PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage

Cell Rep. 2016 Apr 12;15(2):423-35. doi: 10.1016/j.celrep.2016.03.023. Epub 2016 Mar 31.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics
  • Animals
  • Base Sequence
  • Brain / metabolism
  • Cells, Cultured
  • Conserved Sequence
  • Evolution, Molecular
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Immunoprecipitation / methods*
  • Mice, Inbred C57BL
  • MicroRNAs / metabolism*
  • Nucleotide Motifs / genetics
  • Poly A / metabolism*
  • Polyadenylation
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Transcriptome / genetics
  • tau Proteins / metabolism*


  • 3' Untranslated Regions
  • MicroRNAs
  • RNA, Messenger
  • tau Proteins
  • Poly A