Computational profiling and identification of the 3' untranslated region within Paramecium tetraurela
The 3' untranslated region of mRNA is of particular interest for determining localization within a cell, and may play a role in evolution of genes. However, the 3' region is not easy to determine for all mRNA within a cell. A profile of the 3' untranslated region within Paramecium tetraurelia is explored. This profile can be used to predict the cleavage site as well through the use of a modified Hidden Markov Model. Also, using conserved domains known to bind to mRNA, different mRNA binding proteins were identified in an attempt to identify those that bind to control localization. Concurrently, a method to experimentally determine the 3' untranslated region was developed as a method to confirm results from the probabilistic model. This was accomplished through first creating cDNA and using a primer 50-200 nt upstream from the stop codon and a poly dT primer to amplify the 3' untranslated region for sequencing. With the methodology, the predictions can be verified.
© Copyright 2012 Tristan Vrolijk