RBFOX1 regulates both splicing and transcriptional networks in human neuronal development.

Present address: Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.
Human Molecular Genetics (Impact Factor: 6.68). 06/2012; 21(19):4171-86. DOI: 10.1093/hmg/dds240
Source: PubMed

ABSTRACT RNA splicing plays a critical role in the programming of neuronal differentiation and, consequently, normal human neurodevelopment, and its disruption may underlie neurodevelopmental and neuropsychiatric disorders. The RNA-binding protein, fox-1 homolog (RBFOX1; also termed A2BP1 or FOX1), is a neuron-specific splicing factor predicted to regulate neuronal splicing networks clinically implicated in neurodevelopmental disease, including autism spectrum disorder (ASD), but only a few targets have been experimentally identified. We used RNA sequencing to identify the RBFOX1 splicing network at a genome-wide level in primary human neural stem cells during differentiation. We observe that RBFOX1 regulates a wide range of alternative splicing events implicated in neuronal development and maturation, including transcription factors, other splicing factors and synaptic proteins. Downstream alterations in gene expression define an additional transcriptional network regulated by RBFOX1 involved in neurodevelopmental pathways remarkably parallel to those affected by splicing. Several of these differentially expressed genes are further implicated in ASD and related neurodevelopmental diseases. Weighted gene co-expression network analysis demonstrates a high degree of connectivity among these disease-related genes, highlighting RBFOX1 as a key factor coordinating the regulation of both neurodevelopmentally important alternative splicing events and clinically relevant neuronal transcriptional programs in the development of human neurons.

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    • "The focus of this study is to define and characterize the Rbfox target splicing-regulatory network in the mammalian brain. An important piece of information missing in previous efforts toward this aim (e.g., Fogel et al., 2012; Gehman et al., 2011, 2012; Ray et al., 2013; Zhang et al., 2008) is a genome-wide, high-resolution map of in vivo Rbfox interaction sites in the brain. Such a map is especially essential due to the functional redundancy of different Rbfox family members, so that simultaneous depletion of more than one member is probably required to uncover a majority of Rbfox-dependent exons in a physiologically relevant condition. "
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    ABSTRACT: The RNA binding proteins Rbfox1/2/3 regulate alternative splicing in the nervous system, and disruption of Rbfox1 has been implicated in autism. However, comprehensive identification of functional Rbfox targets has been challenging. Here, we perform HITS-CLIP for all three Rbfox family members in order to globally map, at a single-nucleotide resolution, their in vivo RNA interaction sites in the mouse brain. We find that the two guanines in the Rbfox binding motif UGCAUG are critical for protein-RNA interactions and crosslinking. Using integrative modeling, these interaction sites, combined with additional datasets, define 1,059 direct Rbfox target alternative splicing events. Over half of the quantifiable targets show dynamic changes during brain development. Of particular interest are 111 events from 48 candidate autism-susceptibility genes, including syndromic autism genes Shank3, Cacna1c, and Tsc2. Alteration of Rbfox targets in some autistic brains is correlated with downregulation of all three Rbfox proteins, supporting the potential clinical relevance of the splicing-regulatory network.
    Cell Reports 03/2014; DOI:10.1016/j.celrep.2014.02.005 · 7.21 Impact Factor
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    • "The numbers of predicted RBFOX1 RNA binding motifs at the 3' untranslated regions (UTRs) of mRNAs positively correlated with the abundance of mRNAs [6]. Using the data of RNA-seq following RBFOX1 knockdown in primary human neural progenitor cells [7], Ray et al. found that the number of predicted FBFOX1 binding sites in mRNAs also positively correlated with the extent to which RBFOX1 knockdown reduced the expression of the mRNAs [6], reminiscent of the finding concerning Hsp90 and clients [4]. As reduced RBFOX1 levels in the brains of autism patients had been noted [8], it was further shown that predicted RBFOX1 targets had progressively lower mRNA expression in these patients [6]. "
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    ABSTRACT: A biological molecule, e.g., an enzyme, tends to interact with its many cognate substrates, targets, or partners differentially. Such a property is termed relative specificity and has been proposed to regulate important physiological functions, even though it has not been examined explicitly in most complex biochemical systems. This essay reviews several recent large-scale studies that investigate protein folding, signal transduction, RNA binding, translation and transcription in the context of relative specificity. These results and others support a pervasive role of relative specificity in diverse biological processes. It is becoming clear that relative specificity contributes fundamentally to the diversity and complexity of biological systems, which has significant implications in disease processes as well.
    Genomics Proteomics & Bioinformatics 02/2014; 12(1). DOI:10.1016/j.gpb.2014.01.001
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    • "Thus, in addition to confirming involvement of synaptic dysfunction in ASD, these findings strongly suggest that transcriptomic approaches can identify molecular commonalities in ASD brains, and we can now address whether hiPSC-derived neurons can identify these molecular signatures. The dominant module was anchored by A2BP1, the gene coding for the neuron-selective splicing factor RBFOX1, thus implicating splicing dysregulation in ASD (Fogel et al. 2012). Since A2BP1 itself had previously been identified as an autism susceptibility gene in humans (Martin et al. 2007), these results provide a strong rationale for creating hPSC-based ASD models with defects in this gene. "
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    ABSTRACT: Autism spectrum disorder (ASD) is characterized by deficits in language development and social cognition and the manifestation of repetitive and restrictive behaviors. Despite recent major advances, our understanding of the pathophysiological mechanisms leading to ASD is limited. Although most ASD cases have unknown genetic underpinnings, animal and human cellular models of several rare, genetically defined syndromic forms of ASD have provided evidence for shared pathophysiological mechanisms that may extend to idiopathic cases. Here, we review our current knowledge of the genetic basis and molecular etiology of ASD and highlight how human pluripotent stem cell-based disease models have the potential to advance our understanding of molecular dysfunction. We summarize landmark studies in which neuronal cell populations generated from human embryonic stem cells and patient-derived induced pluripotent stem cells have served to model disease mechanisms, and we discuss recent technological advances that may ultimately allow in vitro modeling of specific human neuronal circuitry dysfunction in ASD. We propose that these advances now offer an unprecedented opportunity to help better understand ASD pathophysiology. This should ultimately enable the development of cellular models for ASD, allowing drug screening and the identification of molecular biomarkers for patient stratification.
    Psychopharmacology 11/2013; DOI:10.1007/s00213-013-3332-1 · 3.99 Impact Factor