Euchromatin is a form of chromatin that is lightly packed—as opposed to heterochromatin, which is densely packed. The presence of euchromatin usually reflects that cells are transcriptionally active, i.e. they are actively transcribing DNA to mRNA. Euchromatin is found in the nucleus of eukaryotes and represents more than 90% of the human genome.
Before understanding the structure of euchromatin, we should comprehend the different ways in which DNA is packaged in cells.
The DNA in eukaryotic cells is arranged in complexes comprising genes and proteins. These complexes are called chromatin, and they exist in two forms: euchromatin and heterochromatin. Briefly, euchromatin (also known as the beads-on-a-string structure) is composed of DNA helices that are condensed at intervals into nucleosomes.
Nucleosomes are the basic unit of chromatin and they consist of packaged complexes containing histone proteins around which DNA is wrapped, i.e. nucleosomes are made of DNA coiled around histones. The DNA that connects nucleosomes is known as the linker DNA. Heterochromatin is euchromatin that has been more densely packed into 30-nm fibers. During interphase, heterochromatin is packaged into denser structures—active chromosomes, which are further condensed into denser structures during mitosis and meiosis—metaphase chromosomes.
the DNA on the left side is condensed into progressively denser structures as we move rightwards, until we reach the densest conformation—the metaphase chromosome that we are used to seeing in micrographs. Note how the double-stranded DNA (first illustration on the left) is wrapped around a center of histone proteins to form nucleosomes (second illustration), which in turn are part of euchromatin or beads-on-a-string (third illustration). The third illustration clearly shows why euchromatin is also known as beads-on-a-string, since one can appreciate the linker DNA (string) connecting the nucleosomes (beads).
The main proteins that form chromatin are called histones. Octomers of histones are assembled together to form the nucleosomes: two copies of H2A, two of H2B, two of H3 and two of H4. About 200 base pairs of DNA are wrapped around each nucleosome. Interestingly, histones are thought to act as switches that swap between the different chromatin conformations—euchromatin and heterochromatin—through methylation and acetylation. For instance, a methylated lysine 4 in a part of the histone called histone tail seems to induce the euchromatin conformation. This methylated lysine 4 is therefore used as a marker for euchromatin.
Despite being actively researched, the structure of chromatin is still poorly understood although it seems that the cycle in which the cell is at a certain time determines the structure of chromatin. Not surprisingly, the structure of euchromatin provides hints regarding its function and why it is present in transcriptionally active cells.
As mentioned above, euchromatin is also called beads-on-a-string because of the resemblance between a necklace of beads connected through a string and the nucleosomes connected through the linker DNA. In this conformation, euchromatin is loose and consequently leaves the linker DNA exposed so that it can be transcribed; this way, RNA and DNA polymerases as well as other proteins can access the DNA. Because of its loose structure, euchromatin is difficult to see under a microscope and appears faintly when stained—in contrast to the easily visible heterochromatin, which is densely packed.
It has been hypothesized that the regulation of the chromatin structure is a way to control gene expression. It is believed that the euchromatic structure is present when genes are turned on, that is, when they are being actively transcribed, while the heterochromatic structure is present when genes are turned off or inactive.
In other words, because euchromatin is present in transcriptionally active cells because of the accessibility to the DNA, folding into heterochromatin may be a way to regulate transcription by preventing the access of RNA polymerases and other regulatory proteins to the DNA. In this line, housekeeping genes, for instance, are always in the euchromatic conformation because they need to be constantly replicated and transcribed to keep the functional activity and survival of the cells.
Euchromatin in prokaryotes and some eukaryotes
Although prokaryotes have a different mechanism to condense DNA, its packaged structure resembles that of euchromatin. It is therefore believed that heterochromatin—the densely packaged chromatin—evolved later, possibly together with the nucleus, to regulate gene expression and to manage large amounts—long strings—of genetic material.
Whereas the DNA in most eukaryotic cells is packaged as described, there are some other eukaryotes that do not conform to this organization. Among these are avian red blood cells and motile sperm cells (spermatozoa), both of which contain chromatin in more densely packaged conformations than most eukaryotes.