Gene transcriptions/TATA binding proteins

< Gene transcriptions
The diagram illustrates the approximate application and location of TBP during gene transcription. Credit: Robert Tjian.

"The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters.[1] TBP, along with a variety of TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex.[2] As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene."[3]

Notations

Notation: let the symbol TBP represent the TATA binding protein, or TATA box binding protein.

DNA melting

"TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β sheet."[3]

"The strain imposed on the DNA through this interaction initiates melting, or separation, of the strands. Because this region of DNA is rich in adenine and thymine residues, which base-pair through only two hydrogen bonds, the DNA strands are more easily separated. Separation of the two strands exposes the bases and allows RNA polymerase II to begin transcription of the gene."[3]

"TBP's C-terminus composes of a helicoidal shape that (incompletely) complements the T-A-T-A region of DNA. It is interesting to note that this incompleteness allows DNA to be passively bent on binding."[3]

Transcription initiation

"The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box.[4][5]"[3]

"TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases."[3]

Modulation of transcription

"TBP [has] a long string of glutamines [Gs] in the N-terminus of the protein. This region modulates the DNA binding activity of the C-terminus, and modulation of DNA-binding affects the rate of transcription complex formation and initiation of transcription."[3]

Research

Hypothesis:

  1. TBP initiates transcription of A1BG.

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).[6] In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.[7]"[8]

Proof of concept

Def. a “short and/or incomplete realization of a certain method or idea to demonstrate its feasibility"[9] 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.[10]

See also

References

  1. ↑ RD Kornberg (2007). "The molecular basis of eukaryotic transcription". Proc. Natl. Acad. Sci. U.S.A. 104 (32): 12955–61. doi:10.1073/pnas.0704138104. PMID 17670940. PMC 1941834. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1941834/.
  2. ↑ TI Lee , RA Young (2000). "Transcription of eukaryotic protein-coding genes". Annu. Rev. Genet. 34: 77–137. doi:10.1146/annurev.genet.34.1.77. PMID 11092823.
  3. 1 2 3 4 5 6 7 "TATA-binding protein, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. July 30, 2012. Retrieved 2012-09-29.
  4. ↑ Hochheimer A, Tjian R (June 2003). "Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression". Genes Dev. 17 (11): 1309-20. doi:10.1101/gad.1099903. PMID 12782648.
  5. ↑ Pugh BF (September 2000). "Control of gene expression through regulation of the TATA-binding protein". Gene 255 (1): 1-14. PMID 10974559.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ "Treatment and control groups, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. May 18, 2012. Retrieved 2012-05-31.
  9. ↑ "proof of concept, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. November 10, 2012. Retrieved 2013-01-13.
  10. ↑ 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.

External links

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