Even while there is still a great deal more to understand about the actions of the various chromatin structures, there is little doubt that the packing of DNA into nucleosomes was very necessary for the evolution of eukaryotic organisms such as ourselves. In order to develop a complex multicellular being, the cells in the various lineages need to specialize by changing the accessibility and activity of many hundreds of genes. This is required in order to generate the creature. Because each cell maintains a record of its previous developmental experience within the regulatory circuits that regulate its numerous genes, "cell memory" plays an important part in the process described here. It would appear that a portion of the data is stored in the chromatin structure.

Higher eukaryotic organisms contain memory circuits that are unrivaled in terms of their level of intricacy. Cell memory systems can also be found in bacteria. When a gene is turned on or off, strategies based on regional variations in chromatin structure, which are unique to eukaryotes, can help the gene remain in that state until a different stimulus acts to change it. These strategies can help the gene remain in that state until a different stimulus acts to change it. One example of an extreme is a structure known as centromeric chromatin, which, once it has been formed, may reliably be passed on from one generation of cells to the next. The primary or "conventional" type of heterochromatin, which is characterized by extensive arrays of the HP1 protein, is also capable of surviving forever. A sort of condensed chromatin that is created by the Polycomb protein family is employed, in contrast, to mute genes that need to be kept quiet under certain circumstances but are active under others. These genes are called "silent" genes. The latter route is responsible for the regulation of a large number of genes, the majority of which encode transcription regulators that play an essential role in early embryonic development. There are many additional types of chromatin, some of which have lifespans that are frequently and significantly shorter than the amount of time it takes for a cell to divide.

In the chromosomes of eukaryotic organisms, the DNA is neatly packaged into nucleosomes, but there is a wide variety of alternative chromatin configurations that are also a possibility. In order to generate this variety, each of the four histones that are found within the nucleosome core has been subjected to a substantial number of reversible covalent modifications. The mono-, di-, and trimethylation of several different lysine side chains is an important reaction that can take place on the same lysines; however, this reaction is incompatible with the acetylation that can take place on the same lysines. Numerous nucleosomes are "marked" in some way by specific combinations of the modifications, and these markings influence how the nucleosomes engage in interactions with other proteins. These marks are read when protein modules that are part of a larger protein complex connect to the altered nucleosomes in a region of chromatin. This attachment process takes place in an area. These reader proteins then recruit other proteins that have a variety of functions.

Some reader protein complexes contain a histone-modifying enzyme, such as a histone lysine methylase, and this enzyme "writes" the same mark that the reader is able to recognize. This enzyme is found in some reader protein complexes. This particular kind of reader-writer-remodeling complex has the ability to transport a particular kind of chromatin along a chromosome. In particular, it is thought that this is how large areas of condensed heterochromatin get their start. In addition to the traditional places on chromosomes near centromeres and telomeres, heterochromatin can also be found in a great number of other regions on chromosomes. The dense packing of DNA in heterochromatin often results in the silencing of any genes that are located there.

A strong indication that condensed states of chromatin are passed down from one cell generation to the next is provided by the phenomenon known as position impact variegation. It would suggest that the specialized chromatin that is found at centromeres is maintained by the same method. The ability to transmit certain chromatin configurations from one cell generation to the next permits an epigenetic cell memory mechanism that helps contribute to the maintenance of a variety of cell states that are required by complex multicellular organisms.

Following our discussion of the DNA and protein molecules that are constituents of the chromatin fiber, we will now examine the overall structure of the chromosome as well as the manner in which its numerous domains are arranged in space. A typical human chromosome would still be 0.1 centimeters long and would be able to make more than 100 complete rotations around the nucleus if it were a 30-nm fiber. Chromosomes must still be folding at a higher level even when they are in the interphase state. This higher-order packing almost certainly involves the folding of the chromatin into a series of loops and coils; however, the specific chemical details are not known at all. This fluid chromatin packing is constantly subject to change as a result of the demands placed on the cell.

Research conducted on the inflexible and extraordinarily lengthy chromosomes seen in developing amphibian oocytes has shed light on the characteristics of the chromosomes found in interphase cells (immature eggs). Even when viewed via a simple light microscope, these incredibly unusual lampbrush chromosomes, which are currently the largest chromosomes that have been identified, are clearly visible when they couple up in preparation for meiosis. It has been discovered that they are organized into a number of huge chromatin loops that extend outward from a chromosomal axis in a linear fashion.

The same DNA sequence is carried by a particular loop in these chromosomes at all times. This DNA sequence continues to be stretched in the same manner as the oocyte develops. The vast majority of the genes that can be located in the DNA loops on these chromosomes are being actively expressed, and as a result, significant quantities of RNA are being produced for the oocyte. On the other hand, the vast majority of the DNA does not exist in loops but is instead still densely packed along the chromosome axis. This is an area of the genome that does not normally allow for the expression of genes.

It is generally accepted that the interphase chromosomes of all eukaryotic organisms are structured in loops, similar to one another. Even though they are typically too small and delicate to be seen clearly under a light microscope, it is possible to infer the existence of these loops through the use of other methods. Modern DNA technologies have made it possible to identify potential candidates for the sites on chromatin that serve as the bases of loop structures. For example, by determining the frequency with which any two loci along an interphase chromosome are held together, it is possible to identify potential candidates for these sites. These studies, along with other ones, have led us to the conclusion that the DNA found in human chromosomes is most likely organized in loops of varying lengths. A typical DNA loop may contain anywhere from 50,000 to 200,000 nucleotide pairs, despite the fact that loops consisting of a million nucleotide pairs have also been proposed.