CDC174, a novel component of the exon junction complex whose mutation underlies a syndrome of hypotonia and psychomotor developmental delay

Detection of polymorphisms in six genes and their association analysis with litter size in sheep

Litter size in sheep is a complex trait controlled by micro-effective polygenes. APAF1, CLSTN2, CTH, PLCB1, PLCB4, and CHST11 are all involved in mammalian reproduction. However, the effects of these genes on litter size in sheep are still unclear. Therefore, in this study, we used Sequenom MassARRAY® SNP assay technology to type the single nucleotide polymorphisms (SNPs) loci of six genes in five sheep breeds. The results showed that most sheep breeds contain three genotypes at each locus. Then, we conducted population genetic analysis on the SNPs of six genes and found that the polymorphic information content in all sheep breeds ranged from 0 to 0.37, and most sheep breeds were in Hardy-Weinberg equilibrium (p > 0.05). In addition, association analysis in Small Tail Han sheep indicated that the rs399534524 locus in CLSTN2 was highly associated with first parity litter size, and litter size in ewes with CT genotype was higher than that in ewes with CC genotype or TT genotype. Furthermore, the rs407142552 locus in CTH was highly associated with second parity litter size in Small Tail Han sheep, and litter size in ewes with CT genotype was higher than that in ewes with TT genotype. Finally, we predicted the CTH and CLSTN2 protein interaction network and found that HTR1E, NOM1, CCDC174 and ALPK3 interact with CLSTN2 and have been reported as candidate genes related to litter size in sheep. These results suggest that they may be useful genetic markers for increasing litter size in sheep.

The Exon Junction Complex Factor RBM8A in Glial Fibrillary Acid Protein-Expressing Astrocytes Modulates Locomotion Behaviors

The role of RNA Binding Motif Protein 8a (RBM8A), an exon junction complex (EJC) component, in neurodevelopmental disorders has been increasingly studied for its crucial role in regulating multiple levels of gene expression. It regulates mRNA splicing, translation, and mRNA degradation and influences embryonic development. RBM8A protein is expressed in both neurons and astrocytes, but little is known about RBM8A's specific role in glial fibrillary acid protein (GFAP)-positive astrocytes. To address the role of RBM8A in astrocytes, we generated a conditional heterozygous knockout (KO) mouse line of Rbm8a in astrocytes using a GFAP-cre line. We confirmed a decreased expression of RBM8A in astrocytes of heterozygous conditional KO mice via RT-PCR and Sanger sequencing, as well as qRT-PCR, immunohistochemistry, and Western blot. Interestingly, these mice exhibit significantly increased movement and mobility, alongside sex-specific altered anxiety in the open field test (OFT) and elevated plus maze (OPM) tests. These tests, along with the rotarod test, suggest that these mice have normal motor coordination but hyperactive phenotypes. In addition, the haploinsufficiency of Rbm8a in astrocytes leads to a sex-specific change in astrocyte density in the dentate gyrus. This study further reveals the contribution of Rbm8a deletion to CNS pathology, generating more insights via the glial lens of an Rbm8a model of neurodevelopmental disorder.

Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites

Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (nuclear RNAi-defective 2), and CCDC174 (coiled-coil domain-containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP-specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use noncanonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice, and accurate pre-mRNA splicing.

Regulatory network and targeted interventions for CCDC family in tumor pathogenesis

CCDC (coiled-coil domain-containing) is a coiled helix domain that exists in natural proteins. There are about 180 CCDC family genes, encoding proteins that are involved in intercellular transmembrane signal transduction and genetic signal transcription, among other functions. Alterations in expression, mutation, and DNA promoter methylation of CCDC family genes have been shown to be associated with the pathogenesis of many diseases, including primary ciliary dyskinesia, infertility, and tumors. In recent studies, CCDC family genes have been found to be involved in regulation of growth, invasion, metastasis, chemosensitivity, and other biological behaviors of malignant tumor cells in various cancer types, including nasopharyngeal carcinoma, lung cancer, colorectal cancer, and thyroid cancer. In this review, we summarize the involvement of CCDC family genes in tumor pathogenesis and the relevant upstream and downstream molecular mechanisms. In addition, we summarize the potential of CCDC family genes as tumor therapy targets. The findings discussed here help us to further understand the role and the therapeutic applications of CCDC family genes in tumors.

The Physiological Roles of the Exon Junction Complex in Development and Diseases

The exon junction complex (EJC) becomes an increasingly important regulator of early gene expression in the central nervous system (CNS) and other tissues. The EJC is comprised of three core proteins: RNA-binding motif 8A (RBM8A), Mago homolog (MAGOH), eukaryotic initiation factor 4A3 (EIF4A3), and a peripheral EJC factor, metastatic lymph node 51 (MLN51), together with various auxiliary factors. The EJC is assembled specifically at exon-exon junctions on mRNAs, hence the name of the complex. The EJC regulates multiple levels of gene expression, from splicing to translation and mRNA degradation. The functional roles of the EJC have been established as crucial to the normal progress of embryonic and neurological development, with wide ranging implications on molecular, cellular, and organism level function. Dysfunction of the EJC has been implicated in multiple developmental and neurological diseases. In this review, we discuss recent progress on the EJC’s physiological roles.

Coiled-Coil Domain-Containing (CCDC) Proteins: Functional Roles in General and Male Reproductive Physiology

The coiled-coil domain-containing (CCDC) proteins have been implicated in a variety of physiological and pathological processes. Their functional roles vary from their interaction with molecular components of signaling pathways to determining the physiological functions at the cellular and organ level. Thus, they govern important functions like gametogenesis, embryonic development, hematopoiesis, angiogenesis, and ciliary development. Further, they are implicated in the pathogenesis of a large number of cancers. Polymorphisms in CCDC genes are associated with the risk of lifetime diseases. Because of their role in many biological processes, they have been extensively studied. This review concisely presents the functional role of CCDC proteins that have been studied in the last decade. Studies on CCDC proteins continue to be an active area of investigation because of their indispensable functions. However, there is ample opportunity to further understand the involvement of CCDC proteins in many more functions. It is anticipated that basing on the available literature, the functional role of CCDC proteins will be explored much further.

Orchestrating the expression levels of sperm mRNAs reveals CCDC174 as an important determinant of semen quality and bull fertility

Bulls with acceptable semen quality vary in actual field fertility and this can be elucidated by studying the expression levels of mRNAs in the sperm. The present study aimed at assessing the variations in the sperm gene expression levels of PRM1, CCDC174, RPL36A, TMCO2, SWI5 and OIT3 in bulls differing in fertility status. Frozen semen samples from Holstein-Friesian bulls were classified into high-fertile (n = 8, average field conception rate = 46.1 ± 0.51, p < 0.001) and sub-fertile (n = 7, average field conception rate = 39.4 ± 0.69) groups. In the post-thaw semen samples, sperm kinematics, structural and functional membrane integrities, mitochondrial membrane potential and chromatin distribution were analyzed. The sperm total RNA was subjected to gene expression studies by Real-Time PCR. Multivariate regression analysis was performed using gene expression levels and conception rates. The sperm functional attributes did not differ significantly between the groups. The relative mRNA levels (fold change) of CCDC174 (6.20), RPL36A (4.66), SWI5 (1.86) and OIT3 (1.53) were higher in high-fertile bulls. Further, the expression level of the CCDC174 gene was significantly (p = 0.02) up-regulated in high-fertile bulls. The fertility prediction multivariate model with genes, CCDC174, RPL36A, TMCO2 and OIT3 had the maximum coefficient of determination (R² = 0.68) with the field conception rate. This model had 93.3% bull fertility prediction accuracy with 100% sensitivity and 87.5% specificity. The study suggests that the expression level of CCDC174 can be used as a potential marker for assessing bull fertility.

Corpus Callosum Agenesis: An Insight into the Etiology and Spectrum of Symptoms

Brain hemispheres are connected by commissural structures, which consist of white matter fiber tracts that spread excitatory stimuli to various regions of the cortex. This allows an interaction between the two cerebral halves. The largest commissure is the corpus callosum (CC) which is located inferior to the longitudinal fissure, serving as its lower border. Sometimes this structure is not completely developed, which results in the condition known as agenesis of the corpus callosum (ACC). The aim of this paper was to review the latest discoveries related to the genetic and metabolic background of ACC, including the genotype/phenotype correlations as well as the clinical and imaging symptomatology. Due to various factors, including genetic defects and metabolic diseases, the development of CC may be impaired in many ways, which results in complete or partial ACC. This creates several clinical implications, depending on the specificity of the malformation and other defects in patients. Epilepsy, motor impairment and intellectual disability are the most prevalent. However, an asymptomatic course of the disease is even more common. ACC presents with characteristic images on ultrasound and magnetic resonance imaging (MRI).

Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep

The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of mutations, mainly in the family of the transforming growth factor β (TGF-β) genes. To explore genetic mechanisms underlying the variation in litter size, we conducted a genome-wide association study in two groups of Pelibuey sheep (multiparous sheep with two lambs per birth vs. uniparous sheep with a single lamb at birth) using the OvineSNP50 BeadChip. We identified a total of 57 putative SNPs markers (p < 3.0 × 10^-3, Bonferroni correction). The candidate genes that may be associated with litter size in Pelibuey sheep are CLSTN2, MTMR2, DLG1, CGA, ABCG5, TRPM6, and HTR1E. Genomic regions were also identified that contain three quantitative trait loci (QTLs) for aseasonal reproduction (ASREP), milk yield (MY), and body weight (BW). These results allowed us to identify SNPs associated with genes that could be involved in the reproductive process related to prolificacy.

The exon junction complex senses energetic stress and regulates contractility and cell architecture in cardiac myocytes

The exon junction complex (EJC) is the main mechanism by which cells select specific mRNAs for translation into protein. We hypothesized that the EJC is involved in the regulation of gene expression during the stress response in cardiac myocytes, with implications for the failing heart. In cultured rat neonatal myocytes, we examined the cellular distribution of two EJC components eukaryotic translation initiation factor 4A isoform 3 (eIF4A3) and mago nashi homologue (Mago) in response to metabolic stress. There was significant relocalization of eIF4A3 and Mago from the nucleus to cytoplasm following 18 h of hypoxia. Treating myocytes with 50 mM NaN₃ for 4 h to mimic the metabolic stress induced by hypoxia also resulted in significant relocalization of eIF4A3 and Mago to the cytoplasm. To examine whether the effects of metabolic stress on the EJC proteins were dependent on the metabolic sensor AMP kinase (AMPK), we treated myocytes with 1 μM dorsomorphin (DM) in combination with NaN₃ DM augmented the translocation of Mago and eIF4A3 from the nucleus to the cytoplasm. Knockdown of eIF4A3 resulted in cessation of cell contractility 96 h post-treatment and a significant reduction in the number of intact sarcomeres. Cell area was significantly reduced by both hypoxia and eIF4A3 knockdown, whilst eIF4A3 knockdown also significantly reduced nuclear size. The reduction in nuclear size is unlikely to be related to apoptosis as it was reversed in combination with hypoxia. These data suggest for the first time that eIF4A3 and potentially other EJC members play an important role in the myocyte stress response, cell contractility and morphology.

Neurogenesis: Regulation by Alternative Splicing and Related Posttranscriptional Processes

The complexity of the mammalian brain requires highly specialized protein function and diversity. As neurons differentiate and the neuronal circuitry is established, several mRNAs undergo alternative splicing and other posttranscriptional changes that expand the variety of protein isoforms produced. Recent advances are beginning to shed light on the molecular mechanisms that regulate isoform switching during neurogenesis and the role played by specific RNA binding proteins in this process. Neurogenesis and neuronal wiring were recently shown to also be regulated by RNA degradation through nonsense-mediated decay. An additional layer of regulatory complexity in these biological processes is the interplay between alternative splicing and long noncoding RNAs. Dysregulation of posttranscriptional regulation results in defective neuronal differentiation and/or synaptic connections that lead to neurodevelopmental and psychiatric disorders.