View source for General factor II D gene transcriptions

'''Editor-In-Chief:''' Henry A. Hoff

The '''general transcription factor II D''' (TF<sub>II</sub>D) is one of several [[general transcription factor]]s that make up the RNA polymerase II preinitiation complex.<ref name=Lewin>{{ cite book
| author = Benjamin Lewin
| title = Genes VIII
| publisher = Pearson Prentice Hall
| location = Upper Saddle River, NJ
| year = 2004
| pages = 636–637
| isbn = 0-13-144946-X }}</ref> Before the start of [[Draft:Gene transcriptions|transcription]], the transcription factor II D (TFIID) complex, binds to the core promoter of the gene.

TFIID is the first protein to bind to DNA during the formation of the pre-initiation transcription complex of RNA polymerase II (RNA Pol II). Binding of TFIID to the TATA box in the [[Gene promoter|promoter]] region of the gene initiates the recruitment of other factors required for RNA Pol II to begin transcription. Some of the other recruited [[transcription factors]] include TFIIA, TFIIB, and TFIIF. Each of these transcription factors is formed from the interaction of many protein subunits, indicating that transcription is a heavily regulated process.

"Several of the TFIID subunits have been implicated in core promoter selectivity (Verrijzer and Tijan, 1996; Hampsey and Reinberg, 1997; Smale, 1997; Hahn, 1998)."<ref name=Chalkley/>

==Genetics==
{{main|Genetics}}
[[Image:Bob, the guinea pig.jpg|thumb|right|250px|This is an image of Bob, the guinea pig. Credit: [http://www.tboggi.de selbst].]]
Genetics involves the expression, transmission, and variation of inherited characteristics.
{{clear}}

==Gene transcriptions==
{{main|Gene transcriptions}}
[[Draft:Deoxyribonucleic acids|DNA]] is a double helix of interlinked nucleotides surrounded by an epigenome. On the basis of biochemical signals, an enzyme, specifically a ribonucleic acid ([[Ribonucleic acids|RNA]]) polymerase, is chemically bonded to one of the strands (the template strand, usually) of this double helix. The polymerase, once phosphorylated, begins to catalyze the formation of RNA using the template strand. Although the catalysis may have more than one beginning nucleotide (a start site) and more than one ending nucleotide (a stop site) along the DNA, each nucleotide sequence catalyzed that ultimately produces approximately the same RNA is part of a gene. The catalysis of each RNA representation from the template DNA is a transcription, specifically a gene transcription. The overall process is also referred to as gene transcription.

==RNA polymerase IIs==
{{main|Gene transcriptions/RNA polymerase IIs|RNA polymerase IIs}}

==RNA polymerase II holoenzyme complexes==
{{main|Gene transcriptions/RNA polymerase II holoenzyme complexes|RNA polymerase II holoenzyme complexes}}

==General transcription factors==
{{main|Gene transcriptions/General factors|General transcription factors}}
[[Image:F2.large.jpg|thumb|right|250px|The diagram illustrates the big picture of how general transcription factors complement transcription. Credit: Development Biologists.]]
'''General transcription factors''' (GTFs), also known as basal transcriptional factors, are a class of [[Draft:Proteins|protein]] [[transcription factor]]s that bind to specific sites on [[Draft:Human DNA|DNA]] to activate [[Draft:gene transcriptions|transcription]]. GTFs, [[RNA polymerase]], and the [[Mediator complex|mediator multiple protein complex]] constitute the basic transcriptional apparatus.<ref name=Pierce>Pierce, Benjamin A. 2002. Genetics : A Conceptual Approach. 1st ed. New York: W.H. Freeman and Co. pg. 367-369.</ref>
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==Phosphates==
{{main|Chemicals/Phosphates|Phosphates}}
[[Image:Triplite gemstone 1.jpg|thumb|right|250px|Triplite is a rare fluoro-hydroxide phosphate mineral that forms in phosphate rich granitic pegmatites and high temperature hydrothermal veins. Credit: [[w:Gemshare|Gemshare]].]]
"The amount of phosphate needed or available for a purpose, including estimates of phosphate in and phosphate out, and the phosphate form, determine the '''phosphate budget''' for a cell or an entire organism."<ref name=HenryAHoffWikidoc>{{ cite book
|author=Henry A. Hoff
|title=Phosphate reserves
|publisher=WikiDoc Foundation
|location=Boston, Massachusetts
|date=June 14, 2009
|url=http://www.wikidoc.org/index.php/Phosphate_reserves
|accessdate=2013-08-23 }}</ref> Bold added. For a "standard man" of 70 kg the available phosphate is ~1.52 x 10<sup>25</sup> molecules of phosphate in some form. The available phosphate of an adult human female may differ from the "standard man".
{{clear}}

==Theoretical general transcription factors==

==Core promoters==
{{main|Gene transcriptions/Core promoters|Core promoters}}
[[Image:Preinitiation complex.png|thumb|right|250px|The diagram shows the RNA polymerase II holoenzyme attached to the DNA template strand. Credit: [[commons:User:ArneLH|ArneLH]].]]
The '''core promoter''' is the minimal portion of the [[Gene transcriptions/Promoters|promoter]] required to properly initiate [[Draft:Gene transcriptions|gene transcription]].<ref name=Smale2003>{{ cite journal
|author=Stephen T. Smale and James T. Kadonaga
|title=The RNA Polymerase II Core Promoter
|journal=Annual Review of Biochemistry
|month=July
|year=2003
|volume=72
|issue=1
|pages=449-79
|url=http://www.lps.ens.fr/~monasson/Houches/Kadonaga/CorePromoterAnnuRev2003.pdf
|arxiv=
|bibcode=
|doi=10.1146/annurev.biochem.72.121801.161520
|pmid=12651739
|accessdate=2012-05-07 }}</ref>

It contains a binding site for [[RNA polymerase]] ([[RNA polymerase I]], [[RNA polymerase II]], or [[RNA polymerase III]]) holoenzymes.

A vast network of regulatory factors that contribute to the initiation of transcription by RNA polymerase ultimately target any specific gene’s core promoter.

The core promoter includes the [[transcription start site]](s) (TSS).

That portion of the core promoter that is upstream of the TSS is also part of the [[proximal promoter]].

The core promoter is approximately -34 bp upstream from the TSS.

"Several factors have been identified that bind to core promoters (reviewed in Smale, 1997)".<ref name=Chalkley>{{ cite journal
|author=Gillian E. Chalkley and C. Peter Verrijzer
|title=DNA binding site selection by RNA polymerase II TAFs: a TAF<sub>II</sub>250-TAF<sub>II</sub>150 complex recognizes the Initiator
|journal=The EMBO Journal
|month=September 1,
|year=1999
|volume=18
|issue=17
|pages=4835-45
|url=http://www.ncbi.nlm.nih.gov/pubmed/10469661
|arxiv=
|bibcode=
|doi=
|pmid=10469661
|pdf=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1171555/pdf/004835.pdf
|accessdate=2012-04-26 }}</ref><ref name=Smale>{{ cite journal
|author=S. T. Smale
|title=Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes
|journal=Biochim. Biophys. Acta.
|month=
|year=1997
|volume=1351
|issue=
|pages=73-88
|url=
|arxiv=
|bibcode=
|doi=
|pmid=
|accessdate=2012-04-26 }}</ref>

TFIID binds to the core promoter to position the polymerase properly.
{{clear}}

==TATA boxes==
{{main|Gene transcriptions/Boxes/TATAs|TATA boxes}}
"The '''TATA box''' (also named the Goldberg-Hogness box after its discoverers) [is] the first core promoter element identified in eukaryotic protein-coding genes."<ref name=Smale/> Bold added. It "is a cis-regulatory element"<ref name=Palmieri>{{ cite journal
|author=M. Cristina Palmieri, Simone Sell, Xi Huang, Matthias Scherf, Thomas Werner, Jörg Durner, and Christian Lindermayr
|title=Nitric oxide-responsive genes and promoters in Arabidopsis thaliana: a bioinformatics approach
|journal=Journal of Experimental Botany
|month=February
|year=2008
|volume=59
|issue=2
|pages=177-86
|url=http://jxb.oxfordjournals.org/content/59/2/177.short
|arxiv=
|bibcode=
|doi=10.1093/jxb/erm345
|pmid=
|accessdate=2012-05-17 }}</ref> found in the promoter region of genes in archaea and eukaryotes.<ref name=Smale2003/> "About 24% of human genes have a TATA-like element and their promoters are generally AT-rich".<ref name=Yang>{{ cite journal
| doi = 10.1016/j.gene.2006.09.029
| author = Chuhu Yang, Eugene Bolotin, Tao Jiang, Frances M. Sladek, and Ernest Martinez
| title = Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters
| journal = Gene
| volume = 389
| issue = 1
| pages = 52–65
|month=March 1,
| year = 2007
| pmid = 17123746
| pmc = 1955227 }}</ref>

==TATA binding proteins==
{{main|Gene transcriptions/TATA binding proteins|TATA binding proteins}}
[[Image:Tjian fig2 lg.gif|thumb|right|250px|The diagram illustrates the approximate application and location of TBP during gene transcription. Credit: Robert Tjian.]]
The '''TATA-binding protein''' ('''TBP''') is a general transcription factor that binds specifically to a [[Draft:Human DNA|DNA]] sequence called the TATA box. This DNA sequence is found about 25 base pairs upstream of the [[transcription start site]] in some [[Draft:Eukaryotes|eukaryotic]] [[Draft:Genes|gene]] [[Gene promoter|promoter]]s.<ref name=Kornberg>{{ cite journal
| author = RD Kornberg
| title = The molecular basis of eukaryotic transcription
| journal = Proc. Natl. Acad. Sci. U.S.A.
| volume = 104
| issue = 32
| pages = 12955–61
| year = 2007
| pmid = 17670940
| pmc = 1941834
| doi = 10.1073/pnas.0704138104 }}</ref>

TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β sheet.

TBP is also a necessary component of RNA polymerase I and RNA polymerase III, and is, it is thought, the only common subunit required by all three of the RNA polymerases.
{{clear}}

==TATA binding protein associated factors==
{{main|Gene transcriptions/TATA binding proteins/Associated factors|TATA binding protein associated factors}}
When there is no TATA box nucleotide sequence in the gene promoter region of the DNA next to a gene, a '''TATA binding protein associated factor''' (TAF) will bind sequence specifically and force the TATA box binding protein to bind non-sequence specifically to the DNA in the promoter region.

"[T]he TAFs contribute to basal activities on non-TATA core elements in the context of TATA-less as well as TATA-containing promoters (Kaufmann and Smale, 1994; Martinez ''et al.'', 1994; Verrijzer ''et al.'', 1994, 1995; Burke and Kadonaga, 1996, 1997)."<ref name=Chalkley/>

"TAF-independent TATA-less transcription has also been described (Aso ''et al.'', 1994; Weis and Reinberg, 1997)."<ref name=Chalkley/>

The TAFs or alternates that compose the general transcription factor II D are TAF1 - TAF4, TAF4B, TAF5 - TAF9, TAF9B, TAF10 - TAF13, and TAF 15.

==Complex assembly==
{{main|Gene transcriptions/Preinitiation complex assembly|Preinitiation complex assembly}}
TFIID serves as the scaffold for assembly of the remainder of the transcription complex.

==Transcription initiations==

TFIID coordinates the activities of more than 70 polypeptides required for initiation of transcription by RNA polymerase II.

==Acknowledgements==

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from [http://www.wikiversity.org Wikiversity].

==See also==
{{div col|colwidth=12em}}
* [[General transcription factor II A]]
* [[General transcription factor II B]]
* [[General transcription factor II C]]
* [[General transcription factor II E]]
* [[General transcription factor II F]]
* [[Initiator element]]
* [[TATA binding protein associated factors]]
* [[Gene transcriptions/A1BG|Transcription of A1BG]]
* [[Gene transcriptions/Start sites|Transcription start sites]]
{{Div col end}}

==References==
{{reflist|2}}

==Further reading==
* {{ cite journal
| author = ST Smale, JT Kadonaga
| title = The RNA polymerase II core promoter
| url = http://www.lpt.ens.fr/~monasson/Houches/Kadonaga/CorePromoterAnnuRev2003.pdf
| journal = Annual review of biochemistry
| volume = 72
| pages = 449–79
| year = 2003
| pmid = 12651739
| doi = 10.1146/annurev.biochem.72.121801.161520 }}

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