Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes

Abstract

Over 95% of human multi-exon genes undergo alternative splicing, a process important in normal development and often dysregulated in disease. We sought to analyze the global splicing regulatory network of CELF2 in human T cells, a well-studied splicing regulator critical to T cell development and function. By integrating high-throughput sequencing data for binding and splicing quantification with sequence features and probabilistic splicing code models, we find evidence of splicing antagonism between CELF2 and the RBFOX family of splicing factors. We validate this functional antagonism through knockdown and overexpression experiments in human cells and find CELF2 represses RBFOX2 mRNA and protein levels. Because both families of proteins have been implicated in the development and maintenance of neuronal, muscle, and heart tissues, we analyzed publicly available data in these systems. Our analysis suggests global, antagonistic coregulation of splicing by the CELF and RBFOX proteins in mouse muscle and heart in several physiologically relevant targets, including proteins involved in calcium signaling and members of the MEF2 family of transcription factors. Importantly, a number of these coregulated events are aberrantly spliced in mouse models and human patients with diseases that affect these tissues, including heart failure, diabetes, or myotonic dystrophy. Finally, analysis of exons regulated by ancient CELF family homologs in chicken, Drosophila, and Caenorhabditis elegans suggests this antagonism is conserved throughout evolution.

Viral-Induced Alternative Splicing of Host Genes Promotes Influenza Replication

“…Notably, only 43 of these genes also exhibit changes in abundance upon viral infection ( Fig. 2c ), consistent with many other studies that have found that genes regulated by splicing and transcription are largely distinct (Gazzara et al, 2017; Ip et al, 2007; Shinde et al, 2017). Moreover, GO analysis of the 588 genes that are differentially spliced, without changes in abundance, finds an enrichment for genes associated with RNA processing, not immune defense ( Fig.…”

Handshakes and Fights: The Regulatory Interplay of RNA-Binding Proteins

“…Outside the hnRNP and SR families, genome-wide analyses found a conserved functional antagonism in splicing regulation between CELF2 and RBFOX2. These RBPs bind to overlapping sites on several pre-mRNAs with opposing consequences on exons inclusion (Gazzara et al, 2017 ). This mechanism is also used by QKI and PTBP1, competing for the splicing of specific exons on almost 200 common targets (Hall et al, 2013 ).…”

“…As these RBPs are frequently under autogenous regulation, RBFOX2 represent a global controller of such behavior (Jangi et al, 2014 ). The stability of RBFOX2 mRNA is, in turn, decreased by CELF2 to tune the outcome of their splicing antagonism (Gazzara et al, 2017 ). AS-NMD is also used by RBM10 to repress RBM5 mRNA (Sun et al, 2017 ), with RBM5 in turn controlling the expression of one splicing variant of RBM10 to reduce its pro-oncogenic role (Loiselle et al, 2017 ).…”

RBFOX2 and alternative splicing in B-cell lymphoma

“…This splicing event is important for erythropoiesis because it increases the affinity of 4.1R for target genes 5 . In a recent study, expression of RBFOX2 was detected in the human T-cell line JURKAT and a functional antagonism of the RBPs RBFOX2 and CELF2 was demonstrated 6 . We wanted to describe the expression patterns of RBFOX2 in hematopoetic malignancies, to discover target genes and to unravel the consequence of RBFOX2 repression for target gene splicing and isoform expression.…”