Talk:Regulation of gene expression

Definition of gene regulation

I disagree with the definition of gene regulation as the regulation of protein expression at the DNA and RNA level. It's true that most of the time, the end product of the expression of a gene is a protein, however, it is not always true, and I think that it is too much of a simplification of what gene regulation is to start of the whole overview with that as a definition.

I think that in the last decade we have learned that proteins are not the only active catalytic moiety that exists in a cell and that the work of a cell sometimes relies on special catalytic RNAs or is regulated by even more specialized RNAi's. In other words, defining gene regulation as regulation of protein expression overlooks the RNA world and places too much emphasis on the end product of a gene being a protein. When the central dogma read DNA -> RNA -> protein, the definition was true, but we now know that there need to be some loops and turns in the central dogma, so the definition is no longer suitable.

I chose to address this change in the talk section because I think that I am proposing a major change in the definition of gene regulation and I didn't want to suppose that my definition is the correct one without some form of discussion.

What do people feel, is this worth a discussion or should I just change the sentence and see what people think?

thanks, Stephen R. Lasky, Institute for Systems Biology User:Srlasky

Dr Lasky, you have every right to modify the page. If it is disliked, someone will change it back! In the present form, the page certainly answers to the old dogma. A mention of the emerging theories would be entirely appropriate. Would you care to elaborate if catalytic RNA is an issue of concern in higher lifeforms?

Your input is most welcomed. There is a dearth of contributors with biological expertise on Wikipedia. JFW | T@lk 13:34, 3 Oct 2004 (UTC)

I agree with Dr. Lasky's comments, and have corrected the definition on this page. Turan P. Urmenyi, Federal University of Rio de Janeiro User:Turan

Prokaryotic gene regulation

This page seems to be exclusively about eukaryotic gene regulation. Fror example this sentence: Octameric protein complexes called histones are responsible for the amount of supercoiling of DNA, is simply not true for prokaryotes. There are two possible solutions, either make a Prokaryotic gene regulation article and a seperate Eukaryotic gene regulation article, or try to be more specific and make less generalisations in this article. I've been doing some work on the lac operon article and it could really do with a parallel article on prokaryotic gene regulation in order to fill in the gaps, so I'm in favour of the first option. What's the general feeling?Alun 05:42, 11 October 2005 (UTC)[reply]

Structural modification

According to the article this is a consequence of phosphorylation and methyation, both are chemical modifications, so it should be under the same heading. Andreas ^(T) 00:03, 9 November 2006 (UTC)[reply]

Up/Down Regulation

Could these terms actually be defined please?

Split for regulatory protein?

Regulatory protein redirects here, but I think regulatory proteins are involved in many more processes in the cell than just regulation of gene expression. Shouldn't they have their own page? - tameeria 18:48, 7 May 2007 (UTC)[reply]

I agree that they should have their own page, or that they are at least described more in their section.-EmilyofWolves

Negative and positive control

Negative control and positive control are mentioned in the gene regulation chapter of intro-bio textbooks and need to be defined in the context of gene expression either here or on their respective pages. - tameeria 18:53, 7 May 2007 (UTC)[reply]

Sort stuff out

I dislike the layout of this page. I used to look like it was a first year undergraduate essay (I am suprised that the main reference is not Alberts. Uh, I might add that as a joke). I think Transcriptional regulation must have its own page as it is for post-transcriptional regulation, which links to a page which is now cool (great save guys!). Is that a good idea or will it make it worse as I suppose this is a high school topic too. --Squidonius (talk) 12:15, 9 May 2008 (UTC)[reply]

3 of the 4 references were actually copied from the post-transcriptional page... --Squidonius (talk) 23:19, 20 May 2008 (UTC)[reply]

Incorrect data?

This page states that "The first discovered example of a gene regulation system was the lac operon, discovered by Jacques Monod" however there seems to be another person who did it ~10 years earlier http://en.wikipedia.org/wiki/Barbara_McClintock —Preceding unsigned comment added by 195.216.211.175 (talk) 01:38, 17 July 2009 (UTC)[reply]

Header demotion

This article has four clear sections:

where and how in gene expression regulation occurs
Examples
circuits
methods to study these

I do not want to barge in and change too much stuff around, but I reckon the titles Modification of DNA, Regulation of transcription, Post-transcriptional regulation, Regulation of translation should be made a tier lower to reflect this and Examples should be below Circuitry. --Squidonius (talk) 03:14, 10 October 2010 (UTC)[reply]

The link to Epigenetics?

Under the "Modification of DNA" subheading, it says that this information is from the main article on Epigenetic regulation. Epigenetics is defined as heritable changes caused by mechanisms other than modifications to DNA.

Why does the main article for "Modification of DNA" take us to a page that is about mechanisms other than modifications to DNA? This doesn’t make sense and is confusing. Nursebhayes (talk) 21:39, 24 August 2011 (UTC)[reply]

There is a key point that you left out of the definition of epigenetic regulation. This type of regulation involves modifications to DNA that are "other than changes in the underlying DNA sequence". Examples of epigenetic modifications to DNA include:

DNA methylation in which a methyl group is attached to a DNA base which blocks transcription (a direct change in the chemical structure of DNA)
histone acetylation or deacetylation that results in change in the conformation of DNA making it more or less available for transcription (an indirect change caused by chemical modifications to the proteins that DNA wraps around) Boghog (talk) 00:49, 25 August 2011 (UTC)[reply]

There should be a link to the epigenetic page, but why is it listed as the main page? Epigenetics is not the only way that DNA is modified. DNA is modified by many different processes, including epigenetics. Where are the links to other processes that modify DNA? Maybe the subheading should be changed from Modification of DNA to Epigenetic Modification? Or something similar Nursebhayes (talk) 15:00, 25 August 2011 (UTC)[reply]

I agree that there is a problem with the link to epigenetics in that not all modifications to DNA that regulate gene expression are inheritable. Hence I have modified the text to clarify that. I hope this is an improvement. Boghog (talk) 17:47, 25 August 2011 (UTC)[reply]

Assessment comment

Molecular Biology: Genetics / MCB

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The comment(s) below were originally left at Talk:Regulation of gene expression/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

Rated "top" as highschool topic and important concept/overview in molecular biology. - tameeria 03:55, 29 April 2007 (UTC)[reply]

Last edited at 03:55, 29 April 2007 (UTC). Substituted at 04:07, 30 April 2016 (UTC)

Please clarify the link to alternative splicing

I think it would be good to add a wikilink to alternative splicing and clarify the link between regulation of gene expression and alternative splicing. There could also be info about the extent of this, including in the mammalian/human cortex.

Relevant to this, 2021 in science currently features the following item:

Scientists report a large extent of alternative splicing – cases of a single gene (a template) being used to create instructions (mRNAs) for building different proteins – in the mouse and human cortex and release the transcriptomes on a public database.^[1]^[2]

Please also reply if you think info about the link and/or the study should (also?) be added to another article (maybe to Transcriptome?).

References

^ "Some genes in the brain may make 100 different proteins". New Scientist. Retrieved 11 December 2021.
^ Leung, Szi Kay; Jeffries, Aaron R.; Castanho, Isabel; Jordan, Ben T.; Moore, Karen; Davies, Jonathan P.; Dempster, Emma L.; Bray, Nicholas J.; O’Neill, Paul; Tseng, Elizabeth; Ahmed, Zeshan; Collier, David A.; Jeffery, Erin D.; Prabhakar, Shyam; Schalkwyk, Leonard; Jops, Connor; Gandal, Michael J.; Sheynkman, Gloria M.; Hannon, Eilis; Mill, Jonathan (16 November 2021). "Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing". Cell Reports. 37 (7). doi:10.1016/j.celrep.2021.110022. ISSN 2211-1247.

Prototyperspective (talk) 16:29, 19 December 2021 (UTC)[reply]

[1] "Some genes in the brain may make 100 different proteins". New Scientist. Retrieved 11 December 2021.

[2] Leung, Szi Kay; Jeffries, Aaron R.; Castanho, Isabel; Jordan, Ben T.; Moore, Karen; Davies, Jonathan P.; Dempster, Emma L.; Bray, Nicholas J.; O’Neill, Paul; Tseng, Elizabeth; Ahmed, Zeshan; Collier, David A.; Jeffery, Erin D.; Prabhakar, Shyam; Schalkwyk, Leonard; Jops, Connor; Gandal, Michael J.; Sheynkman, Gloria M.; Hannon, Eilis; Mill, Jonathan (16 November 2021). "Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing". Cell Reports. 37 (7). doi:10.1016/j.celrep.2021.110022. ISSN 2211-1247.

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