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Gene transcriptions/Elements/Downstream promoters

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The diagram is an overview of four core promoter elements. Credit: Jennifer E.F. Butler & James T. Kadonaga.

The figure on the right is an overview of four core promoter elements: the B recognition element (BRE), TATA box, initiator element (Inr), and downstream promoter element (DPE), showing their respective consensus sequences and their distance from the transcription start site.[1]

"The downstream promoter element (DPE) is a core promoter element ... present in other species including humans and excluding Saccharomyces cerevisiae.[2]"[3]

"Like all core promoters, the DPE plays an important role in the initiation of gene transcription by RNA polymerase II."[3]

Gene transcriptions

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Main resource: Gene transcriptions

"Transcription by RNA polymerase II is directed by cis-acting [close-acting] DNA sequences that typically consist of a core promoter along with regulatory elements, such as enhancers [trans-acting, or distant-acting, protein factors], that contain binding sites for sequence-specific transcriptional activator and/or repressor proteins."[4]

Core promoters

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Main resources: Gene transcriptions/Core promoters and Core promoters

"[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"[4].

"[T]he core sequence of the DPE is located at precisely +28 to +32 relative to the A+1 nucleotide in the Inr"[5]. It is located about 28–33 nucleotides downstream of the transcription start site.[2]

"DPE-dependent basal transcription depends highly on the Inr (and vice versa) and on correct spacing between the two elements.[6][4][7]"[8]

Initiator elements

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Main resources: Gene transcriptions/Initiator elements and Initiator elements

"There is a strict requirement for spacing between the [Initiator element] Inr and DPE motifs, as an increase or decrease of 3 nucleotides in the distance between the Inr and DPE causes a seven- to eightfold reduction in transcription as well as a significant reduction in the binding of purified TFIID."[4]

Consensus sequences

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Main resources: Gene transcriptions/Consensus sequences and Consensus sequences

"The DPE consensus sequence was originally thought to be RGWCGTG[6], however more recent studies have suggested it to be the similar but more general sequence RGWYV(T). In nucleic acid notation for DNA, R (puRine) stands for A/G (adenine or guanine, which are both purines); W (Weak) stands for A/T (adenine or thymine, which both form only two hydrogen bonds); Y (pYrimidine) stands for C/T (cytosine or thymine, which are both pyrimidines); and V stands for A/C/G.[2][1][9]"[3]

DPE-containing promoters

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"The ... Drosophila Antennapedia P2 (Antp P2) [promoter contains] a 7-nucleotide sequence that conforms to the DPE consensus"[4]. GeneID: 40835 Antp Antennapedia [Drosophila melanogaster] is also known as Antp P2.[10] GeneID: 3204 HOXA7 homeobox A7 [ Homo sapiens ] is also known as ANTP and "[t]his gene is highly similar to the antennapedia (Antp) gene of Drosophila."[11] As GeneID: 3204 is " highly similar to the antennapedia (Antp) gene of Drosophila"[11], it may have a DPE like the Drosophila gene core promoter does.

"[T]he TATA-less Drosophila Abdominal-B (Abd-B) promoter [has a] partial DPE sequence"[4]. GeneID: 3205 HOXA9 homeobox A9 [ Homo sapiens] is also known as ABD-B and "[t]his gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila."[12] GeneID: 3205 may also be TATA-less and have a DPE.

General transcription factor II Ds

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Main resources: Gene transcriptions/General factors/II Ds and General transcription factor II Ds

The DPE "is required for the binding of purified [general transcription factor II D] TFIID to a subset of TATA-less promoters"[5].

"Photo-cross-linking analysis of purified TFIID with a TATA-less DPE-containing promoter revealed specific cross-linking of dTAFII60 [TAF6 GeneID: 6878] and dTAFII40 [TAF11 GeneID: 6882] to the DPE, with a higher efficiency of cross-linking to dTAFII60 than to dTAFII40. These data, combined with the previously well-characterized interactions between the two TAFs and their homology to histones H4 and H3, suggest that a dTAFII60–dTAFII40 heterotetramer binds to the DPE."[4]

Hypotheses

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Main resource: Hypotheses
  1. The DPE is not used to transcribe A1BG.

See also

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References

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  1. ↑ 1.0 1.1 Jennifer E.F. Butler, James T. Kadonaga (October 15, 2002). "The RNA polymerase II core promoter: a key component in the regulation of gene expression". Genes & Development 16 (20): 2583–92. doi:10.1101/gad.1026202. PMID 12381658. http://genesdev.cshlp.org/content/16/20/2583.full. 
  2. ↑ 2.0 2.1 2.2 Tamar Juven-Gershon, James T. Kadonaga (March 15, 2010). "Regulation of Gene Expression via the Core Promoter and the Basal Transcriptional Machinery". Developmental Biology 339 (2): 225–9. doi:10.1016/j.ydbio.2009.08.009. PMID 19682982. PMC 2830304. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2830304/. 
  3. ↑ 3.0 3.1 3.2 "Downstream promoter element". San Francisco, California: Wikimedia Foundation, Inc. May 6, 2012. Retrieved 2012-05-20.
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 Thomas W. Burke and James T. Kadonaga (November 15, 1997). "The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila". Genes & Development 11 (22): 3020–31. doi:10.1101/gad.11.22.3020. PMID 9367984. PMC 316699. http://genesdev.cshlp.org/content/11/22/3020.long. 
  5. ↑ 5.0 5.1 Stephen T. Smale and James T. Kadonaga (July 2003). "The RNA Polymerase II Core Promoter". Annual Review of Biochemistry 72 (1): 449-79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739. http://www.lps.ens.fr/~monasson/Houches/Kadonaga/CorePromoterAnnuRev2003.pdf. Retrieved 2012-05-07. 
  6. ↑ 6.0 6.1 T.W. Burke and James T. Kadonaga (15 March 1996). "Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters". Genes & Development 10 (6): 711–724. doi:10.1101/gad.10.6.711. PMID 8598298. http://genesdev.cshlp.org/content/10/6/711.full.pdf. 
  7. ↑ Kutach, Alan K.; Kadonaga, James T. (July 2000). "The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters". Molecular and Cellular Biology 20 (13): 4754–4764. doi:10.1128/MCB.20.13.4754-4764.2000. PMID 10848601. PMC 85905. //www.ncbi.nlm.nih.gov/pmc/articles/PMC85905/. 
  8. ↑ "Downstream promoter element, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. November 8, 2012. Retrieved 2013-01-23.
  9. ↑ James T. Kadonaga (September 2002). "The DPE, a core promoter element for transcription by RNA polymerase II". Experimental & Molecular Medicine 34 (4): 259–264. PMID 12515390. http://www.e-emm.or.kr/article/article_files/emm34-4-1.pdf. 
  10. ↑ FlyBase (February 3, 2013). "Antp Antennapedia [ Drosophila melanogaster ]". Bethesda, MD, USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.
  11. ↑ 11.0 11.1 HGNC (February 5, 2013). "HOXA7 homeobox A7 [ Homo sapiens ]". Bethesda, MD, USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.
  12. ↑ HGNC (February 5, 2013). "HOXA9 homeobox A9 [ Homo sapiens ]". Bethesda, MD, USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.

Further reading

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{{Phosphate biochemistry}}

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