The AU-rich element landscape across human transcriptome reveals a large proportion in introns and regulation by ELAVL1/HuR

Abstract Adenylate-uridylate ( AU)- rich elements(AREs) are sequence instability elements that are known to be located in the 3′ untranslated regions (UTR) in thousands of human transcripts. AREs regulate the expression of many genes at the post-transcriptional level, and they are essential for many normal cellular functions. We conducted a transcriptome-wide screen for AREs and found that they are most abundant in introns, with up to 25% of intronscontaining AREs corresponding to 58% of human genes. Clustering studies of ARE size, complexity, and distribution revealed that, in introns, longer AREs with two or more overlapping repeats are more abundant than in the 3′UTR, and only intronscan contain very long AREs with 6–14 overlapping AUUUA pentamers. We found that intronicsites of the ARE binding proteins HuR/ELAVL1, ZFP36/TTP, AUF1, and BRF1/ZFP36L1 overlap with the intronicAREs with HuR being most abundant. Accordingly, RNA-IP experiments demonstrated a specific association of HuR with reporter and endogenous pre-mRNAs that contain intronicAREs. Moreover, HuR knockdown led to a significant general reduction in the mRNA levels of genes that contain intronicAREs and to a specific reduction in the expression of ARE- intronicreporters. The data represent bioinformatics analysis for key RNA-binding proteinsinteractions with intronicAREs and provide experimental evidence for HuR binding to AREs. The widespread distribution of intronicAREs and their particular association with HuR and HuR binding sites indicates that more than half of human genes can be regulated post-transcriptionally by AREs.