Genome-wide assessment of AU-rich elements by the AREScore algorithm

PLoS Genet. 2012 Jan;8(1):e1002433. doi: 10.1371/journal.pgen.1002433. Epub 2012 Jan 5.

Abstract

In mammalian cells, AU-rich elements (AREs) are well known regulatory sequences located in the 3' untranslated region (UTR) of many short-lived mRNAs. AREs cause mRNAs to be degraded rapidly and thereby suppress gene expression at the posttranscriptional level. Based on the number of AUUUA pentamers, their proximity, and surrounding AU-rich regions, we generated an algorithm termed AREScore that identifies AREs and provides a numerical assessment of their strength. By analyzing the AREScore distribution in the transcriptomes of 14 metazoan species, we provide evidence that AREs were selected for in several vertebrates and Drosophila melanogaster. We then measured mRNA expression levels genome-wide to address the importance of AREs in SL2 cells derived from D. melanogaster hemocytes. Tis11, a zinc finger RNA-binding protein homologous to mammalian tristetraprolin, was found to target ARE-containing reporter mRNAs for rapid degradation in SL2 cells. Drosophila mRNAs whose expression is elevated upon knock down of Tis11 were found to have higher AREScores. Moreover high AREScores correlate with reduced mRNA expression levels on a genome-wide scale. The precise measurement of degradation rates for 26 Drosophila mRNAs revealed that the AREScore is a very good predictor of short-lived mRNAs. Taken together, this study introduces AREScore as a simple tool to identify ARE-containing mRNAs and provides compelling evidence that AREs are widespread regulatory elements in Drosophila.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics
  • Animals
  • Computational Biology / methods
  • Consensus Sequence
  • Drosophila Proteins / genetics
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / genetics*
  • Drosophila melanogaster / metabolism*
  • Evolution, Molecular
  • Gene Expression Regulation
  • Genome
  • Genome-Wide Association Study
  • RNA Stability / genetics
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Regulatory Sequences, Ribonucleic Acid / genetics*
  • Sequence Homology, Amino Acid
  • Software
  • Transcriptome / genetics*
  • Tristetraprolin / genetics*
  • Tristetraprolin / metabolism

Substances

  • 3' Untranslated Regions
  • Drosophila Proteins
  • RNA, Messenger
  • RNA-Binding Proteins
  • Regulatory Sequences, Ribonucleic Acid
  • Tis11 protein, Drosophila
  • Tristetraprolin

Associated data

  • RefSeq/NM_010556
  • RefSeq/NM_165011