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Gene transcriptions/Elements

A gene transcription element is a DNA nucleotide sequence that is a part or aspect of a promoter, especially one that is essential or characteristic for a specific gene or related genes.

Theoretical gene transcription elements

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Def. one "of the simplest or essential parts or principles of which anything consists, or upon which the constitution or fundamental powers of anything are based"[1] is called an element.

Angiotensinogen core promoter elements

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Main resources: Gene transcriptions/Elements/Angiotensinogen core promoters and Angiotensinogen core promoter elements
 
This is a restored image of a group of Ainu men between 1863 and early 1870s. Credit: Felice Beato.

Angiotensinogen core promoter element 1 (AGCE1) is an example of a core promoter element that may occur in a DNA sequence for only one gene (the human angiotensinogen gene angiotensin).

X core promoter elements

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Main resources: Gene transcriptions/Elements/X core promoters and X core promoter elements
 
The image shows a group of people gathered to promote a computer game. Credit: - EMR -.

The core promoter element X core promoter element 1 (XCPE1) directs activator-, mediator-, protein-dependent but TFIID-independent RNA polymerase II transcription from TATA box-less promoters.[2]

This promoter element appears to be exclusively human such as the group in the image at the right.

Metal responsive elements

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Main resources: Gene transcriptions/Elements/Metal responsives and Metal responsive elements

Metal responsive elements (MRE)s, or TGC boxes, may occur in the core promoter of some human DNA genes.

Notation: let the symbol MT stand for metallothionein.

"The metallothionein (MT) genes provide a good example of eucaryotic promoter architecture. MT genes specify the synthesis of low-molecular-weight metal-binding proteins. They are transcriptionally regulated by the metal ions cadmium and zinc (11), glucocorticoid hormones (18), interferon (14), interleukin-1 (22), and tumor promoters (2). The metal ion regulation of MTs is conferred by a short sequence element called the metal-responsive element (MRE [21]) or TGC box (31, 34), which functions as a metal ion-dependent enhancer."[3]

cAMP response elements

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Main resources: Gene transcriptions/Elements/cAMP responses and cAMP response elements

"cAMP-response-element modulator (CREM), a transcription factor responsive to the cAMP signal transduction pathway, drives expression of key testis-specific genes."[4]

"Transcription factors of the cAMP-response-element binding protein (CREB)–CREM family target genes with cAMP response elements (CREs) constituted by the palindromic consensus sequence TGACGTCA (Sassone-Corsi et al. 1988)."[4]

"Within the activation domain is the P-(phosphorylation) box containing the target residue for PKA phosphorylation, among other phosphoacceptor sites."[4]

EIF4E basal elements

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Main resources: Gene transcriptions/Elements/EIF4E basals and EIF4E basal elements
 
Eimeria oocysts vary in size, with E. maxima being the largest (about 20 x 30 microns) and E. mitis the smallest (about 14 x 16 microns). Credit: USDA ARS.

The EIF4E basal element, also eIF4E, (4EBE) is a basal promoter element for the eukaryotic translation initiation factor 4E. "Interactions between 4EBE and upstream activator sites are position, distance, and sequence dependent."[5]

GAAC elements

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Main resources: Gene transcriptions/Elements/GAACs and GAAC elements
 
This micrograph stained with chlorazol black, reveals an Entamoeba histolytica cyst. Credit: CDC/ Dr. George Healy.

The GAAC element is usually a core promoter element containing guanine (G), adenine (A), and cytosine (C), "able to direct a new transcription start site 2-7 bases downstream of itself, independent of TATA and Inr regions."[6]

Motif ten elements

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Main resources: Gene transcriptions/Elements/Motif ten and Motif ten elements

The motif ten element (MTE) "promotes transcription by RNA polymerase II when it is located precisely at positions +18 to +27 relative to A+1 in the initiator (Inr) element."[7]

Factor II B recognition elements

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Main resources: Gene transcriptions/Elements/Factor II B recognitions and Factor II B recognition elements
 
This is an electron microscope image the archaean Halobacteria species strain NRC-1. Credit: NASA.

"The B recognition element (BRE) is a DNA sequence found in the promoter region of most genes in eukaryotes and Archaea.[8][9]"[10]

"The BRE is a cis-regulatory element that is found immediately upstream of the TATA box, and consists of 7 nucleotides."[10]

In the archaean from the Dead Sea imaged at the right, "We have completely fragmented their DNA. I mean we have completely destroyed it by bombarding it with [radiation]. And they can reassemble their entire chromosome and put it back into working order within several hours."[11]

Downstream TFIIB recognition elements

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Main resources: Gene transcriptions/Elements/Downstream TFIIB recognitions and Downstream TFIIB recognition elements
 
This image is of a gray slender loris (Loris lydekkerianus nordicus) from Northern Sri Lanka. Credit: Dr. K.A.I. Nekaris.

The downstream B recognition element designated as the BREd,[12] or dBRE, is an additional core promoter element that occurs downstream of the TATA box and is recognized by general transcription factor II B.[12]

Initiator elements

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Main resources: Gene transcriptions/Elements/Initiators and Initiator elements

In the biosynthesis of any human protein, the gene that contains the nucleotide sequence which is translated into that protein must be transcribed. For RNA polymerase II holoenzyme to transcribe the gene, the gene's promoter must be located. After the promoter is located, the transcription start site (TSS) is pinpointed by using nucleotide sequences that include the TSS. Within the promoter, most human genes lack a TATA box and have an initiator element (Inr) or downstream promoter element instead.

Downstream core elements

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Main resources: Gene transcriptions/Elements/Downstream cores and Downstream core elements

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

Downstream promoter downstream promoters

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Main resources: Gene transcriptions/Elements/Downstream promoters and Downstream promoter downstream promoters
 
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.[13]

"The downstream promoter element (DPE) is a core promoter element ... present in other species including humans and excluding Saccharomyces cerevisiae.[14]"[15]

"Like all core promoters, the DPE plays an important role in the initiation of gene transcription by RNA polymerase II."[15]

Hypotheses

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Main resource: Hypotheses
  1. No gene transcription element is used to transcribe A1BG.

See also

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References

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  1. ↑ "element, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. 7 January 2016. Retrieved 2016-01-16.
  2. ↑ Yumiko Tokusumi, Ying Ma, Xianzhou Song, Raymond H. Jacobson, and Shinako Takada (March 2007). "The New Core Promoter Element XCPE1 (X Core Promoter Element 1) Directs Activator-, Mediator-, and TATA-Binding Protein-Dependent but TFIID-Independent RNA Polymerase II Transcription from TATA-Less Promoters". Molecular and Cellular Biology 27 (5): 1844-58. doi:10.1128/MCB.01363-06. PMID 17210644. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820453/. Retrieved 2013-02-09. 
  3. ↑ Robert D. Andersen, Susan J. Taplitz, Sandy Wong, Greg Bristol, Bill Larkin, and Harvey R. Herschman (October 1987). "Metal-Dependent Binding of a Factor In Vivo to the Metal-Responsive Elements of the Metallothionein 1 Gene Promoter". Molecular and Cellular Biology 7 (10): 3574-81. doi:10.1128/​MCB.7.10.3574. http://mcb.asm.org/content/7/10/3574.short. Retrieved 2013-04-15. 
  4. ↑ 4.0 4.1 4.2 Sarah Kimmins, Noora Kotaja, Irwin Davidson and Paolo Sassone-Corsi (1 July 2004). "Testis-specific transcription mechanisms promoting male germ-cell differentiation". Reproduction 128 (1): 5-12. doi:10.1530/rep.1.00170. http://www.reproduction-online.org/content/128/1/5.full. Retrieved 2017-02-19. 
  5. ↑ Mary Lynch, Li Chen, Michael J. Ravitz, Sapna Mehtani, Kevin Korenblat, Michael J. Pazin and Emmett V. Schmidt (August 2005). "hnRNP K Binds a Core Polypyrimidine Element in the Eukaryotic Translation Initiation Factor 4E (eIF4E) Promoter, and Its Regulation of eIF4E Contributes to Neoplastic Transformation". Molecular and Cellular Biology 25 (15): 6436-53. doi:10.1128/​MCB.25.15.6436-6453.2005. http://mcb.asm.org/content/25/15/6436.full. Retrieved 2013-03-17. 
  6. ↑ Upinder Singh, Joshua B. Rogers (August 21, 1998). "The Novel Core Promoter Element GAAC in the hgl5 Gene of Entamoeba histolytica Is Able to Direct a Transcription Start Site Independent of TATA or Initiator Regions". The Journal of Biological Chemistry 273 (34): 21663-8. doi:10.1074/jbc.273.34.21663. http://www.jbc.org/content/273/34/21663.full. Retrieved 2013-02-13. 
  7. ↑ Chin Yan Lim, Buyung Santoso, Thomas Boulay, Emily Dong, Uwe Ohler, and James T. Kadonaga (July 1, 2004). "The MTE, a new core promoter element for transcription by RNA polymerase II". Genes & Development 18 (13): 1606-17. doi:10.1101/gad.1193404. PMID 15231738. http://genesdev.cshlp.org/content/18/13/1606.full. Retrieved 2013-02-10. 
  8. ↑ Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH (1998). "New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB". Genes & Development 12 (1): 34–44. doi:10.1101/gad.12.1.34. PMID 9420329. PMC 316406. //www.ncbi.nlm.nih.gov/pmc/articles/PMC316406/. 
  9. ↑ Littlefield O, Korkhin Y, Sigler PB (1999). "The structural basis for the oriented assembly of a TBP/TFB/promoter complex". Proceedings of the National Academy of Sciences of the USA 96 (24): 13668–73. doi:10.1073/pnas.96.24.13668. PMID 10570130. PMC 24122. //www.ncbi.nlm.nih.gov/pmc/articles/PMC24122/. 
  10. ↑ 10.0 10.1 "B recognition element, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. January 30, 2013. Retrieved 2013-01-30.
  11. ↑ Adrienne Kish (September 10, 2004). "Secrets of a Salty Survivor A microbe that grows in the Dead Sea is teaching scientists about the art of DNA repair". Washington, DC USA: NASA. Retrieved 2014-05-15.
  12. ↑ 12.0 12.1 Wensheng Deng, Stefan G.E. Roberts (October 15, 2005). "A core promoter element downstream of the TATA box that is recognized by TFIIB". Genes & Development 19 (20): 2418–23. doi:10.1101/gad.342405. PMID 16230532. http://genesdev.cshlp.org/content/19/20/2418.full. 
  13. ↑ 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. 
  14. ↑ 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/. 
  15. ↑ 15.0 15.1 "Downstream promoter element, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. May 6, 2012. Retrieved 2012-05-20.
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