Gene transcriptions/Downstream TFIIB recognition elements

< Gene transcriptions
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,[1] or dBRE, is an additional core promoter element that occurs downstream of the TATA box and is recognized by general transcription factor II B.[1]

Consensus sequences

A consensus sequence is 5'-A/G-T-A/G/T-G/T-G/T-G/T-G/T-3' or in the transcription direction on the template strand 3'-A/G-T-A/G/T-G/T-G/T-G/T-G/T-5'.[1]

Genes/Eukaryote genes

Of 140 promoters from the eukaryotic promoter database, "[S]ix percent ... [contain] at least six out of seven bases of the consensus sequence, 18% contain at least five of seven bases and 37% contain at least four of seven".[1]

Human genes

GeneID: 9555 H2A histone family, member Y (H2AFY)[2] "contains a poor TATA element, but both a consensus Inr and DPE in addition to a six/seven match BREd."[1]

General transcription factor II Bs

A TFIIB recognition element (BRE) functions to determine the orientation of the TFIIB-TBP-TATA complex that projects the zinc ribbon of TFIIB toward the TSS.[3]

General transcription factor II B can recognize two distinct sequence elements that flank the TATA box.[1] "The selected sequences contain a strong representation of [ guanine (G) and thymine (T)] bases and a striking preference against [ adenine (A)] (especially between bases -17 and -20)."[1]

"[T]here are ... some weakly conserved features including the TFIIB-Recognition Element (BRE), approximately 5 nucleotides upstream (BREu) and 5 nucleotides downstream (BREd) of the TATA box.[4]"[5]

The TFIIB-DNA contact with the BREd takes place via the minor groove, while that with the upstream B recognition element (BREu) takes place through the major groove.[1]

Transcription start sites

dBRE is cis-TATA box, between the TATA box and the Inr or transcription start site (TSS) and trans-TSS.[1]

Research

Hypothesis:

  1. The dBRE is not involved in the 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. 1 2 3 4 5 6 7 8 9 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.
  2. ↑ HGNC (February 10, 2013). "H2AFY H2A histone family, member Y [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-11.
  3. ↑ Tsai FTP, Sigler PB (2000). "Structural basis of preinitiation complex assembly on human Pol II promoters". EMBO J. 19: 25–36.
  4. ↑ "Polymerase II".
  5. ↑ "RNA polymerase II holoenzyme, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. January 19, 2013. Retrieved 2013-02-11.
  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.

Further reading

External links

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