Talk:Cis-regulatory element

Poor quality article
This article draws on a few references for a subject where hundreds of scientists publish valid work. Many of the references used are from outliers, views not representative of the core of research. Please develop it. — Preceding unsigned comment added by 208.80.117.214 (talk) 09:04, 4 January 2022 (UTC)

Merging
There is a lot of overlap between the entries cis-regulatory element cis-acting element and regulatory element they could all be merged with cis-regulatory element which has the best sources and evidence.
 * I have merged the cis-acting page with this one. Sarahburge (talk) 09:53, 7 June 2011 (UTC)

Example
Suggestion for merged article follows, with modifications.

{|class="wikitable" Jason-pi 09:26, 10 April 2007 (UTC) But first, a reaction on this suggested merge from someone else (sorry for posting in between but it seems to make most sense to me). My opinion: it's a little unclear and ambiguous, for example what does 'species' refer to?. Main point should be:

Consider gene X. This gene should be regulated. DNA sequences play an important role in this. Cis-elements are parts of the DNA located IN or CLOSE TO gene X which are directly necceccary for a proper expression of this gene X (e.g. its promotor area, if you mess it up, so will be the expression levels of gene X).

Trans-elements are parts of the DNA located remote from X which are indirectly necceccary for a proper expression level of X (e.g. a promotor area of a gene Y which codes for a transcription factor for our gene X, if you mess up this promotor area, so will be the expression levels of transcription factor Y, which inderectly has an influence on X's expression levels).

Notes: in my view the 'direct' vs 'indirect' is more important than the 'close by' vs 'remote'. I can imagine pieces of not-so-close DNA still being directly involved in regulating a gene.

Notes: The actual mechanism by which the cis- and trans- regions have an (in)direct effect on expression are very versatile and probably new mechanisms will be discovered in the future - for example: genes also have elements which are not recognized by binding-things until they are transcriped to RNA. The same reasoning still yields in this case however: messing up these sites in the DNA will have an effect on the translation of that same gene.

Notes: I did't spell check this, sorry, I'm not english but I think others are better at correcting texts, even in my native language :)

TransControl 08:54, 4 December 2006 (UTC)

Regulation of gene expression must be gene specific. Regulatory systems therefore require targeting sequences physically linked to the target gene as an address to tell the trans-acting factors that the particular genes should be regulated. These sequences, which can be in the DNA, the RNA are called cis-acting elements (or cis-regulatory elements) if their action depends on their being physically linked to the target.

A cis-regulatory element, cis-element, or cis-sequence is a region of DNA or RNA which regulates the expression of genes located nearby on the same strand. This term is constructed from the Latin root -cis, which means "on the same side as". These cis-regulatory elements are often binding sites of one or more trans-acting factors, usually proteins. A cis-element may be located in the promoter region 5' to the gene it controls, in the mRNA, in the introns, or in the 3' flanking region.

Trans factors or regulatory proteins such as transcription factors bind preferentially. They control gene expression and thus protein expression.

In contrast, trans-regulatory factors are species which may modify the expression of genes distant from the gene that was originally transcribed to create them. To demonstrate the concept, a transcription factor for example GATA1which binds to an element in a promoter for the globin gene on chromosome 11 is transcribed from a gene on the X chromosome. This term is constructed from the Latin root -trans, which means "across from".

Regulatory sequences or elements can also be found in messenger RNA, but they are generally not as well studied as those in DNA. They may be bound by RNA-binding proteins or RNAs (eg miRNAs) and are often found in the 3'UTR.

regulatory elements can, of course, be cis- or trans- acting. and that is disregarding several other important mechanisms. is there any particular reason you're pushing to merge cis-acting elements and regulatory elements? Opposed Lesotho 04:20, 6 December 2006 (UTC)

External References
Recent articles over cis-regulation of gene expression

Gompel et al. 2005. Chance caught on the wing: cis regulation evolution and the origin of pigmentation patterns in Drosophila. Nature 433: 481-487.

Prud'homme et al. 2006. Repeated morphological evolution through cis regulatory changes in a pleiotropic gene. Nature 440: 1050-1053.

Stern, D.L. 2000. Perspective: Evolutionary developmental biology and the problem of variation. Evolution 54: 1079-1091.

Carroll, S.B., Grenier, J.K. and Weatherbee, S.D. 2005. "From DNA to diversity: Molecular genetics and the evolution of animal design" Blackwell publishing.

Comments
Merge all articles will definitely clean things up a bit. Article on GC Box should be added to the "See Also" section. The link for this article is: http://en.wikipedia.org/wiki/GC_box GC Box is a promoter region which is an example of a cis-acting element. Jeremy Kimmelstiel (talk) 06:26, 16 February 2011 (UTC) —Preceding unsigned comment added by 149.125.181.193 (talk)

I find it a good idea to merge all these articles into one. Feel free to make that article. I tried to clean up a little here in the discussion as well by putting some headers. Feel free to correct that too. Mikael Häggström (talk) 07:58, 24 February 2009 (UTC)

Good idea to merge the cis-articles. Cis and trans should definitely not be merged. They are two very different aspects of gene regulation. —Preceding unsigned comment added by 118.209.82.214 (talk) 10:26, 13 November 2010 (UTC)


 * Agreed that the cis and trans articles should not be merged. I have therefore removed the merger banners.  Boghog (talk) 05:32, 28 June 2011 (UTC)

Edit request (done)
This has all been handled by 171...171's edit. -- Jo3sampl (talk) 19:56, 27 February 2012 (UTC)

The lead has this: "A cis-element may be located 5' to the coding sequence of the gene it controls (in the promoter region or further upstream), in an intron, or 3' to the gene's coding sequence, either in the untranslated or untranscribed region." I have no clue what the mark next to the 5 (and the 3) indicates. Clarification would be appreciated.

-- Thanks -- Jo3sampl (talk) 22:28, 2 December 2011 (UTC)

From Promoter_(biology): As promoters are typically immediately adjacent to the gene in question, positions in the promoter are designated relative to the transcriptional start site, where transcription of RNA begins for a particular gene (i.e., positions upstream are negative numbers counting back from -1, for example -100 is a position 100 base pairs upstream). I added a wikilink to that explanation. -- Jo3sampl (talk) 22:56, 2 December 2011 (UTC)

Should Cis-regulatory module be merged?
Cis-regulatory module seems to treat "element" and "module" as roughly synonymous. Is there a reason to have two articles? --Animalparty-- (talk) 21:58, 10 February 2014 (UTC)
 * I'd similarly support a merge given the overlap. Element may be a subset of module, but the module page goes into plenty of details on the individual elements! (here from 's post at WT:MCB). T.Shafee(Evo &#38; Evo)talk 11:06, 25 July 2020 (UTC)
 * Merge: Yes, I wrote (over there): Cis-regulatory module and Cis-regulatory element seem to overlap largely, and to a non-geneticist they seem extremely similar if not a WP:FORK. It doesn't look as if a simple redirect would do the job, so perhaps someone could look at the matter, and either make the articles clearly distinct or merge them. Editors have noted the issue since, ah, 2011. With T.Shafee's confirmation, I'm happy to support the merge. Chiswick Chap (talk) 11:09, 25 July 2020 (UTC)
 * ✅ I've left the nomenclature unchanged, just in case someone comes up with a referenced way of distinguishing between the two. My reading is that use is mixed, so they're certainly best discussed together. Klbrain (talk) 11:21, 13 February 2021 (UTC)

Is this a meaningful statement?
"cis-regulatory elements are present on the same molecule of DNA" That means it is present on the same chromosome. First, it seems clearer to use "chromosome" than "DNA molecule." Second, the statement continues with "whereas trans-regulatory elements can regulate genes distant from the gene from which they were transcribed." That generally happens on the same chromosome as well. Hence the statement is meaningless. It is preceded by a hypothetical illustration of a trans-regulatory element acting from a different chromosome, which lacks reference or actual example.

Very thin references
Not useful discussions of categories of cis-regulators. "Billboards" as described in the referenced Jeziorska et al. 2009 article ignore physical, electrostatic, pi-interaction basis. "Enhancers affect the probability of a gene being activated, but have little or no effect on rate," also referenced to the the Jeziorska et al. article, is nonsense. The process of chromatin looping, with enhancers working both through recruitment and their own encoding, as well as elements like eRNA interactions, signalling transcription machinery, mediates gene transcription level gradients. Where to begin? Perhaps "Pennacchio, L. A., Bickmore, W., Dean, A., Nobrega, M. A., & Bejerano, G. (2013). Enhancers: five essential questions. Nature reviews. Genetics, 14(4), 288–295. https://doi.org/10.1038/nrg3458."

Another thinly referenced description is "enhancers ... can be found upstream, downstream, within the introns, or even relatively far away from the gene they regulate," from the reference given. There is a big debate about the distance that enhancers engage genes is, which is not reflected in this reference or statement. Research finds the distance often 2 or 3 Mb away. Is that "relatively far"?