Euchromatin (also called "open chromatin") is a lightly packed form of
chromatin
Chromatin is a complex of DNA and protein found in eukaryote, eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important ...
(
DNA,
RNA, and
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
) that is enriched in
gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
s, and is often (but not always) under active
transcription. Euchromatin stands in contrast to
heterochromatin
Heterochromatin is a tightly packed form of DNA or '' condensed DNA'', which comes in multiple varieties. These varieties lie on a continue between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a rol ...
, which is tightly packed and less accessible for transcription. 92% of the human genome is euchromatic.
In
eukaryote
Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...
s, euchromatin comprises the most active portion of the
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...
within the
cell nucleus
The cell nucleus (pl. nuclei; from Latin or , meaning ''kernel'' or ''seed'') is a membrane-bound organelle found in eukaryotic cells. Eukaryotic cells usually have a single nucleus, but a few cell types, such as mammalian red blood cells, h ...
. In
prokaryotes
A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...
, euchromatin is the ''only'' form of chromatin present; this indicates that the heterochromatin structure evolved later along with the
nucleus
Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to:
* Atomic nucleus, the very dense central region of an atom
*Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA
Nucl ...
, possibly as a mechanism to handle increasing genome size.
Structure
Euchromatin is composed of repeating subunits known as
nucleosome
A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundame ...
s, reminiscent of an unfolded set of beads on a string, that are approximately 11 nm in diameter.
At the core of these nucleosomes are a set of four
histone
In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn a ...
protein pairs:
H3,
H4,
H2A, and
H2B.
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
In the chemical sciences, methylation denotes the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These ...
and
acetylation
:
In organic chemistry, acetylation is an organic esterification reaction with acetic acid. It introduces an acetyl group into a chemical compound. Such compounds are termed ''acetate esters'' or simply '' acetates''. Deacetylation is the oppos ...
states, which determine the overall arrangement of the chromatin.
Approximately 147 base pairs of
DNA are wound around the histone octamers, or a little less than 2 turns of the helix. Nucleosomes along the strand are linked together via the histone,
H1, and a short space of open
linker DNA
In molecular biology, linker DNA is double-stranded DNA (38-53 base pairs long) in between two nucleosome cores that, in association with histone H1, holds the cores together. Linker DNA is seen as the string in the "beads and string model", whi ...
, ranging from around 0-80 base pairs. The key distinction between the structure of euchromatin and
heterochromatin
Heterochromatin is a tightly packed form of DNA or '' condensed DNA'', which comes in multiple varieties. These varieties lie on a continue between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a rol ...
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.
Appearance
Euchromatin resembles a set of beads on a string at large magnifications.
From farther away, it can resemble a ball of tangled thread, such as in some
electron microscope
An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. As the wavelength of an electron can be up to 100,000 times shorter than that of visible light photons, electron microscopes have a hi ...
visualizations.
In both optical and electron microscopic visualizations, euchromatin appears lighter in color than
heterochromatin
Heterochromatin is a tightly packed form of DNA or '' condensed DNA'', which comes in multiple varieties. These varieties lie on a continue between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a rol ...
- which is also present in the
nucleus
Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to:
* Atomic nucleus, the very dense central region of an atom
*Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA
Nucl ...
and appears darkly - due to its less compact structure.
When visualizing
chromosome
A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins ar ...
s, 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. One such example is
G banding
G-banding, G banding or Giemsa banding is a technique used in cytogenetics to produce a visible karyotype by staining condensed chromosomes. It is the most common chromosome banding method. It is useful for identifying genetic diseases through t ...
, otherwise known as
Giemsa staining where euchromatin appears lighter than heterochromatin.
Function
Transcription
Euchromatin participates in the active
transcription of
DNA to
mRNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein.
mRNA is created during the ...
products. The unfolded structure allows gene regulatory proteins and
RNA polymerase
In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template.
Using the enzyme helicase, RNAP locally opens th ...
complexes to bind to the DNA sequence, which can then initiate the transcription process.
While not all euchromatin is necessarily transcribed, as the euchromatin is divided into transcriptionally active and inactive domains, 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
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. T ...
and
replication, since such processes behave differently on densely compacted chromatin. This is known as the 'accessibility hypothesis'. 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.
Epigenetics
Epigenetics
In biology, epigenetics is the study of stable phenotypic changes (known as ''marks'') that do not involve alterations in the DNA sequence. The Greek prefix '' epi-'' ( "over, outside of, around") in ''epigenetics'' implies features that are ...
involves changes in the
phenotype
In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (biology), morphology or physical form and structure, its Developmental biology, developmental proc ...
that can be inherited without changing the DNA sequence. This can occur through many types of environmental interactions. Regarding euchromatin,
post-translational modifications of the histones can alter the structure of chromatin, resulting in altered gene expression without changing the DNA. Additionally, a loss of heterochromatin and increase in euchromatin has been shown to correlate with an accelerated
aging process
Ageing ( BE) or aging ( AE) is the process of becoming older. The term refers mainly to humans, many other animals, and fungi, whereas for example, bacteria, perennial plants and some simple animals are potentially biologically immortal. In ...
, especially in
diseases known to resemble premature aging. Research has shown epigenetic markers on histones for a number of additional diseases.
Regulation
Euchromatin is primarily regulated by
post-translational modification
Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribo ...
s to its nucleosomes’
histone
In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn a ...
s, conducted by many
histone-modifying enzymes. These modifications occur on the histones’
N-terminal
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the ami ...
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
Heterochromatin is a tightly packed form of DNA or '' condensed DNA'', which comes in multiple varieties. These varieties lie on a continue between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a rol ...
.
Histone acetylation, for instance, is typically associated with euchromatin structure, whereas
histone methylation
Histone methylation is a process by which methyl groups are transferred to amino acids of histone proteins that make up nucleosomes, which the DNA double helix wraps around to form chromosomes. Methylation of histones can either increase or decr ...
promotes heterochromatin remodeling.
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.
Acetylation can occur on multiple
lysine
Lysine (symbol Lys or K) is an α-amino acid that is a precursor to many proteins. It contains an α-amino group (which is in the protonated form under biological conditions), an α-carboxylic acid group (which is in the deprotonated − ...
residues of a histone's
N-terminal
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the ami ...
tail and in different histones of the same nucleosome, which is thought to further increase DNA accessibility for
transcription factor
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The f ...
s.
Phosphorylation
In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...
of histones is another method by which euchromatin is regulated.
This tends to occur on the N-terminal tails of the histones, however some sites are present in the core.
Phosphorylation is controlled by
kinases and
phosphatase
In biochemistry, a phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol. Because a phosphatase enzyme catalyzes the hydrolysis of its substrate, it is a subcategory of hydrolase ...
s, which add and remove the phosphate groups respectively. This can occur at
serine
Serine (symbol Ser or S) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α- amino group (which is in the protonated − form under biological conditions), a carboxyl group (which is in the deprotonated − for ...
,
threonine
Threonine (symbol Thr or T) is an amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form under biological conditions), a carboxyl group (which is in the deprotonated −COO� ...
, or
tyrosine
-Tyrosine or tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a non-essential amino acid with a polar side group. The word "tyrosine" is from the G ...
residues present in euchromatin.
Since the phosphate groups added to the structure will incorporate a negative charge, it will promote the more relaxed “open” form, similar to acetylation.
In regards to functionality, histone phosphorylation is involved with gene expression, DNA damage repair, and
chromatin remodeling
Chromatin remodeling is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression. Such remodeling is principally carried out ...
.
Another method of regulation that incorporates a negative charge, thereby favoring the “open” form, is
ADP ribosylation.
This process adds one or more
ADP-ribose units to the histone, and is involved in the
DNA damage response pathway.
See also
*
Histone Modifying Enzymes
*
Constitutive Heterochromatin
Constitutive heterochromatin domains are regions of DNA found throughout the chromosomes of eukaryotes. The majority of constitutive heterochromatin is found at the pericentromeric regions of chromosomes, but is also found at the telomeres and thro ...
References
Further reading
* Heterochromatin formation involves changes in histone modifications over multiple cell generations –
* Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin –
* Epigenetic inheritance and the missing heritability –
* Histone epigenetic marks in heterochromatin and euchromatin of the Chagas' disease vector, ''Triatoma infestans'' –
{{Chromo
Molecular genetics
Nuclear organization
sv:Eukromatin