View source for Biology:RNA polymerase II

{{short description|Protein complex that transcribes DNA}}
[[File:Label RNA pol II.png|thumb|Function of RNA polymerase II (transcription). Green: newly synthesized RNA strand by enzyme]]
'''RNA polymerase II''' ('''RNAP II''' and '''Pol II''') is a [[Biology:Protein complex|multiprotein complex]] that [[Biology:Transcription|transcribes]] [[Biology:DNA|DNA]] into precursors of [[Biology:Messenger RNA|messenger RNA]] (mRNA) and most [[Biology:Small nuclear RNA|small nuclear RNA]] (snRNA) and [[Biology:MicroRNA|microRNA]].<ref name="Kornberg">{{cite journal | vauthors = Kornberg RD | title = Eukaryotic transcriptional control | journal = Trends in Cell Biology | volume = 9 | issue = 12 | pages = M46–9 | date = December 1999 | pmid = 10611681 | doi = 10.1016/S0962-8924(99)01679-7 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Sims RJ, Mandal SS, Reinberg D | title = Recent highlights of RNA-polymerase-II-mediated transcription | journal = Current Opinion in Cell Biology | volume = 16 | issue = 3 | pages = 263–71 | date = June 2004 | pmid = 15145350 | doi = 10.1016/j.ceb.2004.04.004 | doi-access = free }}</ref> It is one of the three [[Biology:RNA polymerase|RNAP]] [[Biology:Enzyme|enzyme]]s found in the nucleus of [[Biology:Eukaryote|eukaryotic]] cells.<ref name=":0" /> A 550 kDa complex of 12 subunits, RNAP II is the most studied type of [[Biology:RNA polymerase|RNA polymerase]]. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.

== Discovery ==
[[Image:RNA polymerase II.fcgi.png|thumb|300px|right|RNA polymerase II of [[Biology:Saccharomyces cerevisiae|Saccharomyces cerevisiae]] consisting of all 12 subunits.<ref name=Meyer>{{cite journal | vauthors = Meyer PA, Ye P, Zhang M, Suh MH, Fu J | title = Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model | journal = Structure | volume = 14 | issue = 6 | pages = 973–82 | date = June 2006 | pmid = 16765890 | doi = 10.1016/j.str.2006.04.003 | doi-access = free }}</ref>]]
Early studies suggested a minimum of two RNAPs: one which synthesized rRNA in the [[Biology:Nucleolus|nucleolus]], and one which synthesized other RNA in the [[Biology:Nucleoplasm|nucleoplasm]], part of the nucleus but outside the nucleolus.<ref name=":2" /> In 1969, biochemists Robert G. Roeder and William Rutter discovered there are total three distinct nuclear RNA polymerases, an additional RNAP that was responsible for transcription of some kind of RNA in the nucleoplasm.<ref name="pmid5344598">{{cite journal |vauthors=Roeder RG, Rutter WJ | title = Multiple forms of DNA-dependent RNA polymerase in eukaryotic organisms | journal = Nature | volume = 224 | issue = 5216 | pages = 234–7 |date=Oct 1969 | pmid = 5344598 | doi =10.1038/224234a0 | bibcode = 1969Natur.224..234R | s2cid = 4283528 }}</ref>  The finding was obtained by the use of ion-exchange chromatography via [[Chemistry:Diethylethanolamine|DEAE]] coated [[Biology:Sephadex|Sephadex]] beads. The technique separated the enzymes by the order of the corresponding elutions, Ι,ΙΙ,ΙΙΙ, by increasing the concentration of ammonium sulfate. The enzymes were named according to the order of the elutions, [[Biology:RNA polymerase I|RNAP I]], RNAP II, [[Biology:RNA polymerase III|RNAP IΙI]].<ref name=":0" /> This discovery demonstrated that there was an additional enzyme present in the nucleoplasm, which allowed for the differentiation between RNAP II and RNAP III.<ref>{{cite journal |vauthors=Roeder RG, Rutter WJ | title = Multiple forms of DNA-dependent RNA polymerase in eukaryotic organisms | journal = Nature | volume = 224 | issue = 5216 | pages = 234–7 |date=Oct 1969 | pmid = 5344598 | doi =10.1038/224234a0 | bibcode = 1969Natur.224..234R | s2cid = 4283528 }}</ref>

RNA polymerase II (RNAP2) undergoes regulated transcriptional pausing during early elongation. Various studies has shown that disruption of transcription elongation is implicated in [[Medicine:Cancer|cancer]], [[Medicine:Neurodegeneration|neurodegeneration]], HIV latency etc.<ref>{{Cite journal|last1=Cermakova|first1=Katerina|last2=Demeulemeester|first2=Jonas|last3=Lux|first3=Vanda|last4=Nedomova|first4=Monika|last5=Goldman|first5=Seth R.|last6=Smith|first6=Eric A.|last7=Srb|first7=Pavel|last8=Hexnerova|first8=Rozalie|last9=Fabry|first9=Milan|last10=Madlikova|first10=Marcela|last11=Horejsi|first11=Magdalena|date=2021-11-26|title=A ubiquitous disordered protein interaction module orchestrates transcription elongation|journal=Science|volume=374|issue=6571|pages=1113–1121|doi=10.1126/science.abe2913|pmid=34822292|pmc=8943916 |bibcode=2021Sci...374.1113C|s2cid=244660781}}</ref>

==Subunits==
[[File:Eukaryotic RNA-polymerase II structure 1WCM.png|thumb|300px|right|Eukaryotic RNA-polymerase II from ''[[Biology:Saccharomyces cerevisiae|Saccharomyces cerevisiae]]'', PDB ID.<ref name=Armache-eal-2019>{{cite journal |last1=Armache |first1=Karim-Jean |last2=Mitterweger |first2=Simone |last3=Meinhart |first3=Anton |last4=Cramer |first4=Patrick |date=2019 |title=Structures of complete RNA polymerase II and its subcomplex, Rpb4/7 |journal=Journal of Biological Chemistry |volume=280 |issue=8 |pages=7131–1734 |doi=10.2210/pdb1wcm/pdb |pmid=15591044 |url=https://www.jbc.org/content/280/8/7131.full.pdf }}</ref> Subunits colored: <span style="color:orange"> RPB3 – orange </span>, <span style="color:gold"> RPB11 – yellow </span>, <span style="color:peru"> RPB2 – wheat</span>, <span style="color:red"> RPB1 – red</span>, <span style="color:pink"> RPB6 – pink</span>, the rest 7 subunits are colored gray. ]]
The [[Biology:Eukaryote|eukaryotic]] core RNA polymerase II was first purified using transcription assays.<ref name=Sawadogo>{{cite journal | vauthors = Sawadogo M, Sentenac A | title = RNA polymerase B (II) and general transcription factors | journal = Annual Review of Biochemistry | volume = 59 | pages = 711–54 | year = 1990 | pmid = 2197989 | doi = 10.1146/annurev.bi.59.070190.003431 }}</ref> The purified enzyme has typically 10–12 subunits (12 in humans and yeast) and is incapable of specific promoter recognition.<ref name=Myer>{{cite journal | vauthors = Myer VE, Young RA | title = RNA polymerase II holoenzymes and subcomplexes | journal = The Journal of Biological Chemistry | volume = 273 | issue = 43 | pages = 27757–60 | date = October 1998 | pmid = 9774381 | doi = 10.1074/jbc.273.43.27757 | doi-access = free }}</ref> Many subunit-subunit interactions are known.<ref name=Acker>{{cite journal | vauthors = Acker J, de Graaff M, Cheynel I, Khazak V, Kedinger C, Vigneron M | title = Interactions between the human RNA polymerase II subunits | journal = The Journal of Biological Chemistry | volume = 272 | issue = 27 | pages = 16815–21 | date = July 1997 | pmid = 9201987 | doi = 10.1074/jbc.272.27.16815 | doi-access = free }}</ref>

* '''DNA-directed RNA polymerase II subunit RPB1''' – an [[Biology:Enzyme|enzyme]] that in humans is encoded by the [[Biology:POLR2A|POLR2A]] [[Biology:Gene|gene]] and in yeast is encoded by RPO21. RPB1 is the largest subunit of RNA polymerase II. It contains a [[Biology:C-terminus|carboxy terminal domain]] (CTD) composed of up to 52 heptapeptide repeats (YSPTSPS) that are essential for polymerase activity.<ref name="Brickey WJ, Greenleaf AL 1995 599–613">{{cite journal | vauthors = Brickey WJ, Greenleaf AL | title = Functional studies of the carboxy-terminal repeat domain of Drosophila RNA polymerase II in vivo | journal = Genetics | volume = 140 | issue = 2 | pages = 599–613 | date = June 1995 | doi = 10.1093/genetics/140.2.599 | pmid = 7498740 | pmc = 1206638 }}</ref> The CTD was first discovered in the laboratory of C.J. Ingles at the University of Toronto and by JL Corden at [[Organization:Johns Hopkins University|Johns Hopkins University]]. In combination with several other polymerase subunits, the RPB1 subunit forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA.<ref name=POLR2A>{{cite web | title = Entrez Gene: POLR2A polymerase (RNA) II (DNA directed) polypeptide A, 220kDa| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5430}}</ref> It strongly interacts with RPB8.<ref name=Acker/>
* '''RPB2''' (POLR2B) – the second-largest subunit that in combination with at least two other polymerase subunits forms a structure within the polymerase that maintains contact in the active site of the enzyme between the DNA template and the newly synthesized RNA.<ref name=POLR2B>{{cite web | title = Entrez Gene: POLR2B polymerase (RNA) II (DNA directed) polypeptide B, 140kDa| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5431}}</ref>
* '''RPB3''' (POLR2C) – the third-largest subunit. Exists as a heterodimer with another polymerase subunit, POLR2J forming a core subassembly. RPB3 strongly interacts with RPB1-5, 7, 10–12.<ref name=Acker/>
* '''RNA polymerase II subunit B4 (RPB4)''' – encoded by the POLR2D [[Biology:Gene|gene]]<ref name= Khazak >{{cite journal | vauthors = Khazak V, Estojak J, Cho H, Majors J, Sonoda G, Testa JR, Golemis EA | title = Analysis of the interaction of the novel RNA polymerase II (pol II) subunit hsRPB4 with its partner hsRPB7 and with pol II | journal = Molecular and Cellular Biology | volume = 18 | issue = 4 | pages = 1935–45 | date = April 1998 | pmid = 9528765 | pmc = 121423 | doi =  10.1128/mcb.18.4.1935}}</ref> is the fourth-largest subunit and may have a stress protective role.
* '''RPB5''' – In humans is encoded by the [[Biology:POLR2E|POLR2E]] gene. Two molecules of this subunit are present in each RNA polymerase II.<ref name=POLR2E>{{cite web | title = Entrez Gene: POLR2E polymerase (RNA) II (DNA directed) polypeptide E, 25kDa| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5434}}</ref> RPB5 strongly interacts with RPB1, RPB3, and RPB6.<ref name=Acker/>
* '''RPB6 ([[Biology:POLR2F|POLR2F]])''' – forms a structure with at least two other subunits that stabilizes the transcribing polymerase on the DNA template.<ref name=POLR2F>{{cite web | title = Entrez Gene: POLR2F polymerase (RNA) II (DNA directed) polypeptide F| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5435}}</ref>
* '''RPB7''' – encoded by POLR2G and may play a role in regulating polymerase function.<ref name=POLR2G>{{cite web | title = Entrez Gene: POLR2G polymerase (RNA) II (DNA directed) polypeptide G| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=5436}}</ref> RPB7 interacts strongly with RPB1 and RPB5.<ref name=Acker/>
* '''RPB8 (POLR2H)''' – interacts with subunits RPB1-3, 5, and 7.<ref name=Acker/>
* '''RPB9''' – The groove in which the DNA template is transcribed into RNA is composed of RPB9 ([[Biology:POLR2I|POLR2I]]) and RPB1.
* '''RPB10''' – the product of gene POLR2L. It interacts with RPB1-3 and 5, and strongly with RPB3.<ref name=Acker/>
* '''RPB11''' – the RPB11 subunit is itself composed of three subunits in humans: POLR2J (RPB11-a), [[Biology:POLR2J2|POLR2J2]] (RPB11-b), and POLR2J3<ref name=POLR2J3>{{ cite web |title=POLR2J3 polymerase (RNA) II (DNA directed) polypeptide J3 |url=https://www.ncbi.nlm.nih.gov/gene/548644?ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum }}</ref> (RPB11-c).
* '''RPB12''' – Also interacts with RPB3 is RPB12 (POLR2K).<ref name=Acker/>

==Assembly==

RPB3 is involved in RNA polymerase II assembly.<ref name=Kolodziej>{{cite journal | vauthors = Kolodziej PA, Young RA | title = Mutations in the three largest subunits of yeast RNA polymerase II that affect enzyme assembly | journal = Molecular and Cellular Biology | volume = 11 | issue = 9 | pages = 4669–78 | date = September 1991 | pmid = 1715023 | pmc = 361357 | url = | doi=10.1128/mcb.11.9.4669}}</ref> A subcomplex of RPB2 and RPB3 appears soon after subunit synthesis.<ref name=Kolodziej/> This complex subsequently interacts with RPB1.<ref name=Kolodziej/> RPB3, RPB5, and RPB7 interact with themselves to form homodimers, and RPB3 and RPB5 together are able to contact all of the other RPB subunits, except RPB9.<ref name=Acker/> Only RPB1 strongly binds to RPB5.<ref name=Acker/> The RPB1 subunit also contacts RPB7, RPB10, and more weakly but most efficiently with RPB8.<ref name=Acker/> Once RPB1 enters the complex, other subunits such as RPB5 and RPB7 can enter, where RPB5 binds to RPB6 and RPB8 and RPB3 brings in RPB10, RPB 11, and RPB12.<ref name=Acker/> RPB4 and RPB9 may enter once most of the complex is assembled. RPB4 forms a complex with RPB7.<ref name=Acker/>

==Kinetics==

[[Biology:Enzyme|Enzyme]]s can catalyze up to several million reactions per second. Enzyme rates depend on solution conditions and substrate concentration. Like other enzymes POLR2 has a saturation curve and a maximum velocity (''V''<sub>max</sub>). It has a ''K''<sub>m</sub> (substrate concentration required for one-half ''V''<sub>max</sub>) and a ''k''<sub>cat</sub> (the number of substrate molecules handled by one active site per second). The specificity constant is given by ''k''<sub>cat</sub>/''K''<sub>m</sub>. The theoretical maximum for the specificity constant is the diffusion limit of about 10<sup>8</sup> to 10<sup>9</sup> (''M''<sup>−1</sup>''s''<sup>−1</sup>), where every collision of the enzyme with its substrate results in catalysis. In yeast, mutation in the Trigger-Loop domain of the largest subunit can change the kinetics of the enzyme.<ref>{{cite journal | vauthors = Kaplan CD, Jin H, Zhang IL, Belyanin A | title = Dissection of Pol II trigger loop function and Pol II activity-dependent control of start site selection in vivo | journal = PLOS Genetics | volume = 8 | issue = 4 | pages = e1002627 | date = April 12, 2012 | pmid = 22511879 | doi = 10.1371/journal.pgen.1002627 | pmc=3325174 | doi-access = free }}</ref>

Bacterial RNA polymerase, a relative of RNA Polymerase II, switches between inactivated and activated states by translocating back and forth along the DNA.<ref name=Abbondanzieri>{{cite journal | vauthors = Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM | title = Direct observation of base-pair stepping by RNA polymerase | journal = Nature | volume = 438 | issue = 7067 | pages = 460–5 | date = November 2005 | pmid = 16284617 | pmc = 1356566 | doi = 10.1038/nature04268 | bibcode = 2005Natur.438..460A }}</ref> Concentrations of [NTP]<sub>eq</sub> = 10 μM GTP, 10 μM UTP, 5 μM ATP and 2.5 μM CTP, produce a mean elongation rate, turnover number, of ~1 bp (NTP)<sup>−1</sup> for bacterial RNAP, a relative of RNA polymerase II.<ref name=Abbondanzieri/>
[[File:Alpha-Amanitin–RNA polymerase II complex 1K83.png|thumb|188x188px|RNA Polymerase II gray. Alpha-amanitin interaction (red).]]

RNA polymerase II undergoes extensive co-transcriptional pausing during transcription elongation.<ref name=":3">{{Cite journal|last1=Hodges|first1=Courtney|last2=Bintu|first2=Lacramioara|last3=Lubkowska|first3=Lucyna|last4=Kashlev|first4=Mikhail|last5=Bustamante|first5=Carlos|date=2009-07-31|title=Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II|journal=Science|volume=325|issue=5940|pages=626–628|doi=10.1126/science.1172926|issn=1095-9203|pmc=2775800|pmid=19644123|bibcode=2009Sci...325..626H}}</ref><ref>{{Cite journal|last1=Churchman|first1=L. Stirling|last2=Weissman|first2=Jonathan S.|date=2011-01-20|title=Nascent transcript sequencing visualizes transcription at nucleotide resolution|journal=Nature|volume=469|issue=7330|pages=368–373|doi=10.1038/nature09652|issn=1476-4687|pmc=3880149|pmid=21248844|bibcode=2011Natur.469..368C}}</ref> This pausing is especially pronounced at nucleosomes, and arises in part through the polymerase entering a transcriptionally incompetent backtracked state.<ref name=":3" /> The duration of these pauses ranges from seconds to minutes or longer, and exit from long-lived pauses can be promoted by elongation factors such as TFIIS.<ref>{{Cite journal|last1=Galburt|first1=Eric A.|last2=Grill|first2=Stephan W.|last3=Wiedmann|first3=Anna|last4=Lubkowska|first4=Lucyna|last5=Choy|first5=Jason|last6=Nogales|first6=Eva|last7=Kashlev|first7=Mikhail|last8=Bustamante|first8=Carlos|date=2007-04-12|title=Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner|journal=Nature|volume=446|issue=7137|pages=820–823|doi=10.1038/nature05701|issn=1476-4687|pmid=17361130|bibcode=2007Natur.446..820G|s2cid=4310108}}</ref> In turn, the transcription rate influences whether the histones of transcribed nucleosomes are evicted from chromatin, or reinserted behind the transcribing polymerase.<ref>{{Cite journal|last1=Bintu|first1=Lacramioara|last2=Kopaczynska|first2=Marta|last3=Hodges|first3=Courtney|last4=Lubkowska|first4=Lucyna|last5=Kashlev|first5=Mikhail|last6=Bustamante|first6=Carlos|date=2011-11-13|title=The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes|journal=Nature Structural & Molecular Biology|volume=18|issue=12|pages=1394–1399|doi=10.1038/nsmb.2164|issn=1545-9985|pmc=3279329|pmid=22081017}}</ref>

=== Alpha-Amanitin ===
{{Main|Chemistry:Alpha-Amanitin}}
RNA polymerase II is inhibited by [[Chemistry:Α-Amanitin|α-Amanitin]]<ref>{{cite journal | vauthors = Kaplan CD, Larsson KM, Kornberg RD | title = The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin | journal = Molecular Cell | volume = 30 | issue = 5 | pages = 547–56 | date = June 2008 | pmid = 18538653 | pmc = 2475549 | doi = 10.1016/j.molcel.2008.04.023 }}</ref> and other [[Chemistry:Amatoxin|amatoxin]]s. α-Amanitin is a highly poisonous substance found in many mushrooms.<ref name=":2" /> The mushroom poison has different effects on each of the RNA Polymerases: I, II, III. RNAP I is completely unresponsive to the substance and will function normally while RNAP III has a moderate sensitivity. RNAP II, however, is completely inhibited by the toxin. Alpha-Amanitin inhibits RNAP II by strong interactions in the enzyme's "funnel", "cleft", and the key "bridge α-helix" regions of the RPB-1 subunit.<ref>{{Cite journal|last1=Gong|first1=Xue Q.|last2=Nedialkov|first2=Yuri A.|last3=Burton|first3=Zachary F.|date=2004-06-25|title=α-Amanitin Blocks Translocation by Human RNA Polymerase II|journal=Journal of Biological Chemistry|language=en|volume=279|issue=26|pages=27422–27427|doi=10.1074/jbc.M402163200|issn=0021-9258|pmid=15096519|doi-access=free}}</ref>

==Holoenzyme==
{{main|Biology:RNA polymerase II holoenzyme}}
'''RNA polymerase II holoenzyme''' is a form of [[Biology:Eukaryote|eukaryotic]] RNA polymerase II that is recruited to the promoters of [[Biology:Protein|protein]]-coding genes in living cells.<ref name="Myer"/> It consists of RNA polymerase II, a subset of general [[Biology:Transcription factor|transcription factor]]s, and [[Biology:Regulation of gene expression|regulatory protein]]s known as SRB proteins.

Part of the assembly of the holoenzyme is referred to as the [[Biology:Transcription preinitiation complex|preinitiation complex]], because its assembly takes place on the [[Biology:Gene|gene]] promoter before the initiation of transcription. The [[Biology:Mediator (coactivator)|mediator complex]] acts as a bridge between RNA polymerase II and the transcription factors.

==Control by chromatin structure==
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This is an outline of an example mechanism of yeast cells by which [[Biology:Chromatin|chromatin]] structure and [[Biology:Histone|histone]] [[Biology:Post-translational modification|post-translational modification]] help regulate and record the transcription of genes by RNA polymerase II.

This pathway gives examples of regulation at these points of transcription:
* Pre-initiation (promotion by Bre1, histone modification)
* Initiation (promotion by TFIIH, Pol II modification and promotion by COMPASS, histone modification)
* Elongation (promotion by Set2, Histone Modification)

This refers to various stages of the process as regulatory steps. It has not been proven that they are used for regulation, but is very likely they are.

RNA Pol II elongation promoters can be summarised in 3 classes.
#Drug/sequence-dependent arrest-affected factors (Various interfering proteins)
#Chromatin structure-oriented factors (Histone posttranscriptional modifiers, e.g., Histone Methyltransferases)
#RNA Pol II catalysis-improving factors (Various interfering proteins and Pol II cofactors; see RNA polymerase II).

==Transcription mechanisms==
* ''Chromatin structure oriented factors:''<br />''(HMTs ('''H'''istone '''M'''ethyl'''T'''ransferases)):''<br /> COMPASS§† – ('''COM'''plex of '''P'''roteins '''AS'''sociated with '''S'''et1) – Methylates lysine 4 of histone H3: Is responsible of repression/silencing of transcription. A normal part of cell growth and transcription regulation within RNAP II.<ref>{{Cite journal|last1=Briggs|first1=Scott D.|last2=Bryk|first2=Mary|last3=Strahl|first3=Brian D.|last4=Cheung|first4=Wang L.|last5=Davie|first5=Judith K.|last6=Dent|first6=Sharon Y. R.|last7=Winston|first7=Fred|last8=Allis|first8=C. David|date=2001-12-15|title=Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae|journal=Genes & Development|language=en|volume=15|issue=24|pages=3286–3295|doi=10.1101/gad.940201|issn=0890-9369|pmc=312847|pmid=11751634}}</ref>
* Set2 – Methylates lysine 36 of histone H3: Set2 is involved in regulation transcription elongation through its direct contact with the CTD.<ref>{{Cite journal|last1=Li|first1=Bing|last2=Howe|first2=LeAnn|last3=Anderson|first3=Scott|last4=Yates|first4=John R.|last5=Workman|first5=Jerry L.|date=2003-03-14|title=The Set2 Histone Methyltransferase Functions through the Phosphorylated Carboxyl-terminal Domain of RNA Polymerase II|journal=Journal of Biological Chemistry|language=en|volume=278|issue=11|pages=8897–8903|doi=10.1074/jbc.M212134200|issn=0021-9258|pmid=12511561|doi-access=free}}</ref><br /> (interesting irrelevant example: Dot1*‡ – Methylates lysine 79 of histone H3.)
* Bre1 – Ubiquinates (adds [[Biology:Ubiquitin|ubiquitin]] to) lysine 123 of histone H2B. Associated with pre-initiation and allowing RNA Pol II binding.

===C-terminal Domain===

The [[Biology:C-terminus|C-terminus]] of RPB1 is appended to form the C-terminal domain (CTD). The carboxy-terminal domain of RNA polymerase II typically consists of up to 52 repeats of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser.<ref>{{cite journal | vauthors = Meinhart A, Cramer P | title = Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors | journal = Nature | volume = 430 | issue = 6996 | pages = 223–6 | date = July 2004 | pmid = 15241417 | doi = 10.1038/nature02679 | bibcode = 2004Natur.430..223M | s2cid = 4418258 | url = http://nbn-resolving.de/urn:nbn:de:bvb:12-bsb00085061-6 | hdl = 11858/00-001M-0000-0015-8512-8 | hdl-access = free }}</ref> The domain stretches from the core of the RNAPII enzyme to the exit channel, this placement is effective due to its inductions of "RNA processing reactions, through direct or indirect interactions with components of the RNA processing machinery".<ref name=":1">{{Cite journal|last1=Egloff|first1=Sylvain|last2=Murphy|first2=Shona|title=Cracking the RNA polymerase II CTD code|journal=Trends in Genetics|volume=24|issue=6|pages=280–288|doi=10.1016/j.tig.2008.03.008|pmid=18457900|year=2008}}</ref> The CTD domain does not exist in RNA Polymerase I or RNA Polymerase III.<ref name=":0">{{Cite journal|last=Young|first=Richard A.|date=2003-11-28|title=RNA Polymerase II|journal=Annual Review of Biochemistry|language=en|volume=60|issue=1|pages=689–715|doi=10.1146/annurev.bi.60.070191.003353|pmid=1883205}}</ref> The RNA Polymerase CTD was discovered first in the laboratory of C.J.Ingles at the University of Toronto and also in the laboratory of J Corden at Johns Hopkins University during the processes of sequencing the DNA encoding the RPB1 subunit of RNA polymerase from Yeast and Mice respectively. Other proteins often bind the C-terminal domain of RNA polymerase in order to activate polymerase activity. It is the protein domain that is involved in the initiation of transcription, the capping of the [[Biology:Messenger RNA|RNA transcript]], and attachment to the [[Biology:Spliceosome|spliceosome]] for [[Biology:RNA splicing|RNA splicing]].<ref name="Brickey WJ, Greenleaf AL 1995 599–613"/>

==== Phosphorylation of the CTD ====
RNA Polymerase II exists in two forms unphosphorylated and phosphorylated, IIA and IIO respectively.<ref name=":2">{{Cite book|title=Molecular biology|author=Weaver, Robert Franklin|date=2012-01-01|publisher=McGraw-Hill|isbn=9780073525327|oclc=789601172}}</ref><ref name=":0" /> The transition between the two forms facilitates different functions for transcription. The [[Biology:Phosphorylation|phosphorylation]] of CTD is catalyzed by one of the six [[Biology:General transcription factor|general transcription factor]]s, TFIIH. TFIIH serves two purposes: one is to unwind the DNA at the transcription start site and the other is to phosphorylate. The form polymerase IIA joins the preinitiation complex, this is suggested because IIA binds with higher affinity to the TBP (TATA-box binding protein), the subunit of the general transcription factor TFIID, than polymerase IIO form. The form polymerase IIO facilitates the elongation of the RNA chain.<ref name=":2" /> The method for the elongation initiation is done by the phosphorylation of [[Chemistry:Serine|Serine]] at position 5 (Ser5), via TFIIH. The newly phosphorylated Ser5 recruits enzymes to cap the 5' end of the newly synthesized RNA and the "3' processing factors to poly(A) sites".<ref name=":1" /> Once the second Serine is phosphorylated, Ser2, elongation is activated. In order to terminate elongation dephosphorylation must occur. Once the domain is completely dephosphorylated the RNAP II enzyme is "recycled" and catalyzes the same process with another initiation site.<ref name=":1" />

==Transcription coupled recombinational repair==

[[Chemistry:DNA oxidation|Oxidative DNA damage]] may block RNA polymerase II [[Biology:Transcription|transcription]] and cause strand breaks.  An RNA templated transcription-associated recombination process has been described that can protect against DNA damage.<ref name="pmid27233112">{{cite journal |vauthors=Wei L, Levine AS, Lan L |title=Transcription-coupled homologous recombination after oxidative damage |journal=DNA Repair (Amst.) |volume=44 |pages=76–80 |year=2016 |pmid=27233112 |doi=10.1016/j.dnarep.2016.05.009 }}</ref>  During the G1/G0 stages of the [[Biology:Cell cycle|cell cycle]], cells exhibit assembly of homologous recombination factors at double-strand breaks within actively transcribed regions.  It appears that transcription is coupled to repair of DNA double-strand breaks by RNA templated homologous recombination.  This repair process efficiently and accurately rejoins double-strand breaks in [[Biology:Gene|gene]]s being actively transcribed by RNA polymerase II.

== See also ==
* [[Biology:Eukaryotic transcription|Eukaryotic transcription]]
* [[Biology:Post-transcriptional modification|Post-transcriptional modification]]
* [[Biology:RNA polymerase I|RNA polymerase I]]
* [[Biology:RNA polymerase II holoenzyme|RNA polymerase II holoenzyme]]
* [[Biology:RNA polymerase III|RNA polymerase III]]
* Transcription (genetics)

== References ==
{{reflist}}

== External links ==
* [https://web.archive.org/web/20041018112937/http://www.als.lbl.gov/als/science/sci_archive/polymerase2.html More information at Berkeley National Lab]
([[Wayback Machine]] copy)
* {{MeshName|RNA+Polymerase+II}}

{{Kinases}}
{{Enzymes}}

{{DEFAULTSORT:Rna Polymerase Ii}}
[[Category:EC 2.7.7]]
[[Category:Proteins]]
[[Category:Gene expression]]

{{Sourceattribution|RNA polymerase II}}