The ubiquitously expressed RNA-binding protein Hu antigen R (HuR) or ELAVL1 is 
implicated in a variety of biological processes as well as being linked with a 
number of diseases, including cancer. Despite a great deal of prior 
investigation into HuR, there is still much to learn about its function. We take 
an important step in this direction by conducting cross-linking and 
immunoprecipitation and RNA sequencing experiments followed by an extensive 
computational analysis to determine the characteristics of the HuR binding site 
and impact on the transcriptome. We reveal that HuR targets predominantly 
uracil-rich single-stranded stretches of varying size, with a strong 
conservation of structure and sequence composition. Despite the fact that HuR 
sites are observed in intronic regions, our data do not support a role for HuR 
in regulating splicing. HuR sites in 3'-UTRs overlap extensively with predicted 
microRNA target sites, suggesting interplay between the functions of HuR and 
microRNAs. Network analysis showed that identified targets containing HuR 
binding sites in the 3' UTR are highly interconnected.