Talk:Five prime untranslated region

DSKireai (talk) 20:43, 5 November 2013 (UTC)

Notice

This article is being edited by members of a Developmental biology class as an educational assignment, and we would appreciate any feedback, such as layout pointers or informational issues. SOTTET05 (talk) 19:42, 4 November 2013 (UTC)

Summary of Revamp Article

In order to create an informative article, we propose an outline as a starting point. First, we shall outline the history and origins of the 5' UTR. Next, we will speak on the organization of the 5' UTR, including the elements located there and what their function is. We will also cover proteins which bind to these specific elements. Next, we shall discuss the specifics to the 5' UTR in prokaryotes, eukaryotes, archea, and viruses. After our discussion of structure, we shall switch over to their roles in disease. There are many disease which utilize miRNAs, which bind to these regions. DSKireai (talk) 23:03, 17 October 2013 (UTC) SOTTET05 (talk) 23:04, 17 October 2013 (UTC)

Peer Review

I like how you've organized the wiki page. It's very logical, and has a lot of detail, that are all linked to other pages, which is great. However (there's more detail in the rest of the post) it would be helpful if you fleshed out your intro, and intros to other sections. Otherwise I have no idea for what information this page has to offer at first glance. The sections themselves are very dense with information, which is good, but it can also be a bit confusing with no diagrams as a visual aide. If you can find some diagrams for sections "uORFs" and "Reinitation" it would be helpful.

Introduction: "differing mechanisms dependent on organism." sounds awkward. Also you should provide more detail on the different mechanism General Structure: Length: I like the example you give to demonstrate size difference.

Role in Translational Regulation: I think it would be helpful if you had a small overview section "Role in Translational Regulation". The section is split up in a very logical way, but it feels a bit disjointed. The overview might help a person approach each section with a greater picture in mind. Prok: Is there a page that outlines the mechanism of Prokaryotic Translation? It would be a good idea to link that information to this section. You say "many other proteins" are recruited, which opens the question of the actual process. It would be good if you include more details on how 5' UTR can be mutated, and what kind of defects it can lead to. It might also be a good idea if you include more information as to what model organisms were used to determine some of the experimental results. Pitpeelorchard (talk) 02:00, 23 November 2013 (UTC)

Bibliography of Relevant Texts for Article Revamp

• Browne, PD (2013 Feb 27). "Contribution of transcriptomics to systems-level understanding of methanogenic Archaea". Archaea. doi:10.1155/2013/586369. PMID 23533330. Retrieved 14 October 2013. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)CS1 maint: date and year (link) CS1 maint: unflagged free DOI (link)

This article is extremely interesting with regards to how the 5' UTR is used in regulation and development in Archaea, which should be touched upon in a comprehensive review of the topic.

• Alekhina, OM (2012). "Translation initiation in eukaryotes: versatility of the scanning model". Biochemistry (Mosc). 13. 77: 1465–77. doi:10.1134/S0006297912130056.. PMID 23379522. Retrieved 14 October 2013. {{cite journal}}: Check |doi= value (help); Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)

This article covers most of the eukaryotic regulation with the 5'UTR holds. This will be very useful in analyzing a comprehensive look.

• Piñeiro, D (2012 Oct 19). "RNA structural elements of hepatitis C virus controlling viral RNA translation and the implications for viral pathogenesis". Viruses. 10. 4: 2233–2250. doi:10.3390/v4102233.. PMID 23202462. {{cite journal}}: Check |doi= value (help); Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)CS1 maint: date and year (link)

Again, as to create a comprehensive article, the above review deals witht he 5' UTR in viruses.

• Farazi, TA (2013). "MicroRNAs in human cancer". Adv Exp Med Biol. 774: 1–20. doi:10.1007/978-94-007-5590-1_1.. PMID 23377965. {{cite journal}}: Check |doi= value (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
• Lee, S (2013). "Post-transcriptional stimulation of gene expression by microRNAs". Adv Exp Med Biol. 768: 97–126. doi:10.1007/978-1-4614-5107-5_7.. PMID 23224967. {{cite journal}}: |access-date= requires |url= (help); Check |doi= value (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

These two reviews deal with how miRNAs regulate different transcripts via the 5' UTR. This is quite interesting, and important to the field.

• van der Velden, AW (1999). "The role of the 5' untranslated region of an mRNA in translation regulation during development". Int J Biochem Cell Biol. 1. 31: 87–106. PMID 10216946. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help); Unknown parameter |month= ignored (help)

This review looks into how the 5' UTR affects development. This looks into how certain initiation factors and other proteins work affect the mRNA during development.

Five prime untranslated region article bibliography

Nahum Sonenberg, Alan G. Hinnebusch, Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets, Cell, Volume 136, Issue 4, 20 February 2009, Pages 731-745, ISSN 0092-8674, http://dx.doi.org/10.1016/j.cell.2009.01.042. (http://www.sciencedirect.com/science/article/pii/S0092867409000907)

Tokumasa Nakamoto, Evolution and the universality of the mechanism of initiation of protein synthesis, Gene, Volume 432, Issues 1–2, 1 March 2009, Pages 1-6, ISSN 0378-1119, http://dx.doi.org/10.1016/j.gene.2008.11.001. (http://www.sciencedirect.com/science/article/pii/S0378111908005702) Keywords: Cumulative specificity mechanism in the initiation of protein synthesis; Multisubstrate enzyme system in the initiation of protein synthesis; Non-unique initiation signals in protein synthesis; Initiation mechanism for eukaryotic protein synthesis; Evolutionarily conserved initiation signals in protein synthesis; Universal initiation mechanism for protein synthesis

Andrey V. Pisarev, Nikolay E. Shirokikh, Christopher U.T. Hellen, Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites, Comptes Rendus Biologies, Volume 328, Issue 7, July 2005, Pages 589-605, ISSN 1631-0691, http://dx.doi.org/10.1016/j.crvi.2005.02.004. (http://www.sciencedirect.com/science/article/pii/S1631069105000296) Keywords: Classical swine fever virus; Cricket paralysis virus; Hepatitis C virus; IRES; Ribosome; Translation initiation

TV Pestova, CU Hellen. The Structure and function of initiation factors in eukaryotic protein synthesis, Cell Mol Life Sci. 2000 Apr; 57(4):651-74

SYLVAIN DE BREYNE, YINGPU YU, TATYANA V. PESTOVA,CHRISTOPHER U.T. HELLEN, Factor requirements for translation initiation on the Simian picornavirus internal ribosomal entry site, RNA. 2008 February; 14(2): 367–380.

Yaser Hashem, Amedee des Georges, Vidya Dhote, Robert Langlois, Hstau Y. Liao, Robert A. Grassucci, Christopher U.T. Hellen, Tatyana V. Pestova, Joachim Frank, Structure of the Mammalian Ribosomal 43S Preinitiation Complex Bound to the Scanning Factor DHX29, Cell, Volume 153, Issue 5, 23 May 2013, Pages 1108-1119, ISSN 0092-8674, http://dx.doi.org/10.1016/j.cell.2013.04.036. (http://www.sciencedirect.com/science/article/pii/S0092867413005126)

This is just a preliminary list with more sources to come. DSKireai (talk) 22:11, 14 October 2013 (UTC) SOTTET05 (talk) 05:21, 15 October 2013 (UTC)

It's called the 5' untranslate region, but this article says that it's sometime translated?? This is either a mistake or else the fact that it isn't a mistake should be further clarified. --129.215.47.59 (talk) 21:59, 17 February 2011 (UTC)

I have added this sentence to the page: "Mutations to sequences within the 5' UTR as well as changes to the length of the 5' UTR have been implicated in various human diseases, such as hereditary thrombocythaemia" along with a reference. Prewmi (talk) 17:04, 14 March 2013 (UTC)

I have added the following information to the end of the article : Alternative splicing and variation of the transcription start site can produce alternative 5′UTRs. Diversity within the 5′UTR of a gene enables variation in expression, which is dependent on the regulatory elements contained in the alternative 5' UTR. I found the information through an article on the ncbi database and the citation is posted in the reference section. Pleusm (talk) 17:05, 14 March 2013 (UTC)

The bullet points under the sentence "Several regulatory sequences may be found in the 5' UTR:" are capable of being expanded, with several examples being able to highlight the importance of the 5'-UTR in protein regulation. Also, the intro sentence does not give good context for the sequence within the genome, nor does it bring the 5'-UTR into focus, instead generalizing its function with the other components of a messenger RNA transcript. Information of the 5'-UTR in prokaryotes is necessary to contrast its role for eukaryotes. This is an article I may be interested in developing for a university assignment. So, to avoid any redundancy or contradicting information, please message me so we can collaborate on the topic. SOTTET05 (talk) 22:45, 6 October 2013 (UTC)

a fun addition- upstream open reading frames

Yes, your team has plenty to do with this article. I do want to point out that there is an interesting beast called the upstream open reading frame, or uORF. These are found in the 5' utr ( or leader sequence!) of some mRNAs and under certain metabolic conditions can recruit and stall the ribosome to slow down translation. Others are thought to encode short peptides that then influence translation of the 'real' open reading frame. Hakeleh (talk) 23:18, 22 October 2013 (UTC)

Indeed. This is covered (not very well) in the Attenuator_(genetics)#Other_operons_controlled_by_attenuation section.--Paul (talk) 22:50, 5 November 2013 (UTC)

Revamp Process

We are currently in the process of revamping this page. The original was completely scrapped as it was just a stub. We will continue to be adding information over the next weeks in order to flesh out the content even more. DSKireai (talk) 17:56, 16 November 2013 (UTC)

Peer Review

This is a really thorough and well-written article with lots of great diagrams and figures! A few small suggestions: the intro is nice and concise but could additionally expound the technical explanation in more basic terms, for instance what is meant by "five prime" and what "untranslated" refers to, for those without a good background in biology. In addition, perhaps it is just me but the concept of "uORFs" is somewhat confusing and could be clarified because they seem to be coding/translated regions of the 5' untranslated region. So does this mean they are exceptions, and parts of the untranslated region actually do get translated? Also, I only made one very tiny grammatical correction under "uORFs" and changed "translated to creates a product" by removing the "s" on "create."

Nia2993 (talk) 17:30, 21 November 2013 (UTC)

Peer Review

The article had a lot of great information. The introduction can be expanded a little more because it seems a little too concise. Maybe it would be nice to give more a general overview of what the article is about in the introduction. It is a little hard to tell apart the different heading font sizes in the middle section. For example, I see that you have multiple smaller sections under uORF but since the font sizes are very similar to uORF it looks like it's just another point for the translational regulation. It would be better to make it clear the hierarchy of the topics by changing the font style or size. The last section on transcriptional regulation looks incomplete because there is only one example so if you want to make a section about transcriptional regulation it would be better to find more information about it or incorporate that information somewhere else.

Choidah (talk) 23:42, 23 November 2013 (UTC)

Repeated links

Is it necessary to link the same word dozens of times in the article? This is not the normal procedure. Generally, the word is linked to other article at the beginning of the article and in a few significative places below, but "translation", "prokaryote", "eukaryote", "secundary structure" and many other words are repeatedly linked a lot of times (too many).--Miguelferig (talk) 12:50, 8 March 2014 (UTC)