RNA binding proteins of the conserved CUGBP1, Elav-like factor (CELF) family contribute to heart and skeletal muscle development and are implicated in myotonic dystrophy (DM). To understand their genome-wide functions, we analyzed the transcriptome dynamics following induction of CELF1 or CELF2 in adult mouse heart and of 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. We identified hundreds of mRNAs bound in their 3 ′ UTRs by both CELF1 and the developmentally induced MBNL1 protein, a threefold greater overlap in target messages than expected, including messages involved in development and cell differentiation. The extent of 3 ′ UTR binding by CELF1 and MBNL1 predicted the degree of mRNA repression or stabilization, respectively, following CELF1 induction. However, CELF1's RNA binding specificity in vitro was not detectably altered by coincubation with recombinant MBNL1. These findings support a model in which CELF and MBNL proteins bind independently to mRNAs but functionally compete to specify down-regulation or localization/stabilization, respectively, of hundreds of mRNA targets. Expression of many alternative 3 ′ UTR isoforms was altered following CELF1 induction, with 3 ′ UTR binding associated with down-regulation of isoforms and genes. The splicing of hundreds of alternative exons was oppositely regulated by these proteins, confirming an additional layer of regulatory antagonism previously observed in a handful of cases. The regulatory relationships between CELFs and MBNLs in control of both mRNA abundance and splicing appear to have evolved to enhance developmental transitions in major classes of heart and muscle genes.[Supplemental material is available for this article.] CELF RNA binding proteins (RBPs) play roles in early embryonic development, heart, and skeletal muscle functions. They are also thought to contribute to DM pathogenesis (Timchenko et al. 1996) and have been suggested to contribute to other diseases (Ladd 2013). The six family members present in mammals can be divided into two subfamilies: CELF1-2, which are expressed most highly in heart, skeletal muscle, and brain, and CELF3-6, which exhibit more restricted expression (Dasgupta and Ladd 2012). The CELF proteins contain two N-terminal RNA recognition motifs (RRMs) and one C-terminal RRM, with which they bind GU-rich RNAs, and a linker region termed the "divergent domain" that separates RRM2 and RRM3 and is involved in the regulation of alternative pre-mRNA splicing and mRNA decay (Han and Cooper 2005;.During normal development, CELF1 and CELF2 proteins are highly expressed in early embryonic stages and are then down-regulated more than 10-fold in skeletal muscle (Ladd et al. 2005) and the heart (Kalsotra et al. 2008) during post-natal development, remaining at low levels in adult tissues. This developmental downregulation occurs through multiple mechanisms, including repression by microRNAs (m...