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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]

Contents

Gene transcriptionsEdit

"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 promotersEdit

"[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 elementsEdit

"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 sequencesEdit

"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 promotersEdit

"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 DsEdit

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]

HypothesesEdit

  1. The DPE is not used to transcribe A1BG.

See alsoEdit

ReferencesEdit

  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, In: Wikipedia". 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 ]". 8600 Rockville Pike, Bethesda MD, 20894 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 ]". 8600 Rockville Pike, Bethesda MD, 20894 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 ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-07.

Further readingEdit

External linksEdit