Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length

Cell Rep. 2012 Jun 28;1(6):753-63. doi: 10.1016/j.celrep.2012.05.003. Epub 2012 Jun 7.


Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we performed transcriptome-wide mapping of both binding sites of 3' end processing factors CPSF-160, CPSF-100, CPSF-73, CPSF-30, Fip1, CstF-64, CstF-64τ, CF I(m)25, CF I(m)59, and CF I(m)68 and 3' end processing sites in HEK293 cells. We found that although binding sites of these factors generally cluster around the poly(A) sites most frequently used in cleavage, CstF-64/CstF-64τ and CFI(m) proteins have much higher positional specificity compared to CPSF components. Knockdown of CF I(m)68 induced a systematic use of proximal polyadenylation sites, indicating that changes in relative abundance of a single 3' end processing factor can modulate the length of 3' untranslated regions across the transcriptome and suggesting a mechanism behind the previously observed increase in tumor cell invasiveness upon CF I(m)68 knockdown.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics*
  • Base Sequence
  • Binding Sites
  • Blotting, Northern
  • Cell Proliferation
  • Gene Knockdown Techniques
  • Genetic Loci / genetics
  • Genome, Human / genetics*
  • HEK293 Cells
  • Humans
  • Models, Biological
  • Molecular Sequence Data
  • Nucleotide Motifs / genetics
  • Poly A / metabolism
  • Polyadenylation / genetics
  • Protein Binding / genetics
  • RNA 3' End Processing / genetics*
  • RNA Precursors / genetics*
  • RNA Precursors / metabolism
  • RNA-Binding Proteins / metabolism
  • mRNA Cleavage and Polyadenylation Factors / metabolism*


  • 3' Untranslated Regions
  • RNA Precursors
  • RNA-Binding Proteins
  • cleavage factor Im, human
  • mRNA Cleavage and Polyadenylation Factors
  • Poly A

Associated data

  • GEO/GSE37401