Gene transcriptions/Boxes/ATA

< Gene transcriptions < Boxes

The ATA box is a variant of the TATA box that appears in the globin and other genes. Instead of a sequence TATA as in the TATA box, the ATA box lacks the first thymine (T) and may be tissue specific.

Consensus sequences

"The 3' flanking area contained the highly conserved hexanucleotide sequence A-A-T-A-A-A found in eukaryotic messages between the terminator codon and the polyadenylylation site (44)."[1]

An ATA box may have the sequence AAATAT.[2] The CArG box has the sequence CCTATTATGG.[2]

This suggests a consensus sequence of 3'-AAATA(A/T)A-5' on the template strand, or perhaps 3'-(A/C/G/T)AATA(A/T)A-5'.

Cystatin genes

The "four cystatin genes [GeneID: 1469 CST1, GeneID: 1470 CST2, GeneID: 1471 CST3, and GeneID: 1472 CST4] contain the ATA-box sequence (ATAAA) in their 5'-flanking regions; however, the CAT-box sequence (CAT), a binding site of the transcription factor, CTF, is found only in the 5'-flanking region of the S-type cystatin genes."[3]

β-thalassemia

"DNA sequence analysis of a cloned β-globin gene from a Chinese patient with β-thalassemia revealed a single nucleotide substitution (A→ G) within the ATA box homology and 28 base pairs upstream from the cap site."[4]

"Comparison of the level of β-globin transcripts in a variety of deletion mutants shows that for efficient transcription, both the ATA or Goldberg–Hogness box, and a region between 100 and 58 base pairs in front of the site at which transcription is initiated, are required. Deletion of either of these regions results in a decrease in the level of β-globin transcripts by an order of magnitude; deletion of the ATA box causes an additional loss in the specificity of the site of initiation of RNA synthesis. The DNA sequences downstream from the ATA box, including the natural β-globin mRNA cap site, are dispensable for transcription in vivo."[5]

"The first is a sequence rich in the nucleic acids adenine and thymine (the Goldberg-Hogness, "TATA," or "ATA" box) which is located 20-30 base pairs upstream from the RNA initiation site (the cap site which is the transcriptional start site for the mRNA) and is characterized by a concensus sequence (5'-TATAA-ATA-3')."[6]

Research

Hypothesis:

  1. A1BG is not transcribed by an ATA 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).[7] In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.[8]"[9]

Proof of concept

Def. a “short and/or incomplete realization of a certain method or idea to demonstrate its feasibility"[10] 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.[11]

See also

References

  1. ↑ Stephen A. Liebhaber, Michel J. Goossens, and Yuet Wai Kan (December 1980). "Cloning and complete nucleotide sequence of human 5'-α-globin gene". Proceedings of the National Academy of Science USA 77 (12): 7054-8. http://www.pnas.org/content/77/12/7054.full.pdf. Retrieved 2013-06-28.
  2. 1 2 Shigemi Kimura, Kuniya Abe, Misao Suzuki, Masakatsu Ogawa, Kowashi Yoshioka, Tadasi Kaname, Teruhisa Miike and Ken-ichi Yamamura (June 1997). "A 900 bp genomic region from the mouse dystrophin promoter directs lacZ reporter expression only to the right heart of transgenic mice". Development, Growth & Differentiation 39 (3): 257-65. doi:10.1046/j.1440-169X.1997.t01-2-00001.x. http://onlinelibrary.wiley.com/doi/10.1046/j.1440-169X.1997.t01-2-00001.x/full. Retrieved 2013-06-28.
  3. ↑ Eiichi Saitoh and Satoko Isemura (January 1, 1993). "Molecular Biology of Human Salivary Cysteine Proteinase Inhibitors". Critical Reviews in Oral Biology and Medicine 4 (3/4): 487-93. doi:10.1177/10454411930040033301. http://cro.sagepub.com/content/4/3/487.full.pdf. Retrieved 2013-06-28.
  4. ↑ Stuart H. Orkin, Julianne P. Sexton, Tu-chen Cheng, Sabra C. Goff, Patricia J. V. Giardina, I. Lee Joseph and Haig H. Hazazian Jr. (1983). "ATA box transcription mutation in β-thalassemia". Nucleic Acids Research 11 (14): 4727-34. doi:10.1093/nar/11.14.4727. http://nar.oxfordjournals.org/content/11/14/4727.short. Retrieved 2014-05-29.
  5. ↑ G. C. Grosveld, E. De Boer, C. K. Shewmaker, & R. A. Flavell (January 14, 1982). "DNA sequences necessary for transcription of the rabbit β-globin gene in vivo". Nature 295 (5845): 120-6. doi:10.1038/295120a0. http://www.nature.com/nature/journal/v295/n5845/abs/295120a0.html. Retrieved 2014-05-29.
  6. ↑ GE Smith, MD Summers (1988). "Method for producing a recombinant baculovirus expression vector". US Patent (4,745,051). http://www.google.com/patents/US4745051. Retrieved 2014-05-29.
  7. ↑ 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.
  8. ↑ 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.
  9. ↑ "Treatment and control groups, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. May 18, 2012. Retrieved 2012-05-31.
  10. ↑ "proof of concept, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. November 10, 2012. Retrieved 2013-01-13.
  11. ↑ 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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