By transcription factors

Figure 37-7. Transcription elements and binding factors in the herpes simplex virus thymidine kinase ffW gene. DNA-dependent RNA polymerase II binds to the region of the TATA box (which is bound by transcription factor TEND) to form a multicomponent preinitiation complex capable of initiating transcription at a single nucleotide (+1).The frequency of this event is increased by the presence of upstream c/s-acting elements (the GC and CAAT boxes). These elements bind frans-acting transcription factors, in this example Spl and CTF (also called C/EBP, NF1, NFY). These cis elements can function independently of orientation (arrows).

The non-linear connections between DNA regions brought together by coiling and which are subject to control by transcription factors. These are then concentration-dependent cooperative features internal to the code. 

Often, it is desirable to block expression of particular genes that are activated by transcription factors. The anti-sense knockout experiments are directed toward this end and require the addition of an antisense oligonucleotide, which will anneal to the cis-acting regulatory element for a particular transcription factor in a specific gene. 

Taniguchi, N. Regulation of the GnT-V promoter by transcription factor Ets-1 in various cancer cell lines. / Biol Chem1999, 274, 22941-22948. 

The requirement for zinc in the regulation of gene expression is exemplified by transcription factor IIIA, which has been shown to contain from two (Hanas et al., 1983) to seven to eleven (Miller et al., 1985) zinc ions bound to a 40K protein molecule. Transcription factor IIIA is obtained from immature Xenopus oocytes in a complex with 5 S RNA, and the protein is required for transcription initiation the apoprotein does not bind to the 5 S RNA gene (Hanas et al, 1983). Uncertainties regarding the stoichiometric requirement for zinc persist, given the report by Shang et al. (1989) that transcription factor IIIA, as either the isolated protein or the 5 S RNA complex, contains two firmly bound zinc ions which are required for transcription activation. 

In prokaryotes and eukaryotes, the expression of individual genes is controlled by activation or inhibition of RNA polymerase on each gene by transcription factors. 

Gene expression may be controlled by transcription factors that bind to the 5 -untranslated region, which encompasses the promoter. 

Cyclin E also performs its function in Gi/S phase. It demonstrates a periodic concentration change with a maximal value at the start of S phase. Afterwards, its concentration falls off sharply within S phase. The gene for cyclin E is also induced by transcription factor E2F which explains the increase in cyclin E at the Gi/S transition. Cyclin E binds and activates CDK2. The activated CDK2 complex is also involved in phosphorylation of the pRb protein. As a consequence, a signal is transmitted, with cooperation of cyclin D, in the direction of the transcription of genes that are essential for the continuation of the cell cycle. 

Lee J, Kosaras B, Aleyasin H, Han JA, Park DS, et al. 2006. Role of cyclooxygenase-2 induction by transcription factor Spl and Sp3 in neuronal oxidative and DNA damage response. FASEB J 20 E1657-E1669. 

One-dimensional diffusion can accelerate the formation of site-specific interactions within biopolymers by up to lO -fold (Berg et al., 1981). Such facihtated diffusion is used by transcription factors and restriction endonucleases to locate specific sites on double-stranded DNA (von Hippel and Berg, 1989). The backbone of RNA, like that of DNA, could allow for the facilitated diffusion of proteins. Yet, the facilitated diffusion of a protein along RNA (or any single-stranded nucleic acid) has not been demonstrated previously. 

Adachi K, Scholer HR (2012) Directing reprogramming to pluripotency by transcription factors. Curr Opin Genet Dev 22(5) 416 22... 

Redox homeostasis regulates activation and binding by transcription factors at the 5 end of the target gene. In the transcription factors, cysteine residues are frequently located in their protein... 

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