Functional Antagonism Between CELF and Mbnl Proteins in the Cytoplasm

Abstract

The conserved CUGBP1, Elav-like (CELF) family of RNA binding proteins contribute to heart and skeletal muscle development and are implicated in myotonic dystrophy (DM). To understand genome-wide functions of CELF proteins, we analyzed transcriptome dynamics following induction of CELF1 or CELF2 in adult mouse heart or CELF1 in muscle by RNA-seq, complemented by crosslinking/immunoprecipitation-sequencing (CLIP-seq) analysis of mouse cells and tissues to distinguish direct from indirect regulatory targets. Analysis of expression and mRNA binding data revealed hundreds of mRNAs bound in their 3' UTRs by both CELF1 and and the developmentally induced Mbnl1 protein, 3-fold more than expected. The relative extent of CELF1 and Mbnl1 binding in 3' UTRs predicted the extent of repression or stabilization, respectively, following CELF induction. These findings support a ?Cytoplasmic Competition? model in which CELF and Mbnl proteins compete to specify degradation or membrane localization/stabilization, respectively, of an overlapping set of targets. Several hundred messages contained proximal CELF1 and Mbnl1 binding sites (within 50 bases), and were more strongly repressed by CELF1 than messages with distal sites. Messages with different spacing of CELF and Mbnl sites in their 3' UTRs exhibited different developmental dynamics, suggesting that spacing is used to tune cytoplasmic competition between these factors to specify the timing of developmental induction. CELF1 also shared dozens of splicing targets with Mbnl1, most regulated oppositely, confirming a phenomenon observed in smaller scale studies but not previously supported by genome-wide methods, which also appears to enhance developmental transitions.