Accurate and precise annotation of 3′ UTRs is critical for understanding how mRNAs are regulated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). Here, we describe a method, poly(A) binding protein-mediated mRNA 3′ end retrieval by crosslinking immunoprecipitation (PAPERCLIP), that shows high specificity for mRNA 3′ ends and compares favorably with existing 3′ end mapping methods. PAPERCLIP uncovers a previously unrecognized role of CstF64/64tau in promoting the usage of a selected group of non-canonical poly(A) sites, the majority of which contain a downstream GUKKU motif. Furthermore, in the mouse brain, PAPERCLIP discovers extended 3′ UTR sequences harboring functional miRNA binding sites and reveals developmentally regulated APA shifts, including one in Atp2b2 that is evolutionarily conserved in humans and results in the gain of a functional binding site of miR-137. PAPERCLIP provides a powerful tool to decipher post-transcriptional regulation of mRNAs through APA in vivo. Display omitted •PAPERCLIP is a high-performance mRNA 3′ end mapping method based on the CLIP technique•PAPERCLIP provides insights into the regulation of alternative polyadenylation•PAPERCLIP expands knowledge of 3′-UTR-mediated mRNA regulation Hwang et al. develop PAPERCLIP, a high-performance mRNA 3′ end mapping method based on the CLIP technique. They use PAPERCLIP to show that CstF64/64tau promotes non-canonical poly(A) site usage through a GUKKU motif. Furthermore, they also discover shifts in alternative polyadenylation and identify novel microRNA binding sites during mouse brain development.