Talk:Transcription factor

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Article Grading: The following comments were left by the quality and importance raters: (edit · refresh) Changed rating to "high" as this is high school/SAT biology content and central to molecular biology. The article needs serious attention, e.g. an explanation how transcription factors work, more general expansion on classes of transcription factors etc. - tameeria 22:34, 18 February 2007 (UTC)

Regarding the need for revision and use of Template:Confusing

I think this article needs a greater level of detail devoted to framing transcription and transcription factors in their relevant context.

I'm going to annotate the first sentence in order to clarify what sort of information seems missing.

"In molecular biology, a transcription factor is a protein that regulates* the activation** of transcription*** in the eukaryotic nucleus****."

* The word regulates is either ambiguous or inconsistent with the word activation. In this context, does it mean triggers? or maybe schedules?

** Be careful about making references to concepts that have not yet been treated in this article. A stickler would never do it. And a pragmatist would almost never do it, and make sure that exceptions to the rule are at least linked to a wiki article that does explain the concept.

*** When I found this article, I was actually (apparently) looking for an article that defined transcription; this is another good reason to try hard to frame Transcription factor in the context of Transcription. Put another way, it seems like transcription is a process with an end goal (duping dna subsequences out into new proteins?), and like transcription factor is a catalyst or an agent in that effort. I think readers would benefit from seeing some info about the nature of the end goal and what exact role transcription factors play in the pursuit.

**** eh, what? this bullet is redundant with the second one. however, its more critical to address. when I read the word activation, I thought hmmm, hope that gets cleared up... and when I read eukaryotic nucleus, I was ambushed by garbled high school memories of eukaryotes vs prokaryotes vs mitochondria, and my head fell off.

Kierah 23:00, 22 October 2006 (UTC)

Ok, first off, regulates is a good word, especially since it is the typical term used in the field to describe the actions of transcription factors. It does regulate the "activation" of transcription. TFs are not truly associated with transcription itself as that is accomplished primarily by the RNA polymerase enzyme. They rather act to control the level of transcription of a particular gene...ie regulating the activation of the gene to produce its protein or other end product. Trigger and schedule are both too narrow as TFs can promote transcription or suppress it. I'll add links in the text to appropriate articles for activation and eukaryotic nuclei as those seem to be unmarked and are better explained in their own articles since this one should focus on how TFs work.Cquan 23:11, 22 October 2006 (UTC)

[edit] Re: Confusing

The bit about the "transcription factor being a protein that regulates the activation of transcription in the eukaryotic nucleus" is very accurate, though a little abstract. I added a few sentences to try to explain specifically where TFs attach and how they interact with RNA pol and the promoter. There is room for a lot more though. For example, we haven't discussed interactions between TFs and the more distal control elements. Some activators promote transcription by attracting proteins that acetylate the surrounding histones (and some repressors vis-versa). That isn't part of the initiation complex. Cheers Doub1etap 22:33, 1 December 2006 (UTC)

[edit] Distinction between eukaryotes, archea, and bacteria?

I suppose the article requires a terse definition of transcription factor. According to Lewin, Genes VIII a transcription factor is a molecule required by RNA polymerase to initiate transcription, that is not itself part of RNApol. Following this definition, there are no bacterial transcription factors in the strict sense (sigma is part of rnapol).

I do not know whether this definition is the one to follow, but maybe it could help to clarify things, because regulation is a only a consequence of the primary effect: enabling the machinery.

Also, according to this definition, activators and repressors in bacteria are not TFs in the strict sense, but just trans-acting elements. The article should thus not refer to them as examples. All other examples in the article come from eukarya, hence they could be kept. The list of DNA-binding domains imho also contains mostly domains from eukarya. In conclusion I vote for more restricted definition but do not dare to add it, because I'm neither a native speaker nor biologist. What do you think?

[edit] Intro paragraph

Added intro paragraph for a very general audience. However, I'm relying a bit more on my skills as a writer than strict knowledge of molecular biology, so it would be a good idea for a true expert to dig in and check this very carefully, not just whether it sounds good, and revise accordingly - hopefully keeping things simple however.

Also, as it stood, the text below seem to imply that T factors ALSO regulated DNA expression; so I've made it clear that this is exactly what they do, and what is being discussed - however someone more expert may wish to clarify further here. Ndaniels 19:28, 24 February 2007 (UTC)

The intro paragraph is, frankly, dumbing down a little much and speaks a lot more on transcription in general than TFs. I've removed it, added a link in the intro paragraph to transcription and a little more to clarify what TFs actually do. -Cquan 19:26, 5 March 2007 (UTC)