Editing Euchromatin

{{short description|Lightly packed form of chromatin that is enriched in genes}}
[[File:Sha-Boyer-Fig1-CCBy3.0.jpg|thumb|300x300px|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 [[gene]]s, and is often (but not always) under active [[Transcription (genetics)|transcription]]. Euchromatin stands in contrast to [[heterochromatin]], which is tightly packed and less accessible for transcription. 92% of the human genome is euchromatic.<ref>{{cite journal | author = International Human Genome Sequencing Consortium | title = Finishing the euchromatic sequence of the human genome | journal = Nature | volume = 431 | issue = 7011 | pages = 931–945 | date = October 2004 | pmid = 15496913 | doi = 10.1038/nature03001 | bibcode = 2004Natur.431..931H | s2cid = 186242248 | doi-access = free }}</ref>

In [[eukaryote]]s, 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 [[Cell nucleus|nucleus]], possibly as a mechanism to handle increasing genome size.

== Structure ==
Euchromatin is composed of repeating subunits known as [[nucleosome]]s, reminiscent of an unfolded set of beads on a string, that are approximately 11&nbsp;nm in diameter.<ref name="Babu_1987">{{cite journal | vauthors = Babu A, Verma RS | title = Chromosome structure: euchromatin and heterochromatin | journal = International Review of Cytology | volume = 108 | pages = 1–60 | date = January 1987 | pmid = 2822591 | doi = 10.1016/s0074-7696(08)61435-7 | publisher = Academic Press | isbn = 978-0-12-364508-1 | veditors = Bourne GH, Jeon KW, Friedlander M }}</ref> At the core of these nucleosomes are a set of four [[histone]] protein pairs: [[Histone H3|H3]], [[Histone H4|H4]], [[Histone H2A|H2A]], and [[Histone H2B|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>{{Cite web|title= Definition: nucleosome/nucleosomes | work = Scitable Nature Education |url=https://www.nature.com/scitable/definition/nucleosome-nucleosomes-30/|access-date=2021-10-06 |language=en}}</ref> Nucleosomes along the strand are linked together via the histone, [[Histone H1|H1]],<ref>{{cite book | vauthors = Mobley AS | chapter = Chapter 4 - Induced Pluripotent Stem Cells|date= January 2019 | title =Neural Stem Cells and Adult Neurogenesis|pages=67–94| veditors = Mobley AS |publisher=Academic Press|language=en|isbn=978-0-12-811014-0 }}</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 (biology)|transcription]].<ref name="Babu_1987" />

==Appearance==
[[File:Heterochromatic versus euchromatic nuclei.jpg|thumb|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 [[Micrograph|electron microscope]] visualizations.<ref name="mmegias">{{Cite web|title=The cell. 4. Nucleus. Chromatin. Atlas of plant and animal histology.|url=https://mmegias.webs.uvigo.es/02-english/5-celulas/4-cromatina.php|access-date=2021-12-02|website=mmegias.webs.uvigo.es}}</ref> In both optical and electron microscopic visualizations, euchromatin appears lighter in color than [[heterochromatin]] - which is also present in the [[Cell nucleus|nucleus]] and appears darkly<ref>{{cite book | vauthors = Enukashvily NI | chapter = Chapter Two - Mammalian Satellite DNA: A Speaking Dumb|date= January 2013 | title = Advances in Protein Chemistry and Structural Biology|volume=90|pages=31–65| veditors = Donev R, Ponomartsev NV |series=Organisation of Chromosomes|publisher=Academic Press |language=en| doi = 10.1016/B978-0-12-410523-2.00002-X | pmid = 23582201| isbn = 978-0-12-410523-2}}</ref> - due to its less compact structure.<ref name="mmegias" /> When visualizing [[chromosome]]s, such as in a [[Karyotype|karyogram]], [[Cytogenetics|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>{{cite book | vauthors = Shen CH | chapter = Chapter 13 - Molecular Diagnosis of Chromosomal Disorders|date= January 2019 | title = Diagnostic Molecular Biology|pages=331–358| veditors = Shen CH |publisher=Academic Press|language=en|isbn=978-0-12-802823-0 | doi = 10.1016/B978-0-12-802823-0.00013-4 | s2cid = 131915096}}</ref> One such example is [[G banding]], otherwise known as [[Giemsa stain]]ing where euchromatin appears lighter than heterochromatin.<ref name="biologyonline">{{Cite web|date=2019-10-07|title=Giemsa banding|url=https://www.biologyonline.com/dictionary/giemsa-banding|access-date=2021-12-02|website=Biology Articles, Tutorials & Dictionary Online|language=en-US}}</ref>
{| class="wikitable"
|+Appearance of Heterochromatin and Euchromatin Under Various Visualization Techniques<ref name="biologyonline" /><ref>{{Cite web|date=2020-09-18|title=Reverse banding - Definition and Examples - Biology Online Dictionary|url=https://www.biologyonline.com/dictionary/reverse-banding|access-date=2021-12-02|website=Biology Articles, Tutorials & Dictionary Online|language=en-US}}</ref><ref>{{Cite web|date=2019-10-07|title=Constitutive heterochromatin banding|url=https://www.biologyonline.com/dictionary/constitutive-heterochromatin-banding|access-date=2021-12-02|website=Biology Articles, Tutorials & Dictionary Online|language=en-US}}</ref><ref>{{Cite web|date=2019-10-07|title=Quinacrine banding|url=https://www.biologyonline.com/dictionary/quinacrine-banding|access-date=2021-12-02|website=Biology Articles, Tutorials & Dictionary Online|language=en-US}}</ref><ref>{{Cite web|date=2019-10-07|title=T-banding|url=https://www.biologyonline.com/dictionary/t-banding|access-date=2021-12-02|website=Biology Articles, Tutorials & Dictionary Online|language=en-US}}</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)
|}

== Function ==
[[File:Human karyotype with bands and sub-bands.png|thumb|Schematic [[karyotype|karyogram]] of a [[human]], showing an overview of the [[human genome]] using [[G banding]], which is a method that includes [[Giemsa stain]]ing, wherein the lighter staining regions are generally more euchromatic, whereas darker regions generally are more heterochromatic.{{further|Karyotype}}]]
=== Transcription ===
Euchromatin participates in the active [[Transcription (biology)|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>{{cite journal | vauthors = Verschure PJ, van Der Kraan I, Manders EM, van Driel R | title = Spatial relationship between transcription sites and chromosome territories | journal = The Journal of Cell Biology | volume = 147 | issue = 1 | pages = 13–24 | date = October 1999 | pmid = 10508851 | pmc = 2164981 | doi = 10.1083/jcb.147.1.13 }}</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 [[DNA replication|replication]], since such processes behave differently on densely compacted chromatin. This is known as the 'accessibility hypothesis'.<ref>{{cite journal | vauthors = Muegge K | title = Modifications of histone cores and tails in V(D)J recombination | journal = Genome Biology | volume = 4 | issue = 4 | page = 211 | date = 2003-04-01 | pmid = 12702201 | pmc = 154571 | doi = 10.1186/gb-2003-4-4-211 | doi-access = free }}</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>{{cite journal | vauthors = Eisenberg E, Levanon EY | title = Human housekeeping genes, revisited | language = English | journal = Trends in Genetics | volume = 29 | issue = 10 | pages = 569–574 | date = October 2013 | pmid = 23810203 | doi = 10.1016/j.tig.2013.05.010 }}</ref>

=== Epigenetics ===
[[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>{{cite journal | vauthors = Arney KL, Fisher AG | title = Epigenetic aspects of differentiation | journal = Journal of Cell Science | volume = 117 | issue = Pt 19 | pages = 4355–4363 | date = September 2004 | pmid = 15331660 | doi = 10.1242/jcs.01390 | s2cid = 24376600 }}</ref> Regarding euchromatin, [[Euchromatin#Regulation|post-translational modifications of the histones]] can alter the structure of chromatin, resulting in altered gene expression without changing the DNA.<ref>{{cite journal | vauthors = Singh NP, Madabhushi SR, Srivastava S, Senthilkumar R, Neeraja C, Khosla S, Mishra RK | title = Epigenetic profile of the euchromatic region of human Y chromosome | journal = Nucleic Acids Research | volume = 39 | issue = 9 | pages = 3594–3606 | date = May 2011 | pmid = 21252296 | pmc = 3089472 | doi = 10.1093/nar/gkq1342 }}</ref> Additionally, a loss of heterochromatin and increase in euchromatin has been shown to correlate with an accelerated [[Ageing|aging process]], especially in [[Progeroid syndromes|diseases known to resemble premature aging]].<ref>{{cite journal | vauthors = Wang J, Jia ST, Jia S | title = New Insights into the Regulation of Heterochromatin | journal = Trends in Genetics | volume = 32 | issue = 5 | pages = 284–294 | date = May 2016 | pmid = 27005444 | doi = 10.1016/j.tig.2016.02.005 | pmc = 4842111 }}</ref> Research has shown epigenetic markers on histones for a number of additional diseases.<ref>{{Cite journal | title = Epigenetic Influences and Disease | vauthors = Simmons D | date = 2008 | journal = Nature Education | volume = 1 | issue = 1 | page = 6 |url= http://www.nature.com/scitable/topicpage/epigenetic-influences-and-disease-895|access-date=2021-12-02 }}</ref><ref>{{cite journal | vauthors = Alaskhar Alhamwe B, Khalaila R, Wolf J, von Bülow V, Harb H, Alhamdan F, Hii CS, Prescott SL, Ferrante A, Renz H, Garn H, Potaczek DP | display-authors = 6 | title = Histone modifications and their role in epigenetics of atopy and allergic diseases | journal = Allergy, Asthma, and Clinical Immunology | volume = 14 | issue = 1 | page = 39 | date = 2018-05-23 | pmid = 29796022 | pmc = 5966915 | doi = 10.1186/s13223-018-0259-4 | doi-access = free }}</ref>

== Regulation ==
Euchromatin is primarily regulated by [[post-translational modification]]s to its nucleosomes' [[histone]]s, conducted by many [[histone-modifying enzymes]]. These modifications occur on the histones' [[N-terminus|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">{{cite journal | vauthors = Bannister AJ, Kouzarides T | title = Regulation of chromatin by histone modifications | journal = Cell Research | volume = 21 | issue = 3 | pages = 381–395 | date = March 2011 | pmid = 21321607 | doi = 10.1038/cr.2011.22 | pmc = 3193420 }}</ref> [[Histone acetylation and deacetylation|Histone acetylation]], for instance, is typically associated with euchromatin structure, whereas [[histone methylation]] promotes heterochromatin remodeling.<ref name="Singh_2020">{{cite book | vauthors = Singh D, Nishi K, Khambata K, Balasinor NH | chapter = Introduction to epigenetics: basic concepts and advancements in the field|date= January 2020 | title = Epigenetics and Reproductive Health|volume=21|pages=xxv–xliv| veditors = Tollefsbol T |series=Translational Epigenetics|publisher=Academic Press|language=en| doi = 10.1016/B978-0-12-819753-0.02001-8 | isbn = 978-0-12-819753-0| s2cid = 235031860}}</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-terminus|N-terminal]] tail and in different histones of the same nucleosome, which is thought to further increase DNA accessibility for [[transcription factor]]s.<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 [[phosphatase]]s, 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|ADP ribosylation]].<ref name="Singh_2020" /> This process adds one or more [[Adenosine diphosphate ribose|ADP-ribose]] units to the histone, and is involved in the [[DNA-damage response|DNA damage response]] pathway.<ref name="Singh_2020" />

== See also ==
* [[Histone-modifying enzymes|Histone Modifying Enzymes]]
* [[Constitutive heterochromatin|Constitutive Heterochromatin]]

== References ==
{{Reflist}}

== Further reading ==
{{refbegin|30em}}
* Heterochromatin formation involves changes in histone modifications over multiple cell generations – {{cite journal | vauthors = Katan-Khaykovich Y, Struhl K | title = Heterochromatin formation involves changes in histone modifications over multiple cell generations | journal = The EMBO Journal | volume = 24 | issue = 12 | pages = 2138–2149 | date = June 2005 | pmid = 15920479 | pmc = 1150886 | doi = 10.1038/sj.emboj.7600692 }}
* Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin – {{cite journal | vauthors = Tedesco M, Giannese F, Lazarević D, Giansanti V, Rosano D, Monzani S, Catalano I, Grassi E, Zanella ER, Botrugno OA, Morelli L, Panina Bordignon P, Caravagna G, Bertotti A, Martino G, Aldrighetti L, Pasqualato S, Trusolino L, Cittaro D, Tonon G | display-authors = 6 | title = Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin | journal = Nature Biotechnology | pages = 235–244 | date = October 2021 | volume = 40 | issue = 2 | pmid = 34635836 | doi = 10.1038/s41587-021-01031-1 | hdl = 11368/3007419 | s2cid = 238637962 | hdl-access = free }}
* Epigenetic inheritance and the missing heritability – {{cite journal | vauthors = Trerotola M, Relli V, Simeone P, Alberti S | title = Epigenetic inheritance and the missing heritability | journal = Human Genomics | volume = 9 | issue = 1 | page = 17 | date = July 2015 | pmid = 26216216 | pmc = 4517414 | doi = 10.1186/s40246-015-0041-3 | doi-access = free }}
* Histone epigenetic marks in heterochromatin and euchromatin of the Chagas' disease vector, ''Triatoma infestans'' – {{cite journal | vauthors = Alvarenga EM, Rodrigues VL, Moraes AS, Naves LS, Mondin M, Felisbino MB, Mello ML | title = Histone epigenetic marks in heterochromatin and euchromatin of the Chagas' disease vector, Triatoma infestans | journal = Acta Histochemica | volume = 118 | issue = 4 | pages = 401–412 | date = May 2016 | pmid = 27079857 | doi = 10.1016/j.acthis.2016.04.002 }}
{{refend}}

{{Chromo}}

[[Category:Molecular genetics]]
[[Category:Nuclear organization]]

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