User talk:Sagarc88-NJITWILL

After reading the Wiki article on 'AU-Rich Elements', I believe there needs to be few changes in order to improve its quality.

1) The definition is insufficient to explain the full concept of ARE's. Moreover, there is no flow in the current definition. It is just presenting different concepts. My own proposal is to change the definition to the following:


 * AU-Rich Elements (Adenylate Uridylate Rich Elements), commonly found in 3’ Untranslated Regions of mRNA’s, are one of the regulatory RNA motifs involved in the control of gene expression. They are known to regulate the stability of mRNA by promoting mRNA degradation or delaying it.

The above definition adds that the ARE’s are found in the 3’ UTR which the original definition didn’t mention. Moreover, the original definition lacks to mention that the ARE’s can both promote or delay mRNA degradation. Hence it can contribute to destabilization or stabilization of mRNA’s. Also, all the information in the definition can be supported using the sources mentioned below. The original definition had no citations for the facts. I believe the above definition is more concise and informative.

2) Some of the facts such as “It is estimated that 5-8% of human mRNAs contain ARE's…” and “This lies within a 50-150 base sequence, repeats of the core AUUUA element are often required for function” are not supported at all in the article. These are facts and they should be supported by external sources. The two sources below can be used to provide citations for the above facts and the definition:
 * Bindra, Richipal Singh., Wang, Jason T.L., & Bagga, Paramjeet Singh. (2010). Bioinformatics methods for studying microRNA and ARE-mediated regulation of post-transcriptional gene expression. International Journal of Knowledge Discovery in Bioinformatics (IJKDB), 1(3), 97-112.
 * Bakheet, Tala., Williams, Bryan R. G., & Khabar, Khalid S. A. (2003). ARED 2.0: an update of AU-rich element mRNA database. Nucleic Acids Research, 31(1), 421–423.
 * Halees, Anason., El-Badrawi, Rashad., & Khabar, Khalid S. A. (2008). ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse. Nucleic Acids Research, 36. Retrieved from http://nar.oxfordjournals.org/content/36/suppl_1/D137 doi: 10.1093/nar/gkm959

All the above sources are from peer reviewed journals and written by highly qualified people. These are sure to add much quality to the topic.

3) The Wikipedia article lacks an important section which I believe should be added. There have been great advancement in finding these ARE sites computationally in mRNA. The article mentions AREsite very briefly. However, more information is needed to explain the functionality of this tool. Also, this tool is only a database of the ARE sites found. There is another group of researchers which used different algorithms to predict these ARE sites. Their website is called ARED. These researchers were the first one to figure out how to computationally find these ARE sites. Their algorithm can be of great help to anyone trying to gain more knowledge about ARE’s. There should be a different section for these tools with more details on what these tools are and how they work.

Even though I do not have a lot experience in Bioinformatics, I have studied the ARE's in enough depth to be qualified to make these changes. For my senior project, I worked on understanding the function and biological importance of ARE's. In Addition, I have studied ARE's in depth including their computational algorithms and their database. Due to this expertise in the subject, I believe I can successfully add to the quality of this article. If you believe the above mentioned changes will improve the quality of this article, please leave me a message and I will be more than happy to make the changes.

--Sagarc88-NJITWILL (talk) 01:46, 1 August 2011 (UTC)