General factor II D gene transcriptions: Difference between revisions

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'''Editor-In-Chief:''' Henry A. Hoff
'''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
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 web
| author = Benjamin Lewin
| author = Benjamin Lewin
| title = Genes VIII
| title = Genes VIII
| publisher = Pearson Prentice Hall
| publisher = Pearson Prentice Hall
| location = Upper Saddle River, NJ
| location = Upper Saddle River, NJ
| year = 2004
| date = 2004
| pages = 636–637
| 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.
| isbn = 0-13-144946-X }}</ref> Before the start of [[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.
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.
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==Gene transcriptions==
==Gene transcriptions==
{{main|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.
[[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==
==RNA polymerase IIs==
{{main|Gene transcriptions/RNA polymerase IIs|RNA polymerase IIs}}
{{main|RNA polymerase II gene transcriptions}}


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


==General transcription factors==
==General transcription factors==
{{main|Gene transcriptions/General factors|General transcription factors}}
{{main|General factor gene transcriptions}}
[[Image:F2.large.jpg|thumb|right|250px|The diagram illustrates the big picture of how general transcription factors complement transcription. Credit: Development Biologists.]]
[[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>
'''General transcription factors''' (GTFs), also known as basal transcriptional factors, are a class of [[Proteins|protein]] [[transcription factor]]s that bind to specific sites on [[Human DNA|DNA]] to activate [[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>
{{clear}}
{{clear}}


==Phosphates==
==Phosphates==
{{main|Chemicals/Phosphates|Phosphates}}
{{main|Phosphate chemicals}}
[[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]].]]
[[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
"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 web
|author=Henry A. Hoff
|author=Henry A. Hoff
|title=Phosphate reserves
|title=Phosphate reserves
Line 52: Line 52:


==Core promoters==
==Core promoters==
{{main|Gene transcriptions/Core promoters|Core promoters}}
{{main|Core promoter gene transcriptions}}
[[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]].]]
[[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
The '''core promoter''' is the minimal portion of the [[Gene transcriptions/Promoters|promoter]] required to properly initiate [[Gene transcriptions|gene transcription]].<ref name=Smale2003>{{ cite journal
|author=Stephen T. Smale and James T. Kadonaga
|author=Stephen T. Smale and James T. Kadonaga
|title=The RNA Polymerase II Core Promoter
|title=The RNA Polymerase II Core Promoter
|journal=Annual Review of Biochemistry
|journal=Annual Review of Biochemistry
|month=July
|date=July 2003
|year=2003
|volume=72
|volume=72
|issue=1
|issue=1
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|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
|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
|journal=The EMBO Journal
|month=September 1,
|date=September 1, 1999
|year=1999
|volume=18
|volume=18
|issue=17
|issue=17
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|title=Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes
|title=Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes
|journal=Biochim. Biophys. Acta.
|journal=Biochim. Biophys. Acta.
|month=
|date=1997
|year=1997
|volume=1351
|volume=1351
|issue=
|issue=
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|title=Nitric oxide-responsive genes and promoters in Arabidopsis thaliana: a bioinformatics approach
|title=Nitric oxide-responsive genes and promoters in Arabidopsis thaliana: a bioinformatics approach
|journal=Journal of Experimental Botany
|journal=Journal of Experimental Botany
|month=February
|date=February 2008
|year=2008
|volume=59
|volume=59
|issue=2
|issue=2
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| issue = 1
| issue = 1
| pages = 52–65
| pages = 52–65
|month=March 1,
|date=March 1, 2007
| year = 2007
| pmid = 17123746
| pmid = 17123746
| pmc = 1955227 }}</ref>
| pmc = 1955227 }}</ref>


==TATA binding proteins==
==TATA binding proteins==
{{main|Gene transcriptions/TATA binding proteins|TATA binding proteins}}
{{main|TATA binding protein gene transcriptions}}
[[Image:Tjian fig2 lg.gif|thumb|right|250px|The diagram illustrates the approximate application and location of TBP during gene transcription. Credit: Robert Tjian.]]
[[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
The '''TATA-binding protein''' ('''TBP''') is a general transcription factor that binds specifically to a [[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 [[Eukaryotes|eukaryotic]] [[Genes|gene]] [[Gene promoter|promoter]]s.<ref name=Kornberg>{{ cite journal
| author = RD Kornberg
| author = RD Kornberg
| title = The molecular basis of eukaryotic transcription
| title = The molecular basis of eukaryotic transcription
Line 153: Line 148:
| issue = 32
| issue = 32
| pages = 12955–61
| pages = 12955–61
| year = 2007
| date = 2007
| pmid = 17670940
| pmid = 17670940
| pmc = 1941834
| pmc = 1941834
Line 164: Line 159:


==TATA binding protein associated factors==
==TATA binding protein associated factors==
{{main|Gene transcriptions/TATA binding proteins/Associated factors|TATA binding protein associated factors}}
{{main|TATA binding protein associated factor gene transcriptions}}
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.
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.


Line 174: Line 169:


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


Line 188: Line 183:


==See also==
==See also==
{{div col|colwidth=12em}}
{{div col|colwidth=20em}}
* [[General transcription factor II A]]
* [[General transcription factor II A]]
* [[General transcription factor II B]]
* [[General transcription factor II B]]
Line 196: Line 191:
* [[Initiator element]]
* [[Initiator element]]
* [[TATA binding protein associated factors]]
* [[TATA binding protein associated factors]]
* [[Gene transcriptions/A1BG|Transcription of A1BG]]
* [[A1BG gene transcriptions]]
* [[Gene transcriptions/Start sites|Transcription start sites]]
* [[Start site gene transcriptions]]
{{Div col end}}
{{Div col end}}


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| volume = 72
| volume = 72
| pages = 449–79
| pages = 449–79
| year = 2003
| date = 2003
| pmid = 12651739
| pmid = 12651739
| doi = 10.1146/annurev.biochem.72.121801.161520 }}
| doi = 10.1146/annurev.biochem.72.121801.161520 }}
Line 240: Line 235:


<!-- categories -->
<!-- categories -->
[[Category:Biochemistry/Lectures]]
[[Category:Biochemistry lectures]]
[[Category:Genetics/Lectures]]
[[Category:Genetics lectures]]
[[Category:Gene transcriptions/Lectures]]
[[Category:Gene transcription lectures]]
[[Category:Resources last modified in October 2019]]
[[Category:Resources last modified in February 2020]]
[[Category:Zoology/Lectures]]
[[Category:Zoology lectures]]

Latest revision as of 05:01, 2 February 2020

Editor-In-Chief: Henry A. Hoff

The general transcription factor II D (TFIID) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex.[1] Before the start of 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 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)."[2]

Genetics

Main article: Genetics
File:Bob, the guinea pig.jpg
This is an image of Bob, the guinea pig. Credit: selbst.

Genetics involves the expression, transmission, and variation of inherited characteristics.

Gene transcriptions

Main article: Gene transcriptions

DNA is a double helix of interlinked nucleotides surrounded by an epigenome. On the basis of biochemical signals, an enzyme, specifically a ribonucleic acid (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 article: RNA polymerase II gene transcriptions

RNA polymerase II holoenzyme complexes

Main article: RNA polymerase II holoenzyme complex gene transcriptions

General transcription factors

Main article: General factor gene transcriptions
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 protein transcription factors that bind to specific sites on DNA to activate transcription. GTFs, RNA polymerase, and the mediator multiple protein complex constitute the basic transcriptional apparatus.[3]

Phosphates

Main article: Phosphate chemicals
File:Triplite gemstone 1.jpg
Triplite is a rare fluoro-hydroxide phosphate mineral that forms in phosphate rich granitic pegmatites and high temperature hydrothermal veins. Credit: 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."[4] Bold added. For a "standard man" of 70 kg the available phosphate is ~1.52 x 1025 molecules of phosphate in some form. The available phosphate of an adult human female may differ from the "standard man".

Theoretical general transcription factors

Core promoters

Main article: Core promoter gene transcriptions
File:Preinitiation complex.png
The diagram shows the RNA polymerase II holoenzyme attached to the DNA template strand. Credit: ArneLH.

The core promoter is the minimal portion of the promoter required to properly initiate gene transcription.[5]

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)".[2][6]

TFIID binds to the core promoter to position the polymerase properly.

TATA boxes

Main articles: Gene transcriptions/Boxes/TATAs and 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."[6] Bold added. It "is a cis-regulatory element"[7] found in the promoter region of genes in archaea and eukaryotes.[5] "About 24% of human genes have a TATA-like element and their promoters are generally AT-rich".[8]

TATA binding proteins

Main article: TATA binding protein gene transcriptions
File:Tjian fig2 lg.gif
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 DNA sequence called the TATA box. This DNA sequence is found about 25 base pairs upstream of the transcription start site in some eukaryotic gene promoters.[9]

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.

TATA binding protein associated factors

Main article: TATA binding protein associated factor gene transcriptions

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)."[2]

"TAF-independent TATA-less transcription has also been described (Aso et al., 1994; Weis and Reinberg, 1997)."[2]

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 article: Preinitiation complex assembly gene transcriptions

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 Wikiversity.

See also

References

  1. ↑ Benjamin Lewin (2004). "Genes VIII". Upper Saddle River, NJ: Pearson Prentice Hall. pp. 636–637. ISBN 0-13-144946-X. Missing or empty |url= (help)
  2. ↑ 2.0 2.1 2.2 2.3 Gillian E. Chalkley and C. Peter Verrijzer (September 1, 1999). "DNA binding site selection by RNA polymerase II TAFs: a TAFII250-TAFII150 complex recognizes the Initiator". The EMBO Journal. 18 (17): 4835–45. PMID 10469661. Retrieved 2012-04-26. Unknown parameter |pdf= ignored (help)
  3. ↑ Pierce, Benjamin A. 2002. Genetics : A Conceptual Approach. 1st ed. New York: W.H. Freeman and Co. pg. 367-369.
  4. ↑ Henry A. Hoff (June 14, 2009). "Phosphate reserves". Boston, Massachusetts: WikiDoc Foundation. Retrieved 2013-08-23.
  5. ↑ 5.0 5.1 Stephen T. Smale and James T. Kadonaga (July 2003). "The RNA Polymerase II Core Promoter" (PDF). Annual Review of Biochemistry. 72 (1): 449–79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739. Retrieved 2012-05-07.
  6. ↑ 6.0 6.1 S. T. Smale (1997). "Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes". Biochim. Biophys. Acta. 1351: 73–88. |access-date= requires |url= (help)
  7. ↑ M. Cristina Palmieri, Simone Sell, Xi Huang, Matthias Scherf, Thomas Werner, Jörg Durner, and Christian Lindermayr (February 2008). "Nitric oxide-responsive genes and promoters in Arabidopsis thaliana: a bioinformatics approach". Journal of Experimental Botany. 59 (2): 177–86. doi:10.1093/jxb/erm345. Retrieved 2012-05-17.
  8. ↑ Chuhu Yang, Eugene Bolotin, Tao Jiang, Frances M. Sladek, and Ernest Martinez (March 1, 2007). "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". Gene. 389 (1): 52–65. doi:10.1016/j.gene.2006.09.029. PMC 1955227. PMID 17123746.
  9. ↑ RD Kornberg (2007). "The molecular basis of eukaryotic transcription". Proc. Natl. Acad. Sci. U.S.A. 104 (32): 12955–61. doi:10.1073/pnas.0704138104. PMC 1941834. PMID 17670940.

Further reading

External links

{{Phosphate biochemistry}}Template:SisterlinksTemplate:Sisterlinks

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