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Mutations in human nonsense-mediated mRNA decay (NMD) factors are enriched in neurodevelopmental disorders. We show that deletion of key NMD factor Upf2 in mouse embryonic neural progenitor cells causes perinatal microcephaly but deletion in immature neurons does not, indicating NMD's critical roles in progenitors. Upf2 knockout (KO) prolongs the cell cycle of radial glia progenitor cells, promotes their transition into intermediate progenitors, and leads to reduced upper-layer neurons. CRISPRi screening identified Trp53 knockdown rescuing Upf2KO progenitors without globally reversing NMD inhibition, implying marginal contributions of most NMD targets to the cell cycle defect. Integrated functional genomics shows that NMD degrades selective TRP53 downstream targets, including Cdkn1a, which, without NMD suppression, slow the cell cycle. Trp53KO restores the progenitor cell pool and rescues the microcephaly of Upf2KO mice. Therefore, one physiological role of NMD in the developing brain is to degrade selective TRP53 targets to control progenitor cell cycle and brain size.

The UPF3B-dependent branch of the nonsense-mediated RNA decay (NMD) pathway is critical for human cognition. Here, we examined the role of UPF3B in the olfactory system. Single-cell RNA-sequencing (scRNA-seq) analysis demonstrated considerable heterogeneity of olfactory sensory neuron (OSN) cell populations in wild-type (WT) mice, and revealed that UPF3B loss influences specific subsets of these cell populations. UPF3B also regulates the expression of a large cadre of antimicrobial genes in OSNs, and promotes the selection of specific olfactory receptor (Olfr) genes for expression in mature OSNs (mOSNs). RNA-seq and Ribotag analyses identified classes of mRNAs expressed and translated at different levels in WT and Upf3b-null mOSNs. Integrating multiple computational approaches, UPF3B-dependent NMD target transcripts that are candidates to mediate the functions of NMD in mOSNs were identified in vivo. Together, our data provides a valuable resource for the olfactory field and insights into the roles of NMD in vivo.

The UPF3B-dependent branch of the nonsense-mediated RNA decay (NMD) pathway is critical for human cognition. Here, we examined the role of UPF3B in the olfactory system. Single-cell RNA-sequencing (scRNA-seq) analysis demonstrated considerable heterogeneity of olfactory sensory neuron (OSN) cell populations in wild-type (WT) mice, and revealed that UPF3B loss influences specific subsets of these cell populations. UPF3B also regulates the expression of a large cadre of antimicrobial genes in OSNs, and promotes the selection of specific olfactory receptor (Olfr) genes for expression in mature OSNs (mOSNs). RNA-seq and Ribotag analyses identified classes of mRNAs expressed and translated at different levels in WT and Upf3b-null mOSNs. Integrating multiple computational approaches, UPF3B-dependent NMD target transcripts that are candidates to mediate the functions of NMD in mOSNs were identified in vivo. Together, our data provides a valuable resource for the olfactory field and insights into the roles of NMD in vivo.

The Nonsense Mediated Decay (NMD) pathway was originally discovered for its role in degrading mRNA transcripts bearing a premature termination codon (PTC). Recently, it has been shown that the NMD pathway also degrades a subset of normal transcripts. This raises the possibility that NMD regulates normal biological events, including development. Indeed, increasing evidence suggests that NMD regulates various developmental events, including governing early cell fate in the specification of the three germ layers: endoderm, mesoderm, and ectoderm, from the pluripotent stem cell. In particular, NMD promotes formation of mesoderm while inhibiting the formation of endoderm. As support of NMD holding developmental importance, to date 11 patients bearing mutations in one NMD factor, UPF3B, have been reported, all of which exhibit neurodevelopmental disorders including intellectual disability, autism spectrum disorder, and schizophrenia. In addition, reports of individuals with copy number variants in NMD factors UPF2, UPF3A, RBM8A, EIF4A3, RNPS1, and SMG6, have been shown to be associated with neurodevelopmental disorders. This evidence suggests a role for NMD in governing neurodevelopment. Using both in vitro and in silico methods, I have elected to identify the role of one such NMD factor, UPF3B in early cell fate. Specifically, focusing on its regulation of the neural induction process from the pluripotent stem cell state. As well as providing speculation on a potential evolutionary significance of the NMD pathway and its implications in neurodevelopment in the transition from early hominid to modern human.

The Nonsense Mediated Decay (NMD) pathway was originally discovered for its role in degrading mRNA transcripts bearing a premature termination codon (PTC). Recently, it has been shown that the NMD pathway also degrades a subset of normal transcripts. This raises the possibility that NMD regulates normal biological events, including development. Indeed, increasing evidence suggests that NMD regulates various developmental events, including governing early cell fate in the specification of the three germ layers: endoderm, mesoderm, and ectoderm, from the pluripotent stem cell. In particular, NMD promotes formation of mesoderm while inhibiting the formation of endoderm. As support of NMD holding developmental importance, to date 11 patients bearing mutations in one NMD factor, UPF3B, have been reported, all of which exhibit neurodevelopmental disorders including intellectual disability, autism spectrum disorder, and schizophrenia. In addition, reports of individuals with copy number variants in NMD factors UPF2, UPF3A, RBM8A, EIF4A3, RNPS1, and SMG6, have been shown to be associated with neurodevelopmental disorders. This evidence suggests a role for NMD in governing neurodevelopment. Using both in vitro and in silico methods, I have elected to identify the role of one such NMD factor, UPF3B in early cell fate. Specifically, focusing on its regulation of the neural induction process from the pluripotent stem cell state. As well as providing speculation on a potential evolutionary significance of the NMD pathway and its implications in neurodevelopment in the transition from early hominid to modern human.

The Nonsense-Mediated RNA Decay (NMD) pathway prevents the accumulation of potentially toxic proteins in the cell by targeting aberrant RNA transcripts with premature termination codons (PTCs) for decay. While originally for its RNA surveillance capacity, NMD was more recently discovered to target not only aberrant RNA transcripts but also normal, wild-type transcripts, regulating 5-20% of the normal transcriptome. This, in turn, has led to the hypothesis that NMD, by fine-tuning gene expression, functions in orchestrating biological processes such as development. Recent studies have identified mutations in the NMD factor gene, UPF3B, as the cause of syndromic and non-syndromic intellectual disability in human patients; these patients also frequently suffer from psychiatric and neurodevelopmental disorders, including schizophrenia, autism, and attention-deficit disorder. The role of NMD in neurodevelopment was further supported by work from our laboratory identifying the function of miR-128 mediated repression of NMD in neural differentiation.For these reasons, I elected to study the role of the NMD factor UPF3B and microRNA regulation of NMD in neurodevelopment. In summary, I have identified a microRNA regulatory circuit in which the neurally enriched microRNAs, miR-132 and miR-9/-124/-128, repress the UPF2 and UPF3B branches of NMD, respectively. To examine the role of the UPF3B branch of NMD in neurodevelopment, I derived iPSCs and NPCs from patients with UPF3B-null mutations. Using these UPF3B-deficient iPSCs and NPCs, I obtained substantial evidence that UPF3B promotes pluripotency, while depletion or absence of UPF3B promotes differentiation.

The Nonsense-Mediated RNA Decay (NMD) pathway prevents the accumulation of potentially toxic proteins in the cell by targeting aberrant RNA transcripts with premature termination codons (PTCs) for decay. While originally for its RNA surveillance capacity, NMD was more recently discovered to target not only aberrant RNA transcripts but also normal, wild-type transcripts, regulating 5-20% of the normal transcriptome. This, in turn, has led to the hypothesis that NMD, by fine-tuning gene expression, functions in orchestrating biological processes such as development. Recent studies have identified mutations in the NMD factor gene, UPF3B, as the cause of syndromic and non-syndromic intellectual disability in human patients; these patients also frequently suffer from psychiatric and neurodevelopmental disorders, including schizophrenia, autism, and attention-deficit disorder. The role of NMD in neurodevelopment was further supported by work from our laboratory identifying the function of miR-128 mediated repression of NMD in neural differentiation.For these reasons, I elected to study the role of the NMD factor UPF3B and microRNA regulation of NMD in neurodevelopment. In summary, I have identified a microRNA regulatory circuit in which the neurally enriched microRNAs, miR-132 and miR-9/-124/-128, repress the UPF2 and UPF3B branches of NMD, respectively. To examine the role of the UPF3B branch of NMD in neurodevelopment, I derived iPSCs and NPCs from patients with UPF3B-null mutations. Using these UPF3B-deficient iPSCs and NPCs, I obtained substantial evidence that UPF3B promotes pluripotency, while depletion or absence of UPF3B promotes differentiation.