@article {10.1371/journal.pgen.1002433,
	title = {{Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm}},
	journal = {PLoS Genet},
	volume = {8},
	number = {1},
	year = {2012},
	month = {01},
	pages = {e1002433},
	abstract = {<title>Author Summary</title> <p>Many genes are regulated at the posttranscriptional level by factors that influence the stability of the messenger RNA. In mammals, AU-rich elements are known to cause rapid degradation of messenger RNAs and thereby suppress gene expression. In order to identify such elements on a genome-wide scale, we developed a bioinformatic tool with which we can score messenger RNAs for the presence of AU-rich elements. Using the ARE<italic>Score</italic> algorithm, we observe that AU-rich elements correlate with reduced messenger RNA stability and expression levels. We then used the ARE<italic>Score</italic> to compare the transcriptomes of 14 metazoan species and found that messenger RNAs with high ARE<italic>Scores</italic> are enriched in several vertebrates and the fruit fly <italic>Drosophila melanogaster</italic>. We identified messenger RNAs whose levels are regulated by the <italic>Drosophila</italic> Tis11 protein, which binds to AU-rich elements. Our study introduces the ARE<italic>Score</italic> as a means to globally assess AU-rich elements and predict short-lived messenger RNAs. Furthermore, it demonstrates the regulatory role of AU-rich elements in suppressing gene expression by accelerating messenger RNA degradation in <italic>D. melanogaster</italic> cells.</p>},
	doi = {10.1371/journal.pgen.1002433},
	author = {Milan Spasic and Caroline C. Friedel and Johanna Schott and Jochen Kreth and Kathrin Leppek and Sarah Hofmann and Sevim Ozgur and Georg Stoecklin}
}