Expression profiling in spinal muscular atrophy reveals an RNA binding protein deficit

CELF2 promotes tau exon 10 inclusion via hinge domain-mediated nuclear condensation

Alternative splicing is a fundamental process that contributes to the functional diversity and complexity of proteins. The regulation of each alternative splicing event involves the coordinated action of multiple RNA-binding proteins, creating a diverse array of alternatively spliced products. Dysregulation of alternative splicing is associated with various diseases, including neurodegeneration. Here we demonstrate that CELF2, a splicing regulator and a GWAS-identified risk factor for Alzheimer's disease, binds to mRNAs associated with neurodegenerative diseases, with a specific interaction observed in the intron adjacent to exon 10 on Tau mRNA. Loss of CELF2 in the mouse brain results in a decreased inclusion of Tau exon 10, leading to a reduced 4R:3R ratio. Further exploration shows that the hinge domain of CELF2 possesses an intrinsically disordered region (IDR), which mediates CELF2 condensation and function. The functionality of IDR in regulating CELF2 function is underscored by its substitutability with IDRs from FUS and TAF15. Using TurboID we identified proteins that interact with CELF2 through its IDR. We revealed that CELF2 co-condensate with NOVA2 and SFPQ, which coordinate with CELF2 to regulate the alternative splicing of Tau exon 10. A negatively charged residue within the IDR (D388), which is conserved among CELF proteins, is critical for CELF2 condensate formation, interactions with NOVA2 and SFPQ, and function in regulating tau exon 10 splicing. Our data allow us to propose that CELF2 regulates Tau alternative splicing by forming condensates through its IDR with other splicing factors, and that the composition of the proteins within the condensates determines the outcomes of alternative splicing events.

RNA splicing regulators play critical roles in neurogenesis

Alternative RNA splicing increases transcript diversity in different cell types and under varying conditions. It is executed with the help of RNA splicing regulators (RSRs), which are operationally defined as RNA-binding proteins (RBPs) that regulate alternative splicing, but not directly catalyzing the chemical reactions of splicing. By systematically searching for RBPs and manually identifying those that regulate splicing, we curated 305 RSRs in the human genome. Surprisingly, most of the RSRs are involved in neurogenesis. Among these RSRs, we focus on nine families (PTBP, NOVA, RBFOX, ELAVL, CELF, DBHS, MSI, PCBP, and MBNL) that play essential roles in the neurogenic pathway. A better understanding of their functions will provide novel insights into the role of splicing in brain development, health, and disease. This comprehensive review serves as a stepping-stone to explore the diverse and complex set of RSRs as fundamental regulators of neural development. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing.

Mitochondrial Dysfunction in Spinal Muscular Atrophy

Spinal muscular atrophy (SMA) is a devastating neuromuscular disorder caused by recessive mutations in the SMN1 gene, globally affecting ~8-14 newborns per 100,000. The severity of the disease depends on the residual levels of functional survival of motor neuron protein, SMN. SMN is a ubiquitously expressed RNA binding protein involved in a plethora of cellular processes. In this review, we discuss the effects of SMN loss on mitochondrial functions in the neuronal and muscular systems that are the most affected in patients with spinal muscular atrophy. Our aim is to highlight how mitochondrial defects may contribute to disease progression and how restoring mitochondrial functionality may be a promising approach to develop new therapies. We also collected from previous studies a list of transcripts encoding mitochondrial proteins affected in various SMA models. Moreover, we speculate that in adulthood, when motor neurons require only very low SMN levels, the natural deterioration of mitochondria associated with aging may be a crucial triggering factor for adult spinal muscular atrophy, and this requires particular attention for therapeutic strategies.

MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy

Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of the dystrophia myotonica-protein kinase (DMPK) gene. Despite its prominence as the most common adult-onset muscular dystrophy, patients with congenital to juvenile-onset forms of DM1 can present with debilitating neurocognitive symptoms along the autism spectrum, characteristic of possible in utero cortical defects. However, the molecular mechanism by which CTG MREs lead to these developmental central nervous system (CNS) manifestations is unknown. Here, we showed that CUG foci found early in the maturation of three-dimensional (3D) cortical organoids from DM1 patient-derived induced pluripotent stem cells (iPSCs) cause hyperphosphorylation of CUGBP Elav-like family member 2 (CELF2) protein. Integrative single-cell RNA sequencing and enhanced cross-linking and immunoprecipitation (eCLIP) analysis revealed that reduced CELF2 protein-RNA substrate interactions results in misregulation of genes critical for excitatory synaptic signaling in glutamatergic neurons, including key components of the methyl-CpG binding protein 2 (MECP2) pathway. Comparisons to MECP2(y/-) cortical organoids revealed convergent molecular and cellular defects such as glutamate toxicity and neuronal loss. Our findings provide evidence suggesting that early-onset DM1 might involve neurodevelopmental disorder-associated pathways and identify N-methyl-d-aspartic acid (NMDA) antagonists as potential treatment avenues for neuronal defects in DM1.

Human cytomegalovirus UL141 protein interacts with CELF5 and affects viral DNA replication

Human cytomegalovirus (HCMV) infection is the primary viral cause of congenital abnormalities and mental retardation in newborns. The HCMV UL141‑encoded glycoprotein has been previously revealed to inhibit the cell‑surface expression of cluster of differentiation (CD)155, CD122, tumor necrosis factor‑related apoptosis‑inducing ligand death (TRAIL)‑receptor 1 (R1) and TRAIL‑receptor 2 (R2), thus protecting virally‑infected cells by allowing them to escape natural killer cell‑mediated cytotoxicity. The present study investigated the interaction between HCMV UL141 and human fetal brain cDNA to elucidate the possible effects of UL141 on the nervous system. The findings of the current study demonstrate that the HCMV UL141 protein directly interacts with the human protein CUGBP Elav‑like family member 5 (CELF5) via yeast two‑hybrid screening, this interaction was confirmed by glutathione S‑transferase pull‑down and co‑immunoprecipitation assays. Additionally, the present study demonstrated that the UL141 protein co‑localizes with CELF5 in the cytoplasm of 293 cells using fluorescence confocal microscopy. CELF5 overexpression in a stably‑expressing cell line significantly increased viral DNA copy number and titer in HCMV‑infected U373MG cells. However, reducing CELF5 expression via specific small interfering RNAs did not affect viral DNA copy number or titer in HCMV‑infected cells. The current findings suggest that the interaction between UL141 and CELF5 may be involved in modulating viral DNA synthesis and progeny production. Therefore, CELF5 may represent a possible mechanism for regulation of HCMV genomic DNA synthesis, which is a key step during HCMV infection leading to neurological disease.

CELF RNA binding proteins promote axon regeneration in C. elegans and mammals through alternative splicing of Syntaxins

Axon injury triggers dramatic changes in gene expression. While transcriptional regulation of injury-induced gene expression is widely studied, less is known about the roles of RNA binding proteins (RBPs) in post-transcriptional regulation during axon regeneration. In C. elegans the CELF (CUGBP and Etr-3 Like Factor) family RBP UNC-75 is required for axon regeneration. Using crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq) we identify a set of genes involved in synaptic transmission as mRNA targets of UNC-75. In particular, we show that UNC-75 regulates alternative splicing of two mRNA isoforms of the SNARE Syntaxin/unc-64. In C. elegans mutants lacking unc-75 or its targets, regenerating axons form growth cones, yet are deficient in extension. Extending these findings to mammalian axon regeneration, we show that mouse Celf2 expression is upregulated after peripheral nerve injury and that Celf2 mutant mice are defective in axon regeneration. Further, mRNAs for several Syntaxins show CELF2 dependent regulation. Our data delineate a post-transcriptional regulatory pathway with a conserved role in regenerative axon extension.

DOI:http://dx.doi.org/10.7554/eLife.16072.001

Nerve cells or neurons carry information around the body along projections known as axons. An injury or trauma, such as a stroke, can damage the axons and lead to permanent disability because the damaged axons fail to regenerate over long distances.

Axon damage triggers large changes in the activity of many genes that promote regeneration. When a gene is active, its DNA is copied to make molecules of messenger RNA (mRNA), which are then used as templates to make proteins. Many mRNAs undergo a process called alternative splicing, in which different combinations of mRNA sections may be removed from the final molecule. This enables a single gene to produce more than one type of protein.

Recent studies point to an important role for so-called RNA binding proteins in regulating the alternative splicing process. An RNA binding protein called UNC-75 in a worm known as Caenorhabditis elegans has previously been shown to be involved in axon regeneration, but it was not clear how UNC-75 acts on neurons. Here, Chen et al. combined a technique called CLIP-seq (Cross-linking ImmunoPrecipitation-deep sequencing) with genetic testing to identify the mRNAs that UNC-75 regulates during axon regeneration.

The experiments found a set of C. elegans genes required for information to pass between neurons whose mRNAs are also targeted by UNC-75. Many of these genes are also required for axon regeneration. Chen et al. studied one of the mRNA targets – which encodes a protein called syntaxin – in more detail and found that the syntaxin mRNA is required for regenerating axons over long distances. UNC-75 alternatively splices this mRNA to produce a particular form of syntaxin that is mainly found in neurons. Mutant worms that lack either UNC-75 or syntaxin are unable to properly regenerate axons over long distances.

Further experiments show that a mouse protein known as CELF2 that is equivalent to worm UNC-75 plays a similar role in regenerating axons. Moreover, mouse CELF2 restores the ability of worm neurons that lack UNC-75 to regenerate. Like worm UNC-75, the mouse protein is also involved in alternative splicing of syntaxin. The next step is to examine the other mRNA targets of UNC-75 to find out what role they play in axon regeneration and other processes in neurons.

DOI:http://dx.doi.org/10.7554/eLife.16072.002

Transcriptome profiling of spinal muscular atrophy motor neurons derived from mouse embryonic stem cells

Proximal spinal muscular atrophy (SMA) is an early onset, autosomal recessive motor neuron disease caused by loss of or mutation in SMN1 (survival motor neuron 1). Despite understanding the genetic basis underlying this disease, it is still not known why motor neurons (MNs) are selectively affected by the loss of the ubiquitously expressed SMN protein. Using a mouse embryonic stem cell (mESC) model for severe SMA, the RNA transcript profiles (transcriptomes) between control and severe SMA (SMN2^+/+;mSmn^−/−) mESC-derived MNs were compared in this study using massively parallel RNA sequencing (RNA-Seq). The MN differentiation efficiencies between control and severe SMA mESCs were similar. RNA-Seq analysis identified 3,094 upregulated and 6,964 downregulated transcripts in SMA mESC-derived MNs when compared against control cells. Pathway and network analysis of the differentially expressed RNA transcripts showed that pluripotency and cell proliferation transcripts were significantly increased in SMA MNs while transcripts related to neuronal development and activity were reduced. The differential expression of selected transcripts such as Crabp1, Crabp2 and Nkx2.2 was validated in a second mESC model for SMA as well as in the spinal cords of low copy SMN2 severe SMA mice. Furthermore, the levels of these selected transcripts were restored in high copy SMN2 rescue mouse spinal cords when compared against low copy SMN2 severe SMA mice. These findings suggest that SMN deficiency affects processes critical for normal development and maintenance of MNs.

Histologic and transcriptional assessment of a mild SMA model

Spinal muscular atrophy (SMA) is caused by survival of motor neuron (SMN) deficiency, leading to specific motor neuron attrition. The time course and molecular pathophysiologic etiology of motor neuron loss observed in SMA remains obscure. Mice heterozygous for Smn show up to 50% motor neuron attrition by 6 months of age and are used as a model for mild SMA in humans. To determine both the rate of cellular loss and the molecular events underlying motor neuron degeneration in SMA, motor neuron counts and mRNA quantification were performed in spinal cords of Smn(+/-) mice and wild-type littermates. Surprisingly, despite the chronic, subclinical nature of motor neuron loss, we find that the bulk of the loss occurs by 5 weeks of age. RNA isolated from the spinal cords of 5 week-old Smn(+/-) mice subjected to microarray analysis reveal alterations in genes involved in RNA metabolism, apoptosis and transcriptional regulation including a general perturbation of transcripts coding for calcium binding proteins. A subset of these changes in expression was further characterized by semi-quantitative RT-PCR and Western blot analysis at various time points. Taken together, these results indicate that spinal cord cells present the first signs of the apoptotic process consistent with a response to the stress of Smn depletion. A picture of comparatively rapid neuronal attrition in spite of the very mild nature of SMA is obtained. Furthermore, changes occur, which may be reactive to and not causative of the cellular loss, involving central cellular functions as well as calcium modulating proteins.

CELFish ways to modulate mRNA decay

The CELF family of RNA-binding proteins regulates many steps of mRNA metabolism. Although their best characterized function is in pre-mRNA splice site choice, CELF family members are also powerful modulators of mRNA decay. In this review we focus on the different modes of regulation that CELF proteins employ to mediate mRNA decay by binding to GU-rich elements. After starting with an overview of the importance of CELF proteins during development and disease pathogenesis, we then review the mRNA networks and cellular pathways these proteins regulate and the mechanisms by which they influence mRNA decay. Finally, we discuss how CELF protein activity is modulated during development and in response to cellular signals. We conclude by highlighting the priorities for new experiments in this field. This article is part of a Special Issue entitled: RNA Decay mechanisms.

CUG-BP, Elav-like family (CELF)-mediated alternative splicing regulation in the brain during health and disease

Alternative splicing is an important mechanism for generating transcript and protein diversity. In the brain, alternative splicing is particularly prevalent, and alternative splicing factors are highly enriched. These include the six members of the CUG-BP, Elav-like family (CELF). This review summarizes what is known about the expression of different CELF proteins in the nervous system and the evidence that they are important in neural development and function. The involvement of CELF proteins in the pathogenesis of a number of neurodegenerative disorders, including myotonic dystrophy, spinocerebellar ataxia, fragile X syndrome, spinal muscular atrophy, and spinal and bulbar muscular atrophy is discussed. Finally, the known targets of CELF-mediated alternative splicing regulation in the nervous system and the functional consequences of these splicing events are reviewed. This article is part of a Special Issue entitled "RNA and splicing regulation in neurodegeneration."

The role of CELF proteins in neurological disorders

CELF (CUG-BP and ETR-3-like factors) proteins are structurally related RNA-binding proteins involved in various aspects of RNA processing including splicing and mRNA stability. The first member of the family, CELF1/CUG-BP1, was identified through its role in myotonic dystrophy, type 1. Several recent studies have uncovered the recurrent implication, to various extents, of CELF proteins or of the functionally related muscleblind-like 1 protein in a number of neurological conditions. This is particularly clear for inherited neurodegenerative disorders caused by expansions of translated or untranslated triplet repeats in the causative gene. Here we review the role played by CELF proteins, at least as modifiers of the pathological phenotype, in a number of neurological diseases. The involvement of CELF proteins suggest that individual pathogenic pathways in a number of neurological conditions overlap at the level of RNA processing.

Biochemical properties and expression profile of human prolyl dipeptidase DPP9

Dipetidyl peptidase 9 (DPP9) is a prolyl dipeptidase preferentially cleaving the peptide bond after the penultimate proline residue. The biological function of DPP9 is unknown. In this study, we have significantly improved the yield using Strep.Tactin purification system and characterized the biochemical property of DPP9. Moreover, the dimer interaction mode was investigated by introducing a mutation (F842A) at the dimer interface, which abolished the enzymatic activity without disrupting its quaternary structure. Furthermore, DPP9 was found ubiquitously expressed in fibroblasts, epithelial, and blood cells. Surprisingly, contrary to previous report, we found that the expression levels of DPP8 and DPP9 did not change upon the activation of the PBMC or Jurkat cells. These results indicate that the biochemical property of DPP9 is very similar to that of DPP8, its homologous protease. DPP9 and DPP8 are likely redundant proteins carrying out overlapping functions in vivo.

Microarray analysis of mdx mice expressing high levels of utrophin: therapeutic implications for dystrophin deficiency

Duchenne Muscular Dystrophy (DMD) is a fatal muscle wasting disorder caused by dystrophin deficiency. Previous work suggested that increased expression of the dystrophin-related protein utrophin in the mdx mouse can reduce the dystrophic pathophysiology. Physiological tests showed that the transgenic mouse muscle functioned in a way similar to normal muscle. More recently, it has become possible to analyse disease pathways using microarrays, a sensitive method to evaluate the efficacy of a therapeutic approach. We thus examined the gene expression profile of mdx mouse muscle compared to wild-type mouse muscle and compared the data with that obtained from the transgenic line overexpressing utrophin. The data confirm that the expression of utrophin in the mdx mouse muscle results in a global gene expression profile more similar to that seen for the wild-type mouse. This study confirms that a strategy to up-regulate utrophin is likely to be beneficial in dystrophin deficiency.

Smn depletion alters profilin II expression and leads to upregulation of the RhoA/ROCK pathway and defects in neuronal integrity

Spinal muscular atrophy (SMA) is the most common genetic disease resulting in infant mortality due to severe loss of alpha-motor neurons. SMA is caused by mutations or deletions of the ubiquitously expressed survival motor neuron (SMN) gene. However, why alpha-motor neurons of SMA patients are specifically affected is not clear. We demonstrate here that Smn knockdown in PC12 cells alters the expression pattern of profilin II, resulting in an increase in the neuronal-specific profilin IIa isoform. Moreover, the depletion of Smn, a known interacting partner of profilin IIa, further contributes to the increased profilin IIa availability. Altogether, this leads to an increased formation of ROCK/profilin IIa complex and an inappropriate activation of the RhoA/ROCK pathway, resulting in altered cytoskeletal integrity and a subsequent defect in neuritogenesis. This study represents the first description of a mechanism underlying SMA pathogenesis and highlights new targets for therapeutic intervention for this devastating disorder.

Distinct domains of the spinal muscular atrophy protein SMN are required for targeting to Cajal bodies in mammalian cells

Mutations of the survival motor neuron gene SMN1 cause the inherited disease spinal muscular atrophy (SMA). The ubiquitous SMN protein facilitates the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs). The protein is detected in the cytoplasm, nucleoplasm and enriched with snRNPs in nuclear Cajal bodies. It is structurally divided into at least an amino-terminal region rich in basic amino acid residues, a central Tudor domain, a self-association tyrosine-glycine-box and an exon7-encoded C-terminus. To examine the domains required for the intranuclear localization of SMN, we have used fluorescently tagged protein mutants transiently overexpressed in mammalian cells. The basic amino acid residues direct nucleolar localization of SMN mutants. The Tudor domain promotes localization of proteins in the nucleus and it cooperates with the basic amino acid residues and the tyrosine-glycine-box for protein localization in Cajal bodies. Moreover, the most frequent disease-linked mutant SMNΔex7 reduces accumulation of snRNPs in Cajal bodies, suggesting that the C-terminus of SMN participates in targeting to Cajal bodies. A reduced number of Cajal bodies in patient fibroblasts associates with the absence of snRNPs in Cajal bodies, revealing that intranuclear snRNA organization is modified in disease. These results indicate that direct and indirect mechanisms regulate localization of SMN in Cajal bodies.

Cajal bodies: a long history of discovery

This review surveys what is known about the structure and function of the subnuclear domains called Cajal bodies (CBs). The major focus is on CBs in mammalian cells but we provide an overview of homologous CB structures in other organisms. We discuss the protein and RNA components of CBs, including factors recently found to associate in a cell cycle-dependent fashion or under specific metabolic or stress conditions. We also consider the dynamic properties of both CBs and their molecular components, based largely on recent data obtained thanks to the advent of improved in vivo detection and imaging methods. We discuss how these data contribute to an understanding of CB functions and highlight major questions that remain to be answered. Finally, we consider the interesting links that have emerged between CBs and alterations in nuclear structure apparent in a range of human pathologies, including cancer and inherited neurodegenerative diseases. We speculate on the relationship between CB function and molecular disease.

Activation of RNA metabolism-related genes in mouse but not human tissues deficient in SMN

Mutations of the survival of motor neuron gene (SMN1) are responsible for spinal muscular atrophies (SMA), a frequent recessive autosomal motor neuron disease. SMN is involved in various processes including RNA metabolism. However, the molecular pathway linking marked deficiency of SMN to SMA phenotype remains unclear. Homozygous deletion of murine Smn exon 7 directed to neurons or skeletal muscle causes severe motor axonal or myofiber degeneration, respectively. With the use of cDNA microarrays, expression profiles of 8,400 genes were analyzed in skeletal muscle and spinal cord of muscular and neuronal mutants, respectively, and compared with age-matched controls. A high proportion of genes (20 of 429, 5%) was involved in pre-mRNA splicing, ribosomal RNA processing, or RNA decay, and 18 of them were upregulated in mutant tissues. By analyzing other neuromuscular disorders, we showed that most of them (14 of 18) were specific to the SMN defect. Quantitative PCR analysis of these transcripts showed that gene activation was an early adaptive response to the lack but not reduced amount of full-length SMN in mouse mutant tissues. In human SMA tissues, activation of this program was not observed, which could be ascribed to the reduction but not the absence of full-length SMN.