Talk:Three prime untranslated region

This article was the subject of an educational assignment in 2013 Q1. Further details were available on the "Education Program:Boston College/Developmental Biology (Spring 2013)" page, which is now unavailable on the wiki.

Pleusm (talk) 15:24, 1 March 2013 (UTC) Prewmi (talk) 16:44, 14 March 2013 (UTC) Dehringb (talk) 16:44, 14 March 2013 (UTC) [reply]

A fact from Three prime untranslated region appeared on Wikipedia's Main Page in the Did you know column on 28 April 2013 (check views). The text of the entry was as follows:

Did you know... that the localization, stability, export, and translation efficiency of a messenger RNA are regulated by its three prime untranslated region?

A record of the entry may be seen at Wikipedia:Recent additions/2013/April. The nomination discussion and review may be seen at Template:Did you know nominations/Three prime untranslated region.

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Untitled

This article was completely revised by a group of students at Boston College as part of a Developmental Biology class. Pleusm (talk) 16:35, 4 April 2013 (UTC) Prewmi (talk) 16:36, 4 April 2013 (UTC)Dehringb (talk) 17:08, 4 April 2013 (UTC)[reply]

A few students and I will be working to improve the content and quality of this page as part of a Developmental Biology course at Boston College. Here is a list of some of the sources that will be used: http://www.biolcell.org/boc/101/0251/1010251.pdf http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3474909/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431537/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194005/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175714/ Prewmi (talk) 21:56, 8 March 2013 (UTC)[reply]

I am also working on editing this article as part of the group at Boston College. Please feel free to ask any questions and we will try to clarify those posted already. Pleusm (talk) 17:08, 14 March 2013 (UTC)Some additional resources that may be used are: http://www.ncbi.nlm.nih.gov/pubmed/21725897 http://onlinelibrary.wiley.com/doi/10.1038/npg.els.0005011/full http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0005009.pub2/full http://www.ncbi.nlm.nih.gov/pubmed/22614827 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431537/ http://www.ncbi.nlm.nih.gov/pubmed/22012871 Pleusm (talk) 20:14, 16 March 2013 (UTC)[reply]

I am the third member of this group at Boston College. Hopefully we can clarify a lot of your questions. Here are some resources I am using: http://www.asbmb.org.au/magazine/2005-December_Issue36-3/Showcase%203%20-%20Stasinopulos%20et%20al..pdf http://pats.atsjournals.org/content/8/2/163.full.pdf http://www.reference.md/files/D020/mD020413.html http://www.nature.com/nm/journal/v6/n6/full/nm0600_637.html http://www.biolcell.org/boc/101/0251/1010251.pdf Dehringb (talk) 20:25, 21 March 2013 (UTC)[reply]

can someone give a layman's explanation too? I have no idea what this article is describing.

I agree, all we want to know is what 3'UTR means and what it relates to: Here is one definition that I find more instructive: Untranslated Region (3' UTR) Sequences on the 3' end of mRNA but not translated into protein. 3' UTR may contain sequences that regulate translation efficiency, mRNA stability, and polyadenylation signals

The article gives some information about a part of every mRNA. The 3' UTR comes after the part of the mRNA that includes the protein coding region. Most genes have extra sequence before the protein coding region begins (5' UTR) and after the protein coding region ends (3' UTR). There are numerous sequence motifs in these regions that help to control how the gene is regulated. Hence, this topic comes under the section about gene expression. The UTR's are not the same as the flanks, before and after the sequence transcribed into mRNA, these regions also contain regulatory motifs, e.g. promoters.

It's tough to decide where a gene starts and ends; most people would agree that the most important part of a gene is the region that contains the code to make protein, though it turns out that not all genes make proteins.

How about siRNAs (a part of RNAi) ... do those also have their targets their?

How about this as a first sentence for laypeople

The 3' UTR is the un-translated region of a mRNA after the protein coding sequence. The 3' UTR is not translated into protein so may have regulatory roles.

TransControl 06:43, 4 December 2006 (UTC)[reply]

The following is the previous version of the 3'-UTR page

mRNA structure, approximately to scale for a human mRNA, where the median length of 3'UTR is 700 nucleotides

In molecular genetics, the three prime untranslated region (3' UTR) is a particular section of messenger RNA (mRNA). It starts with the nucleotide immediately following the stop codon of the coding region.

A mRNA molecule codes for a protein through translation. The mRNA also contains regions that are not translated. In eukaryotes these regions are the cap, 5' untranslated region, 3' untranslated region, and polyA tail (see diagram).

In prokaryotes mRNA structures have some differences (see mRNA) as do histone mRNAs. However, both have 3' UTRs.

Several regulatory sequences are found in the 3' UTR:

A polyadenylation signal, usually AAUAAA, or a slight variant. This marks the site of cleavage of the transcript approximately 30 base pairs past the signal, followed by the addition of several hundred adenine residues (poly-A tail).^[1]^[2]
Binding sites for proteins, that may affect the mRNA's stability or location in the cell, like SECIS elements (which direct the ribosome to translate the codon UGA as selenocysteines rather than as a stop codon), or AU-rich elements (AREs), stretches consisting of mainly adenine and uracil nucleotides (which can either stabilize or destabilize the mRNA depending on the protein bound to it).^[3]
Binding sites for miRNAs, a type of RNAi.^[4]^[5]

Genetic alterations to the 3'UTR can be used to increase or decrease the half-life of the mRNA, leading to greater or lesser protein levels.^[6]

References

^ Neilson JR, Sandberg R. (2010). "Heterogeneity in mammalian RNA 3' end formation". Exp Cell Res. 316 (8): 1357–64. doi:10.1016/j.yexcr.2010.02.040. PMC 2866830. PMID 20211174. {{cite journal}}: Unknown parameter |month= ignored (help)
^ Ryan K, Bauer DL. (2008). "Finishing touches: post-translational modification of protein factors involved in mammalian pre-mRNA 3' end formation". Int J Biochem Cell Biol. 40 (11): 2384–96. doi:10.1016/j.biocel.2008.03.016. PMC 2548416. PMID 18468939. {{cite journal}}: Cite has empty unknown parameter: |month= (help)
^ von Roretz C, Gallouzi IE. (2008). "Decoding ARE-mediated decay: is microRNA part of the equation?". J Cell Biol. 181 (2): 189–94. doi:10.1083/jcb.200712054. PMC 2315667. PMID 18411313. {{cite journal}}: Unknown parameter |month= ignored (help)
^ Chen K, Song F, Calin GA, Wei Q, Hao X, Zhang W. (2008). "Polymorphisms in microRNA targets: a gold mine for molecular epidemiology". Carcinogenesis. 29 (7): 1306–11. doi:10.1093/carcin/bgn116. PMID 18477647. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
^ Ha M, Pang M, Agarwal V, Chen ZJ. (2008). "Interspecies regulation of microRNAs and their targets". Biochim Biophys Acta. 1779 (11): 735–42. doi:10.1016/j.bbagrm.2008.03.004. PMC 2586835. PMID 18407843. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
^ Makhanova N, Hagaman J, Kim HS, Smithies O. (2008). "Salt-sensitive blood pressure in mice with increased expression of aldosterone synthase". Hypertension. 51 (1): 134–40. doi:10.1161/HYPERTENSIONAHA.107.098897. PMID 18039983. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

External links

Brief introduction to mRNA regulatory elements
UTResource 3' UTR analysis
UTRome.org 3' UTRs in nematodes
Medical Subject Heading: 3' Untranslated Regions

[[Category:RNA]] [[Category:Gene expression]]

Peer Review

Overall, the article turned out really well with everything new added and edited. The content of the subject is strong with good examples supporting the concepts and useful pictures to help with understanding some of the structures discussed. Also, it is well written in a "wikificated" manner where laypeople will be able to understand the scientific information presented. I also liked how you guys ended on an optimistic note with the future development section.

The first two paragraphs giving a brief summary and definition of 3'-UTR is very strong and gave a good overview of what is to come in the section below. The second of the two seems a bit long for its purpose and could be edited down a bit since you repeat some of the information later in the other sections. Also, I noticed that there was no citation in your first paragraph; I only comment on this because our ambassador said there should be one in every paragraph.

The physical characteristics section has good information, but the way it is presented seems choppy and a bit awkward at some times. I think what may help with it is to add a little more information explaining some of the features instead of just jumping from one to the next or drawing conclusions prematurely. One specific area I found a bit awkward and could a bit of work was when discussing the G+C percentage of the mRNA transcript.

The role in gene expression section to me was your strongest! You guys have really good content here that is presented well and easy to understand. Also, the examples of the different regulations really helped to prove the points and the pictures chosen helped as well. My only suggestion is to add a picture of a stem-loop structure since it is discussed often and I feel like could be very useful as well to the laypeople to understand the mechanisms more.

The methods of study section needs a little more work. Adding a couple sentences about the techniques of the mapping and sequencing would improve it so readers can understand how the results are determined and analyzed. Also, the first sentence is a bit off-putting. When you say the methods are tedious, then the reader will assume the paragraph will be as well and will not want to read the rest of it. Mention that it can be tedious further in the paragraph and have a topic sentence stating the methods used to analyze the 3-UTRs.

The disease section has interesting information but I feel like its just a list of alterations that will cause the various diseases. Making it more fluid or expanding on one of the diseases could give the reader a better grasp on the subject. The diagram of the different mutations in the 3'-UTR was my favorite of all the pictures used.

In the end, I think you guys have a really good article and should be proud of the work you have done. Congrats!! We are almost at the end! Ekern529 (talk) 19:49, 13 April 2013 (UTC)[reply]

Adenine / AMP / poly(A) tail

I think poly(A) tails are made of AMP rather than adenine. The article says: "...addition of several hundred adenine residues called the poly(A) tail". Everybody understands the sentence but I think it is more correct with AMP.--Miguelferig (talk) 11:43, 11 March 2014 (UTC)[reply]

Merge with 5'UTR and general UTR article

In the talk page of the UTR article, it was suggested to merge the 5', 3' and general UTR article into just one article. I think this would be very helpful, what do you think? — Preceding unsigned comment added by Ilikelifesciences (talk • contribs) 16:47, 17 June 2016 (UTC)[reply]

[pmid20211174-1] Neilson JR, Sandberg R. (2010). "Heterogeneity in mammalian RNA 3' end formation". Exp Cell Res. 316 (8): 1357–64. doi:10.1016/j.yexcr.2010.02.040. PMC 2866830. PMID 20211174. {{cite journal}}: Unknown parameter |month= ignored (help)

[pmid18468939-2] Ryan K, Bauer DL. (2008). "Finishing touches: post-translational modification of protein factors involved in mammalian pre-mRNA 3' end formation". Int J Biochem Cell Biol. 40 (11): 2384–96. doi:10.1016/j.biocel.2008.03.016. PMC 2548416. PMID 18468939. {{cite journal}}: Cite has empty unknown parameter: |month= (help)

[pmid18411313-3] von Roretz C, Gallouzi IE. (2008). "Decoding ARE-mediated decay: is microRNA part of the equation?". J Cell Biol. 181 (2): 189–94. doi:10.1083/jcb.200712054. PMC 2315667. PMID 18411313. {{cite journal}}: Unknown parameter |month= ignored (help)

[pmid18477647-4] Chen K, Song F, Calin GA, Wei Q, Hao X, Zhang W. (2008). "Polymorphisms in microRNA targets: a gold mine for molecular epidemiology". Carcinogenesis. 29 (7): 1306–11. doi:10.1093/carcin/bgn116. PMID 18477647. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

[pmid18407843-5] Ha M, Pang M, Agarwal V, Chen ZJ. (2008). "Interspecies regulation of microRNAs and their targets". Biochim Biophys Acta. 1779 (11): 735–42. doi:10.1016/j.bbagrm.2008.03.004. PMC 2586835. PMID 18407843. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

[pmid18039983-6] Makhanova N, Hagaman J, Kim HS, Smithies O. (2008). "Salt-sensitive blood pressure in mice with increased expression of aldosterone synthase". Hypertension. 51 (1): 134–40. doi:10.1161/HYPERTENSIONAHA.107.098897. PMID 18039983. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

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