Francisco Bustos

Neurodevelopmental disorders are lifelong debilitating conditions that affect cognition and originate during embryonic development. Being heterogeneous and with a variety of etiologies, most of these disorders have no targeted treatment or cures, due to our lack of knowledge on the underlying molecular mechanisms disrupted in their pathogenesis. An emerging epigenetic mechanism recently associated with neurodevelopmental disorders is ubiquitylation of histone H2B. This posttranslational modification controls gene expression during neurodevelopment, where histone H2B ubiquitylation levels are tightly regulated by multiple deubiquitylase protein complexes ensuring correct gene expression. Components of deubiquitylase complexes regulating histone H2B ubiquitylation are the protein scaffolds ATXN7L3 and ENY2, and the deubiquitylating enzymes USP22, USP27X, and USP51. Recent clinical studies have highlighted a potential role of H2B ubiquitylation in human neurodevelopment, including the identification of neurodevelopmental disorders associated with gene variants in the ATXN7L3 , USP27X and USP51 genes. Here, we summarize our knowledge of the functions of deubiquitylase complexes that regulate histone H2B ubiquitylation and their components in neurodevelopment, and describe ATXN7L3 , USP27X , and USP51 -associated disorders, proposing future directions on the required research on their fundamental biology that could lead to targeted therapies.

The E3 ubiquitin ligase RLIM (also known as RNF12) plays a central role in ubiquitin‐dependent signaling pathways that regulate mammalian development. Missense variants in the RLIM gene cause Tønne–Kalscheuer syndrome (TOKAS), an X‐linked recessive neurodevelopmental disorder affecting males, characterized by intellectual disability, developmental delay, and congenital abnormalities affecting the craniofacial, urogenital, ocular, and skeletal systems, as well as congenital diaphragmatic hernia. Additionally, RLIM duplications lead to a similar neurodevelopmental disorder, Chromosome Xq13 duplication syndrome. That both loss and gain of RLIM function produce overlapping neurodevelopmental phenotypes highlights the dosage sensitivity of this E3 ligase and points to its tightly regulated roles in human development. Despite an increasing number of reported cases, RLIM‐associated disorders remain underdiagnosed and poorly understood, with no cure or targeted treatments, largely due to limited insight into the cellular and molecular mechanisms underlying their pathogenesis. Here, we review current knowledge of RLIM biology across molecular, cellular, and genetic levels. We summarize the genetic basis, diagnostic criteria, and clinical spectrum of RLIM‐associated disorders and integrate this with current understanding of RLIM‐dependent ubiquitin signaling. By bringing together insights from biochemistry, cell signaling, and genetics, this review aimed to serve as a mechanistically informed reference for researchers and clinicians working on RLIM variants. We rank candidate RLIM substrates by the strength of the evidence linking them to disease. Finally, we discuss the key open questions that must be addressed to achieve a comprehensive cellular and molecular understanding of RLIM‐associated disorders and thus lay the foundation for future therapeutic interventions.

Neurodevelopmental disorders (NDDs) are associated with impairments in nervous system function but often remain poorly understood at the molecular level. ...

Neurodevelopmental disorders (NDDs) are associated with impairments in nervous system function but often remain poorly understood at the molecular level. ...

Protein ubiquitylation regulates key biological processes including transcription. This is exemplified by the E3 ubiquitin ligase RNF12/RLIM, which controls developmental gene expression by ubiquitylating the REX1 transcription factor and is mutated in an X-linked intellectual disability disorder. However, the precise mechanisms by which ubiquitylation drives specific transcriptional responses are not known. Here, we show that RNF12 is recruited to specific genomic locations via a consensus sequence motif, which enables co-localisation with REX1 substrate at gene promoters. Surprisingly, RNF12 chromatin recruitment is achieved via a non-catalytic basic region and comprises a previously unappreciated N-terminal autoinhibitory mechanism. Furthermore, RNF12 chromatin targeting is critical for REX1 ubiquitylation and downstream RNF12-dependent gene regulation. Our results demonstrate a key role for chromatin in regulation of the RNF12-REX1 axis and provide insight into mechanisms by which protein ubiquitylation enables programming of gene expression.

Neurodevelopmental disorders with intellectual disability (ND/ID) are a heterogeneous group of diseases driving lifelong deficits in cognition and behavior with no definitive cure. X-linked intellectual disability disorder 105 (XLID105, #300984; OMIM) is a ND/ID driven by hemizygous variants in theUSP27Xgene encoding a protein deubiquitylase with a role in cell proliferation and neural development. Currently, only four genetically diagnosed individuals from two unrelated families have been described with limited clinical data. Furthermore, the mechanisms underlying the disorder are unknown. Here, we report 10 new XLID105 individuals from nine families and determine the impact of gene variants on USP27X protein function. Using a combination of clinical genetics, bioinformatics, biochemical, and cell biology approaches, we determined that XLID105 variants alter USP27X protein biology via distinct mechanisms including changes in developmentally relevant protein–protein interactions and deubiquitylating activity. Our data better define the phenotypic spectrum of XLID105 and suggest that XLID105 is driven by USP27X functional disruption. Understanding the pathogenic mechanisms of XLID105 variants will provide molecular insight into USP27X biology and may create the potential for therapy development.

In female mice, the gene dosage from X chromosomes is adjusted by a process called X chromosome inactivation (XCI) that occurs in two steps. An imprinted form of XCI (iXCI) that silences the paternally inherited X chromosome (Xp) is initiated at the 2- to 4-cell stages. As extraembryonic cells including trophoblasts keep the Xp silenced, epiblast cells that give rise to the embryo proper reactivate the Xp and undergo a random form of XCI (rXCI) around implantation. Both iXCI and rXCI require the lncRNA Xist , which is expressed from the X to be inactivated. The X-linked E3 ubiquitin ligase Rlim (Rnf12) in conjunction with its target protein Rex1 (Zfp42), a critical repressor of Xist , have emerged as major regulators of iXCI. However, their roles in rXCI remain controversial. Investigating early mouse development, we show that the Rlim–Rex1 axis is active in pre-implantation embryos. Upon implantation Rex1 levels are downregulated independently of Rlim specifically in epiblast cells. These results provide a conceptual framework of how the functional dynamics between Rlim and Rex1 ensures regulation of iXCI but not rXCI in female mice.

The E3 ubiquitin ligase RNF12 plays essential roles during development, and the gene encoding it, RLIM , is mutated in the X-linked human developmental disorder Tonne-Kalscheuer syndrome (TOKAS). Substrates of RNF12 include transcriptional regulators such as the pluripotency-associated transcriptional repressor REX1. Using global quantitative proteomics in male mouse embryonic stem cells, we identified the deubiquitylase USP26 as a putative downstream target of RNF12 activity. RNF12 relieved REX1-mediated repression of Usp26 , leading to an increase in USP26 abundance and the formation of RNF12-USP26 complexes. Interaction with USP26 prevented RNF12 autoubiquitylation and proteasomal degradation, thereby establishing a transcriptional feed-forward loop that amplified RNF12-dependent derepression of REX1 targets. We showed that the RNF12-USP26 axis operated specifically in mouse testes and was required for the expression of gametogenesis genes and for germ cell differentiation in vitro. Furthermore, this RNF12-USP26 axis was disrupted by RLIM and USP26 variants found in TOKAS and infertility patients, respectively. This work reveals synergy within the ubiquitylation cycle that controls a key developmental process in gametogenesis and that is disrupted in human genetic disorders.