going to be inserted into a mammalian genome. This is done to prevent a gene from being silenced due to the spread of heterochromatin. According to the findings of the investigation, this barrier sequence has a number of binding sites for the enzyme histone acetylase. Since the acetylation of a lysine side chain is incompatible with the methylation of the same side chain, and particular lysine methylations are required for heterochromatin to spread, histone acetylases are plausible candidates for the creation of DNA barriers that prevent spreading. It is common knowledge that in addition to these chromatin modifications, there are a variety of others that can prevent genes from being silenced.