Gene transcriptions/Boxes/Enhancers

< Gene transcriptions < Boxes
This is an image of Dendromus mysticalis, the chestnut climbing mouse. Credit: Kenneth Worm.

"An E-box (Enhancer Box) is a DNA sequence which usually lies upstream of a gene in a promoter region."[1]

Enhancers

The illustration characterizes a DNA enhancer near a gene. Credit: .

"[A]n enhancer is a short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene cluster. While enhancers are usually cis-acting, an enhancer does not need to be particularly close to the genes it acts on, and sometimes need not be located on the same chromosome.[2]"[3]

"In eukaryotic cells the structure of the chromatin complex of DNA is folded in a way ... that although the enhancer DNA is far from the gene in regard to the number of nucleotides, it is geometrically close to the promoter and gene."[3]

"An enhancer may be located upstream or downstream of the gene it regulates."[3]

"Enhancers do not act on the promoter region itself, but are bound by activator proteins. These activator proteins interact with the mediator complex, which recruits polymerase II and the general transcription factors which then begin transcribing the genes. Enhancers can also be found within introns. An enhancer's orientation may even be reversed without affecting its function. Additionally, an enhancer may be excised and inserted elsewhere in the chromosome, and still affect gene transcription."[3]

Boxes

A "repeating sequence of nucleotides that forms a transcription or a regulatory signal"[4] is a box.

Immunoglobulin domains

"The immunoglobulin domain is a type of protein domain that consists of a 2-layer sandwich of between 7 and 9 antiparallel β-strands arranged in two β-sheets with a Greek key topology.[5][6]"[7]

"The E-box [is] a control element in immunoglobulin heavy-chain promoters[8]".[1]

Consensus sequences

"The consensus sequence for the E-box element is CANNTG, with a palindromic canonical sequence of CACGTG[9]."[1]

Proximal promoters

"[T]he proximal sequence upstream of the gene that tends to contain primary regulatory elements" is a proximal promoter.[10]

It is "[a]pproximately 250 base pairs [or nucleotides, nts] upstream of the [transcription] start site".[10]

There may be an E box in the proximal promoter of some genes.[9]

Distal promoters

An E-box usually lies within the distal promoter starting at or near -300 nts, the proximal promoter, or both.[9]

Research

Hypothesis:

  1. A1BG is not transcribed by an enhancer box.

Control groups

This is an image of a Lewis rat. Credit: Charles River Laboratories.

The findings demonstrate a statistically systematic change from the status quo or the control group.

“In the design of experiments, treatments [or special properties or characteristics] are applied to [or observed in] experimental units in the treatment group(s).[11] In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.[12]"[13]

Proof of concept

Def. a “short and/or incomplete realization of a certain method or idea to demonstrate its feasibility"[14] is called a proof of concept.

Def. evidence that demonstrates that a concept is possible is called proof of concept.

The proof-of-concept structure consists of

  1. background,
  2. procedures,
  3. findings, and
  4. interpretation.[15]

See also

References

  1. 1 2 3 "E-box, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. April 13, 2013. Retrieved 2013-04-17.
  2. ↑ Charalampos G. Spilianakis, Maria D. Lalioti, Terrence Town, Gap Ryol Lee, Richard A. Flavell (2005). "Interchromosomal associations between alternatively expressed loci". Nature 435 (7042): 637–45. doi:10.1038/nature03574. PMID 15880101.
  3. 1 2 3 4 "Enhancer (genetics), In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. April 27, 2013. Retrieved 2013-06-15.
  4. ↑ "Box (disambiguation), In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. May 23, 2013. Retrieved 2013-06-15.
  5. ↑ Bork P, Holm L, Sander C (September 1994). "The immunoglobulin fold. Structural classification, sequence patterns and common core". Journal of Molecular Biology 242 (4): 309–20. doi:10.1006/jmbi.1994.1582. PMID 7932691.
  6. ↑ Brümmendorf T, Rathjen FG (1995). "Cell adhesion molecules 1: immunoglobulin superfamily". Protein Profile 2 (9): 963–1108. PMID 8574878.
  7. ↑ "Immunoglobulin domain, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. June 29, 2012. Retrieved 2012-07-15.
  8. ↑ George M. Church, Anne Ephrussi, Walter Gilbert, Susumu Tonegawa (1985). Nature 313 (6005): 798-801.
  9. 1 2 3 Jaideep Chaudhary and Michael K. Skinner (May 1999). "Basic Helix-Loop-Helix Proteins Can Act at the E-Box within the Serum Response Element of the c-fos Promoter to Influence Hormone-Induced Promoter Activation in Sertoli Cells". Molecular Endocrinology 13 (5): 774-86. doi:10.1210/me.13.5.774. PMID 10319327. http://mend.endojournals.org/content/13/5/774.short. Retrieved 2013-06-14.
  10. 1 2 "Promoter (genetics), In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. June 14, 2013. Retrieved 2013-06-15.
  11. ↑ Klaus Hinkelmann, Oscar Kempthorne (2008). Design and Analysis of Experiments, Volume I: Introduction to Experimental Design (2nd ed.). Wiley. ISBN 978-0-471-72756-9. http://books.google.com/?id=T3wWj2kVYZgC&printsec=frontcover.
  12. ↑ R. A. Bailey (2008). Design of comparative experiments. Cambridge University Press. ISBN 978-0-521-68357-9. http://www.cambridge.org/uk/catalogue/catalogue.asp?isbn=9780521683579.
  13. ↑ "Treatment and control groups, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. May 18, 2012. Retrieved 2012-05-31.
  14. ↑ "proof of concept, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. November 10, 2012. Retrieved 2013-01-13.
  15. ↑ Ginger Lehrman and Ian B Hogue, Sarah Palmer, Cheryl Jennings, Celsa A Spina, Ann Wiegand, Alan L Landay, Robert W Coombs, Douglas D Richman, John W Mellors, John M Coffin, Ronald J Bosch, David M Margolis (August 13, 2005). "Depletion of latent HIV-1 infection in vivo: a proof-of-concept study". Lancet 366 (9485): 549-55. doi:10.1016/S0140-6736(05)67098-5. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894952/. Retrieved 2012-05-09.

Further reading

External links

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