Euchromatin

File:Sha-Boyer-Fig1-CCBy3.0.jpg

Distinction between Euchromatin and Heterochromatin

Euchromatin (also called "open chromatin") is a lightly packed form of chromatin (DNA, RNA, and protein) that is enriched in genes, and is often (but not always) under active transcription. Euchromatin stands in contrast to heterochromatin, which is tightly packed and less accessible for transcription. 92% of the human genome is euchromatic.<ref>Template:Cite journal</ref>

In eukaryotes, euchromatin comprises the most active portion of the genome within the cell nucleus. In prokaryotes, euchromatin is the only form of chromatin present; this indicates that the heterochromatin structure evolved later along with the nucleus, possibly as a mechanism to handle increasing genome size.

StructureEdit

Euchromatin is composed of repeating subunits known as nucleosomes, reminiscent of an unfolded set of beads on a string, that are approximately 11 nm in diameter.<ref name="Babu_1987">Template:Cite journal</ref> At the core of these nucleosomes are a set of four histone protein pairs: H3, H4, H2A, and H2B.<ref name="Babu_1987" /> Each core histone protein possesses a 'tail' structure, which can vary in several ways; it is thought that these variations act as "master control switches" through different methylation and acetylation states, which determine the overall arrangement of the chromatin.<ref name="Babu_1987" /> Approximately 147 base pairs of DNA are wound around the histone octamers, or a little less than 2 turns of the helix.<ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> Nucleosomes along the strand are linked together via the histone, H1,<ref>Template:Cite book</ref> and a short space of open linker DNA, ranging from around 0-80 base pairs. The key distinction between the structure of euchromatin and heterochromatin is that the nucleosomes in euchromatin are much more widely spaced, which allows for easier access of different protein complexes to the DNA strand and thus increased gene transcription.<ref name="Babu_1987" />

AppearanceEdit

File:Heterochromatic versus euchromatic nuclei.jpg

Microscopy of heterochromatic versus euchromatic nuclei (H&E stain).

Euchromatin resembles a set of beads on a string at large magnifications.<ref name="Babu_1987" /> From farther away, it can resemble a ball of tangled thread, such as in some electron microscope visualizations.<ref name="mmegias">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> In both optical and electron microscopic visualizations, euchromatin appears lighter in color than heterochromatin - which is also present in the nucleus and appears darkly<ref>Template:Cite book</ref> - due to its less compact structure.<ref name="mmegias" /> When visualizing chromosomes, such as in a karyogram, cytogenetic banding is used to stain the chromosomes. Cytogenetic banding allows us to see which parts of the chromosome are made up of euchromatin or heterochromatin in order to differentiate chromosomal subsections, irregularities or rearrangements.<ref>Template:Cite book</ref> One such example is G banding, otherwise known as Giemsa staining where euchromatin appears lighter than heterochromatin.<ref name="biologyonline">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref>

citation
CitationClass=web }}</ref><ref>{{#invoke:citation/CS1\|citation	CitationClass=web }}</ref><ref>{{#invoke:citation/CS1\|citation	CitationClass=web }}</ref><ref>{{#invoke:citation/CS1\|citation	CitationClass=web }}</ref><ref name="Babu_1987" />		Giemsa (G-) Banding	Reverse (R-) Banding	Constitutive Heterochromatin (C-) banding	Quinacrine (Q-) banding	Telomeric R (T-) banding
Euchromatin	Lighter	Darker	Lighter	Dull	Light
Heterochromatin	Darker	Lighter	Darker	Bright (Fluorescent)	Darker (Faint)

FunctionEdit

File:Human karyotype with bands and sub-bands.png

Schematic karyogram of a human, showing an overview of the human genome using G banding, which is a method that includes Giemsa staining, wherein the lighter staining regions are generally more euchromatic, whereas darker regions generally are more heterochromatic.Template:Further

TranscriptionEdit

Euchromatin participates in the active transcription of DNA to mRNA products. The unfolded structure allows gene regulatory proteins and RNA polymerase complexes to bind to the DNA sequence, which can then initiate the transcription process.<ref name="Babu_1987" /> While not all euchromatin is necessarily transcribed, as the euchromatin is divided into transcriptionally active and inactive domains,<ref>Template:Cite journal</ref> euchromatin is still generally associated with active gene transcription. There is therefore a direct link to how actively productive a cell is and the amount of euchromatin that can be found in its nucleus.

It is thought that the cell uses transformation from euchromatin into heterochromatin as a method of controlling gene expression and replication, since such processes behave differently on densely compacted chromatin. This is known as the 'accessibility hypothesis'.<ref>Template:Cite journal</ref> One example of constitutive euchromatin that is 'always turned on' is housekeeping genes, which code for the proteins needed for basic functions of cell survival.<ref>Template:Cite journal</ref>

EpigeneticsEdit

Epigenetics involves changes in the phenotype that can be inherited without changing the DNA sequence. This can occur through many types of environmental interactions.<ref>Template:Cite journal</ref> Regarding euchromatin, post-translational modifications of the histones can alter the structure of chromatin, resulting in altered gene expression without changing the DNA.<ref>Template:Cite journal</ref> Additionally, a loss of heterochromatin and increase in euchromatin has been shown to correlate with an accelerated aging process, especially in diseases known to resemble premature aging.<ref>Template:Cite journal</ref> Research has shown epigenetic markers on histones for a number of additional diseases.<ref>Template:Cite journal</ref><ref>Template:Cite journal</ref>

RegulationEdit

Euchromatin is primarily regulated by post-translational modifications to its nucleosomes' histones, conducted by many histone-modifying enzymes. These modifications occur on the histones' N-terminal tails that protrude from the nucleosome structure, and are thought of to recruit enzymes to either keep the chromatin in its open form, as euchromatin, or in its closed form, as heterochromatin.<ref name="Bannister_2011">Template:Cite journal</ref> Histone acetylation, for instance, is typically associated with euchromatin structure, whereas histone methylation promotes heterochromatin remodeling.<ref name="Singh_2020">Template:Cite book</ref> Acetylation makes the histone group more negatively charged, which in turn disrupts its interactions with the DNA strand, essentially "opening" the strand for easier access.<ref name="Bannister_2011" /> Acetylation can occur on multiple lysine residues of a histone's N-terminal tail and in different histones of the same nucleosome, which is thought to further increase DNA accessibility for transcription factors.<ref name="Bannister_2011" />

Phosphorylation of histones is another method by which euchromatin is regulated.<ref name="Bannister_2011" /> This tends to occur on the N-terminal tails of the histones, however some sites are present in the core.<ref name="Bannister_2011" /> Phosphorylation is controlled by kinases and phosphatases, which add and remove the phosphate groups respectively. This can occur at serine, threonine, or tyrosine residues present in euchromatin.<ref name="Bannister_2011" /><ref name="Singh_2020" /> Since the phosphate groups added to the structure will incorporate a negative charge, it will promote the more relaxed "open" form, similar to acetylation.<ref name="Singh_2020" /> In regards to functionality, histone phosphorylation is involved with gene expression, DNA damage repair, and chromatin remodeling.<ref name="Singh_2020" />

Another method of regulation that incorporates a negative charge, thereby favoring the "open" form, is ADP ribosylation.<ref name="Singh_2020" /> This process adds one or more ADP-ribose units to the histone, and is involved in the DNA damage response pathway.<ref name="Singh_2020" />

ReferencesEdit

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