Despite current understanding of 3′-UTRs, they are still relative mysteries. Since mRNAs usually contain several overlapping control elements, it is often difficult to specify the identity and function of each 3′-UTR element, let alone the regulatory factors that may bind at these sites. Additionally, each 3′-UTR contains many alternative AU-rich elements and polyadenylation signals. These cis- and trans-acting elements, along with miRNAs, offer a virtually limitless range of control possibilities within a single mRNA. Future research through the increased use of deep-sequencing based ribosome profiling will reveal more regulatory subtleties as well as new control elements and AUBPs.