MicroRNAs (miRNAs) function via targeting of messenger RNAs, suppressing protein levels, and playing important roles in biological processes of plants and animals. The pathway for miRNA biogenesis is well established, but less is known about miRNA turnover, largely due to difficulties in capturing miRNAs during the process of decay, in which they are both rare and ephemeral. The HEN1 protein methylates the 3' terminus of small RNAs (small RNAs), protecting them from polyurydilation and degradation. Recent progress using deep sequencing to study small RNAs in HEN1 reveals the potential for HEN1 to serve as a platform for studies of miRNA turnover, with the sequencing data providing unprecedented precision and detail in the characterization of 3’ modifications.