Gene transcriptions/Factors

< Gene transcriptions

"[A] transcription factor ... is a protein that binds to specific DNA sequences ... [to control] the flow (or transcription) of genetic information from DNA to [messenger RNA] mRNA.[1][2]"[3]

"Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes.[4][5][6]"[3]

Gene transcriptions

Once the DNA double helix and its associated epigenome have been melted so that the template strand is available for binding, a transcription factor binds to a specific nucleotide sequence to biochemically influence gene transcription.

Transcription factor glossary
• coactivator – a protein that works with transcription factors to increase the rate of gene transcription
• corepressor – a protein that works with transcription factors to decrease the rate of gene transcription
• downregulation, repression, or suppression – decrease the rate of gene transcription
• factor – a substance, such as a protein, that contributes to the cause of a specific biochemical reaction or bodily process
• general transcription factor – a transcription factor that activates gene transcription
• gene transcription - copying of DNA into messenger RNA by RNA polymerase
• transcriptional regulation – modulating the rate of gene transcription
• upregulation, activation, or promotion – increase the rate of gene transcription

Theoretical transcription factors

Def. a substance that contains one or more DNA-binding domains that are nucleotide-sequence specific is called a transcription factor.

Def. “[a] protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA”[3] is called a transcription factor.

DNA-binding domains

"There are approximately 2600 proteins in the human genome that contain DNA-binding domains, and most of these are presumed to function as transcription factors.,[7] though other studies indicate it to be a smaller number.[8] Therefore, approximately 10% of genes in the genome code for transcription factors, which makes this family the single largest family of human proteins. Furthermore, genes are often flanked by several binding sites for distinct transcription factors, and efficient expression of each of these genes requires the cooperative action of several different transcription factors (see, for example, hepatocyte nuclear factors). Hence, the combinatorial use of a subset of the approximately 2000 human transcription factors easily accounts for the unique regulation of each gene in the human genome during development.[9]"[3]

"A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA sequence (a recognition sequence) or have a general affinity to DNA.[10] Some DNA-binding domains may also include nucleic acids in their folded structure."[11]

General transcription factors

"General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors that bind to specific sites on DNA to activate transcription. GTFs, RNA polymerase, and the mediator multiple protein complex constitute the basic transcriptional apparatus.[12]"[13]

Research

Hypothesis:

  1. Some transcription factors transcribe 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).[14] In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.[15]"[16]

Proof of concept

Def. a “short and/or incomplete realization of a certain method or idea to demonstrate its feasibility"[17] 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.[18]

See also

References

  1. ↑ Latchman DS (1997). "Transcription factors: an overview". Int. J. Biochem. Cell Biol. 29 (12): 1305–12. doi:10.1016/S1357-2725(97)00085-X. PMID 9570129.
  2. ↑ Karin M (1990). "Too many transcription factors: positive and negative interactions". New Biol. 2 (2): 126–31. PMID 2128034.
  3. 1 2 3 4 "Transcription factor, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. December 14, 2012. Retrieved 2012-12-14.
  4. ↑ Roeder RG (1996). "The role of general initiation factors in transcription by RNA polymerase II". Trends Biochem. Sci. 21 (9): 327–35. doi:10.1016/0968-0004(96)10050-5. PMID 8870495.
  5. ↑ Nikolov DB, Burley SK (1997). "RNA polymerase II transcription initiation: A structural view". Proc. Natl. Acad. Sci. U.S.A. 94 (1): 15–22. doi:10.1073/pnas.94.1.15. PMID 8990153. PMC 33652. //www.ncbi.nlm.nih.gov/pmc/articles/PMC33652/.
  6. ↑ Lee TI, Young RA (2000). "Transcription of eukaryotic protein-coding genes". Annu. Rev. Genet. 34: 77–137. doi:10.1146/annurev.genet.34.1.77. PMID 11092823.
  7. ↑ Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA (2004). "Structure and evolution of transcriptional regulatory networks". Curr. Opin. Struct. Biol. 14 (3): 283–91. doi:10.1016/j.sbi.2004.05.004. PMID 15193307.
  8. ↑ http://www.biostars.org/p/53590/
  9. ↑ Brivanlou AH, Darnell JE (2002). "Signal transduction and the control of gene expression". Science 295 (5556): 813–8. doi:10.1126/science.1066355. PMID 11823631.
  10. ↑ Lilley, David M. J. (1995). DNA-protein: structural interactions. Oxford: IRL Press at Oxford University Press. ISBN 0-19-963453-X.
  11. ↑ "DNA-binding domain, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. November 13, 2012. Retrieved 2012-12-14.
  12. ↑ Pierce, Benjamin A. 2002. Genetics : A Conceptual Approach. 1st ed. New York: W.H. Freeman and Co. pg. 367-369.
  13. ↑ "General transcription factor, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. August 8, 2012. Retrieved 2012-09-30.
  14. ↑ 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.
  15. ↑ 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.
  16. ↑ "Treatment and control groups, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. May 18, 2012. Retrieved 2012-05-31.
  17. ↑ "proof of concept, In: Wiktionary". San Francisco, California: Wikimedia Foundation, Inc. November 10, 2012. Retrieved 2013-01-13.
  18. ↑ 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.

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