Talk:Transcription factor

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Article Grading: The following comments were left by the quality and importance raters: (edit · history · refresh · how to use this template) 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)

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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)

• Molecular Biology has haphazardly invented an entirely new language for itself, re-defining words like "activation", "regulation", "transcription", and so on, to the point where any new student entering the field is presented with a sheer cliff of a learning-curve. In saying this, I mean to point out that the use of these terms is not the fault of the article writer, but rather the fault of the field itself. A logical naming convention, such as that formulated for Organic Chemistry (IUPAC system) would greatly benefit this field. Until then, we are left with a legacy of hopelessly ill-defined words and terms which, to the scientist, layman, and student all, paint a sad picture of confusion and ambiguity. Dbsanfte 06:42, 16 April 2007 (UTC)

• • I agree that it is not the fault of the author for adopting the language of the field to describe the topic. On the other hand, both Wikipedia and science in general strive to make what was previously not understood, clear to anyone (paraphrasing Paul Dirac). So if the fields terminology is unclear and confusing, it is our job to try to do better. The added glossary is my humble attempt to make things clearer. Boghog2 20:32, 11 June 2007 (UTC)

Contents 1 Re: Confusing 2 Distinction between eukaryotes, archea, and bacteria? 3 Intro paragraph 4 References 5 Breadth 6 Medicine Collaboration of the Week 7 Suggestion for reorganization 8 Technical problem with layout 9 Non DNA binding factors

[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)

[edit] References

I am a little puzzled why this and similar articles do not have references. Obviously any detailed refs to research articles go on the most specific page, but shouldn't the articles at each level have at least some appropriate textbook chapters or review articles in easily found sources? There must have been a policy decision at some point ,because this practice seems fairly uniform in this general topic area.DGG 08:21, 16 April 2007 (UTC)

[edit] Breadth

When trying to track down appropriate references, I quickly came to the conclusion that the main problem with this topic is that it is too broad. Transcription factors cover a very large and mechanistically heterogeneous set of regulatory proteins. There were very few references that I could find that attempted to review the entire class as a whole. It might be better just to give a general definition and list the major classes of transcription factors (e.g., figure 1 of [1]) with the appropriate internal Wikipedia links.Boghog2 19:52, 22 April 2007 (UTC)

[edit] Medicine Collaboration of the Week

• To get things rolling, some relatively recent and hopefully relevant publications which we might try to work into this Wiki article:

^{[1] [2]}

My biggest problem still is finding good review articles that cover the entire area of transcription factors. Once one finds a good source, the article almost writes itself. Any suggestions? Boghog2 19:05, 25 July 2007 (UTC)

• I have made some fairly significant changes to the article including adding new references and deleting the details on the STAT proteins which I think would be better to include in the STAT specific articles. Comments, suggestions, and especially help in directly editing the article would be greatly appreciated. Boghog2 22:45, 28 July 2007 (UTC)

[edit] Suggestion for reorganization

For me, this article seems needlessly complicated. In particular, DNA binding domains/motifs are discussed in at least 4 different sections/subsections. I propose the following headings:

-- Intro

-- DNA binding domains (a general discussion of a transcription factor's sequence/structure that binds DNA. Maybe keep the short DBD list currently found in Classes:Structural)

-- DNA sequence motifs (I might have the wrong name for this, but characteristics of the DNA sequences transcription factors bind to and the chemical nature of the interaction. So far there's almost no discussion on this)

-- Mechanisms of regulation (Talk about the various ways transcription factors regulate transcription. Combine the current sections Mechanisms of Action and Classes:Mechanistic Functional. Fold in info about TADs and SSDs.)

-- Transcription factors in different organisms (Put info from Significance here. Maybe mention role/lack of role in bacteria and viruses. Conservation/lack of conservation among eukaryotes, including plants)

-- Classification based on DBD (Put the list from Classes:Homology here)

Maybe even a section on important roles, giving a nod to HOX genes in Drosophila, heat shock transcription factors, etc.?

Any suggestions/comments are appreciated! --Forluvoft 20:43, 5 August 2007 (UTC)

• Your edits so far are greatly appreciated and your suggestions about reorganization sound good to me. This Medicine Collaboration of the Week has finally turned into a collaboration! I agree that adding section on "DNA sequence motifs/response elements" which also included information on the physicochemical nature of the various types DNA/transcription factor interactions would be very appropriate. This is the area I would be most comfortable/qualified to contribute. I have a definite bias towards mammalian proteins so any info you could add concerning bacteria and plants would be most welcome. Boghog2 21:24, 5 August 2007 (UTC)

• Although a genuinely gallant intent is undoubtedly behind the desire to enumerate the specifics of transcription factor/DNA association, this is far too broad a field for which to develop such generalizations. The nature of the associations between transcription factors and the DNA sequences to which they bind is not only highly varied and complex in nature, but also relatively poorly understood. I think the general idea of certain amino acid residues in particular proteins possessing the ability to bind to certain base residues in DNA is sufficient. To launch into a list of how, where, and why such interactions occurs begs perusal of NCBI databases, and would be far too voluminous to justify its inclusion in a general knowledge article. Otherwise, your suggestions are great. Time permitting, I would be more than happy to help beef up this article. Eganio 00:35, 14 November 2007 (UTC)

[edit] Technical problem with layout

In Firefox, the "Transcription factor glossary" table is overlayed on the "Contents" table, making both unreadable, unless Firefox is put into full screen mode. In IE, the overlaying doesn't happen usually, but the "Contents" table is long and skinny except in full screen mode; but if the browser window is made a little narrower, the "Transcription factor glossary" DOES overlay "Contents" and obscures it.

I don't know how to fix this, but it would be good if it is addressed by someone with technical expertise. —Preceding unsigned comment added by 207.172.220.9 (talk) 20:04, 14 November 2007 (UTC)

In Firefox version 2.0.0.9 for the Macintosh, the glossary and table of contents tables only overlay if the browser window is very narrow. I have decreased the width of the glossary table from 500 to 450 pixels. This allows viewing with slightly narrower window widths without overlap. Is this any better? Other than this, I can't do much else except to display the glossary in the next section the article, but I think the glossary is better near the top of the article, and in particular adjacent to the table of contents to make more efficient use of screen real estate. Boghog2 21:06, 14 November 2007 (UTC)

[edit] Non DNA binding factors

Should there be a mention of transcription factors that do not bind to DNA? Also what can be said about non-protein transcription factors? Though they make up the small minority there should be a mention of these as exceptions and redirections to their specific function and activity. —Preceding unsigned comment added by 129.171.49.78 (talk) 01:47, 22 January 2008 (UTC)

By definition, a protein which regulates transcription but does not directly bind DNA is not a transcription factor, but rather a transcription coregulator. RNA can also regulate gene expression, however (and correct me if I am wrong) this only occurs at the level of mRNA (see RNA interference) and not at the level of transcription of DNA into RNA. Cheers. Boghog2 (talk) 20:15, 2 March 2008 (UTC)