Downstream core element gene transcriptions: Difference between revisions

Revision as of 01:25, 13 October 2019

Editor-In-Chief: Henry A. Hoff

Template:TOCright The downstream core element (DCE) is a transcription core promoter sequence that is within the transcribed portion of a gene.

Downstream

Def. lower "down, in relation to a river or stream ... [f]ollowing the path of a river or stream"^[1] is called downstream.

By analogy, gene transcription follows a path along the human DNA template strand once the RNA polymerase II holoenzyme locates the transcription start site (TSS).

Cores

Def. the "central part ... heart ... center or inner part ... [t]he most important part of a thing ... [an] inside"^[2] is called a core.

Consensus sequences

The consensus sequence for the DCE is CTTC...CTGT...AGC.^[3] These three consensus elements are referred to as subelements: "S_I is CTTC, S_II is CTGT, and S_III is AGC."^[3]

The number of nucleotides between each subelement can apparently vary down to none.

Core promoters

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.^[4]

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

"[T]he core promoter [consists of] the DNA sequences, which encompass the transcription start site (within about -40 and +40 [nucleotides] relative to the +1 start site"^[5].

"Several factors have been identified that bind to core promoters (reviewed in Smale, 1997)"^[6]^[7].

A core promoter that contains all three subelements of the downstream core element may be much less common than one containing only one or two.^[3] "S_I resides approximately from +6 to +11, S_II from +16 to +21, and S_III from +30 to +34."^[3]

Transcription start sites

Notation: let the subscript (+1) indicate the specific nucleobase (nucleotide) along the template strand that is a transcription start site. For example, A₊₁.

The transcription start site (TSS) is the location on the DNA template strand where transcription begins at the 3'-end of a gene.^[8] This location corresponds to the 5'-end of the mRNA which by convention is used to designate DNA locations.^[8]

Nucleotides downstream from the TSS (N₊₁, where N stands for any nucleotide) are numbered increasing from +1.

TSS location

One method to perform a TSS location is to test for portions of the downstream core element (DCE) within the about to be transcribed portion of the gene.

S_I as 3'-CTTC-5' can occur as 3 of 4 (CTT, TTC) or 4 of 4 (CTTC). S_II as 3'-CTGT-5' can also occur as 3 of 4 (CTG, TGT) or 4 of 4 (CTGT). S_III as AGC is not known to vary.

DCE S_III can function independently of SI and SII.^[3]

General transcription factor II Ds

Transcription factor II D (TFIID), a transcription factor that is part of the RNA polymerase II holoenzyme, interacts with promoters containing only S_III of the DCE suggesting a critical spacing parameter between S_III and the TATA box, initiator element, or some combination of the two.^[3] TFIID probably serves as a core promoter recognition complex.^[3]

TAF1 interacts with the DCE in a sequence-dependent manner.^[3]

The differences between core promoters with downstream elements may be explained by

"TATA- and DPE-dependent promoters are specific for particular enhancers"^[3],
"preferences of activators for specific core promoter architectures"^[3], and
"the presence of a DCE or [downstream core promoter element (DPE)] might be indicative of an architecture designed for specific regulatory networks, such as the regulation of housekeeping promoters versus tissue-specific promoters (or other highly regulated promoters) or the regulation of subsets of viral promoters."^[3]

Hypotheses

The downstream core element is not involved in the transcription of A1BG.

References

↑ downstream. San Francisco, California: Wikimedia Foundation, Inc. August 30, 2012. Retrieved 2013-06-28.
↑ core. San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-06-28.
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 Dong-Hoon Lee, Naum Gershenzon, Malavika Gupta, Ilya P. Ioshikhes, Danny Reinberg and Brian A. Lewis (2005). "Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1". Molecular and Cellular Biology. 25 (21): 9674–86. doi:10.1128/MCB.25.21.9674-9686.2005. PMID 16227614. Retrieved 2010-10-23. Unknown parameter |month= ignored (help)
↑ Stephen T. Smale and James T. Kadonaga (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. Unknown parameter |month= ignored (help)
↑ Thomas W. Burke and James T. Kadonaga (1997). "The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAF_II60 of Drosophila". Genes & Development. 11 (22): 3020–31. doi:10.1101/gad.11.22.3020. PMC 316699. PMID 9367984. Unknown parameter |month= ignored (help)
↑ Gillian E. Chalkley and C. Peter Verrijzer (1999). "DNA binding site selection by RNA polymerase II TAFs: a TAF_II250-TAF_II150 complex recognizes the Initiator" (PDF). The EMBO Journal. 18 (17): 4835–45. PMID 10469661. Retrieved 2012-04-26. Unknown parameter |month= ignored (help)
↑ 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)
↑ ^8.0 ^8.1 Marketa J. Zvelebil, Jeremy O. Baum (2008). Dom Holdsworth, ed. Understanding bioinformatics. New York: Garland Science. p. 772. ISBN 978-0815340249.

External links

Template:Sisterlinks

[DownstreamWikt-1] downstream. San Francisco, California: Wikimedia Foundation, Inc. August 30, 2012. Retrieved 2013-06-28.

[CoreWikt-2] core. San Francisco, California: Wikimedia Foundation, Inc. June 18, 2013. Retrieved 2013-06-28.

[Lee-3] 3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 Dong-Hoon Lee, Naum Gershenzon, Malavika Gupta, Ilya P. Ioshikhes, Danny Reinberg and Brian A. Lewis (2005). "Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1". Molecular and Cellular Biology. 25 (21): 9674–86. doi:10.1128/MCB.25.21.9674-9686.2005. PMID 16227614. Retrieved 2010-10-23. Unknown parameter |month= ignored (help)

[Smale03-4] Stephen T. Smale and James T. Kadonaga (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. Unknown parameter |month= ignored (help)

[Burke1997-5] Thomas W. Burke and James T. Kadonaga (1997). "The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAF_II60 of Drosophila". Genes & Development. 11 (22): 3020–31. doi:10.1101/gad.11.22.3020. PMC 316699. PMID 9367984. Unknown parameter |month= ignored (help)

[Chalkley-6] Gillian E. Chalkley and C. Peter Verrijzer (1999). "DNA binding site selection by RNA polymerase II TAFs: a TAF_II250-TAF_II150 complex recognizes the Initiator" (PDF). The EMBO Journal. 18 (17): 4835–45. PMID 10469661. Retrieved 2012-04-26. Unknown parameter |month= ignored (help)

[Smale-7] 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)

[Zvelebil-8] 8.0 ^8.1 Marketa J. Zvelebil, Jeremy O. Baum (2008). Dom Holdsworth, ed. Understanding bioinformatics. New York: Garland Science. p. 772. ISBN 978-0815340249.

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Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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