Alternative polyadenylation regulates CELF1/CUGBP1 target transcripts following T cell activation

•Global polyadenylation site usage was determined following T cell activation.•CELF1 targets were preferentially shortened via APA following T cell activation.•Shortening of CELF1 targets caused loss of the GRE and increased expression.•CELF1 targets shortened via APA encode regulators of cellular proliferation.•A model for CELF1-mediated regulation of APA was proposed.

Alternative polyadenylation (APA) is an evolutionarily conserved mechanism for regulating gene expression. Transcript 3′ end shortening through changes in polyadenylation site usage occurs following T cell activation, but the consequences of APA on gene expression are poorly understood. We previously showed that GU-rich elements (GREs) found in the 3′ untranslated regions of select transcripts mediate rapid mRNA decay by recruiting the protein CELF1/CUGBP1. Using a global RNA sequencing approach, we found that a network of CELF1 target transcripts involved in cell division underwent preferential 3′ end shortening via APA following T cell activation, resulting in decreased inclusion of CELF1 binding sites and increased transcript expression. We present a model whereby CELF1 regulates APA site selection following T cell activation through reversible binding to nearby GRE sequences. These findings provide insight into the role of APA in controlling cellular proliferation during biological processes such as development, oncogenesis and T cell activation.