Biology subjects

Iminitoff, M.

Publications and source records attributed to Iminitoff, M..

8 recordsLinked to original sources

bioRxiv2026

Magel2 deficiency drives microglial synaptic engulfment and alters neuron-microglia interactions in Prader-Willi syndrome

Prader-Willi syndrome (PWS) is a neurodevelopmental disorder characterized by hypothalamic dysfunction, developmental delay, hyperphagia, and cognitive impairment, yet the cellular mechanisms underlying circuit abnormalities remain unclear. Here, we show that loss of the imprinted gene Magel2 remodels microglial state and function in a mouse model of PWS. Three-dimensional morphometric analysis of hypothalamic microglia revealed reduced structural complexity and contracted territorial domains, emerging early in development and largely independent of obesity. Single-nucleus RNA sequencing of hypothalamic brain tissue identified extensive transcriptional reprogramming involving immune signaling, cellular communication, ribosome function, synaptic organization, and protein translation, with stronger effects in females. Magel2 deficiency also increased microglia-neuron contacts and synaptic engulfment, accompanied by reduced synaptic marker density, suggesting aberrant refinement of hypothalamic circuits. Analyses of human post-mortem hypothalamic tissue from individuals with PWS confirmed microglial structural alterations and increased complement engagement. Ligand-receptor inference further revealed reorganization of microglia-centered communication networks, including altered adhesion, trophic, and immune signaling consistent with enhanced phagocytic states. Together, these findings identify microglial remodeling and increased synaptic engagement as central features of Magel2 deficiency, implicate microglia in hypothalamic circuit dysfunction in PWS, and highlight excessive synaptic pruning as a novel dysfunctional mechanism of PWS.

neuroscience↗

bioRxiv2026

Regulation of Human Erythroferrone Expression

Erythroferrone (ERFE) is an erythroblast-secreted hormone that suppresses hepatic hepcidin expression to increase iron availability for erythropoiesis, ensuring recovery from anaemia. ERFE excess drives iron overload in disorders of ineffective erythropoiesis. Despite its pivotal role in systemic iron homeostasis and diseases of erythropoiesis, ERFEs molecular regulation has remained undefined. Here, we applied a genomic approach to characterise the molecular mechanisms governing ERFE expression. Using the HUDEP-2 human erythroid progenitor model, integrative ATAC-seq, CUT&RUN and micro capture-C analysis we identified a stage-specific accessible chromatin region within the ERFE 3 UTR that interacts with the promotor. We also identified enhancer-associated chromatin marks including H3K4me1 and H3K27ac in this region, and demonstrate that this cis-regulatory element is bound by key erythroid transcription factors KLF1, GATA1, TAL1 and STAT5. Functional dissection using CRISPR-Cas9-mediated deletion of the central 3 UTR enhancer element led to marked reduction in ERFE mRNA expression, and we show a corresponding reduction in nascent mRNA, confirming a key role for this region in transcriptional regulation. We define the transcriptional regulatory mechanism by which maturing human erythroblasts activate ERFE, the endocrine signal that coordinates erythropoietic demand with systemic iron mobilisation.

molecular biology↗

bioRxiv2026

SMCHD1 is a novel target for gene-activation therapy to treat Prader-Willi Syndrome

Prader-Willi Syndrome (PWS) is a neurodevelopmental disorder caused by lack of gene expression from the active paternal allele at an imprinted gene cluster on chromosome 15. Current treatments have limited efficacy as they target individual symptoms rather than the underlying cause of disease. All patients preserve a normal, yet epigenetically-silenced, copy of the PWS cluster genes; activation of this imprinted copy to restore necessary gene expression is an appealing option for tackling the root of the disorder. Here we have addressed the potential to activate these silent maternal genes by targeting the epigenetic regulator Structural Maintenance of Chromosomes Hinge domain containing 1 (SMCHD1). First, we expanded the role of SMCHD1 in repressing the PWS cluster from mice to humans, a critical step if SMCHD1 is to be a drug target. Second, we discovered that SMCHD1 represses the entire PWS locus in neural lineages, extending its previously known role at only half of the PWS genes. We show that deleting Smchd1 after early development in vivo is effective at causing PWS gene-activation in disease-relevant mouse tissues including hypothalamus, and that this has beneficial effects on phenotypes observed in a PWS mouse model. Despite SMCHD1 having a role in gene silencing elsewhere in the genome, our data suggest that targeting SMCHD1 after early development is remarkably safe. Taken together, these data propose SMCHD1 as a novel target for gene-activation therapy for PWS.

genetics↗

bioRxiv2026

DNA binding by ATPase-adjacent domains stimulates SMCHD1 ATPase activity

SMCHD1 is an epigenetic regulator in which heterozygous variants are reported in facioscapulohumeral muscular dystrophy (FSHD), as well as Bosma arhinia microphthalmia syndrome (BAMS). While we have previously shown that SMCHD1 is able to interact with nucleic acids via its hinge domain, we have now identified a second DNA-binding site that is located C-terminal to the ATPase domain and formed by two domains: the Bromo-adjacent homology (BAH) and immunoglobulin-like 1 (IGL-1) domains. Here, we report their mode of DNA-interaction and we present the first high-resolution structure of the wild-type human SMCHD1 ATPase using site-directed mutagenesis and structural analysis via cryo-EM. We also reveal that DNA-binding at the BAH-IGL-1 domains stimulates the ATPase activity of full-length SMCHD1 in vitro, and demonstrate in a mouse model that ATP hydrolysis is essential for SMCHD1 function in vivo. Together, these findings establish bidentate DNA binding and DNA-stimulated ATP hydrolysis as central features of SMCHD1 function, providing new mechanistic insight into how SMCHD1 regulates gene silencing. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/704097v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@12b2fd5org.highwire.dtl.DTLVardef@5152c7org.highwire.dtl.DTLVardef@111c487org.highwire.dtl.DTLVardef@17d8d0d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

A method for stabilising the XX karyotype in female mESC cultures

Female mouse embryonic stem cells (mESCs) present differently to male mESCs in several fundamental ways, however complications with their in vitro culture have resulted in an underrepresentation of female mESCs in the literature. Recent studies show that the second X chromosome in female, and more specifically the transcriptional activity from both of these chromosomes due to absent X chromosome inactivation, sets female mESCs apart from males. To avoid this undesirable state, female mESCs in culture preferentially adopt an XO karyotype, with this adaption leading to loss of their unique properties in favour of a state near indistinguishable from male. If female pluripotency is to be studied effectively in this system, it is critical that high quality cultures of XX mESCs are available. Here we report a method for better maintaining XX female mESCs in culture, which also stabilises the male karyotype, and makes study of female specific pluripotency more feasible.

cell biology↗

bioRxiv2020

The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read tools

Application of Oxford Nanopore Technologies long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such analysis can be challenging due to small library sizes and high sequence error, which decreases quantification accuracy and reduces power for statistical testing. Here, we report the analysis of two nanopore sequencing RNA-seq datasets with the goal of obtaining gene-level and isoform-level differential expression information. A dataset of synthetic, spliced, spike-in RNAs ("sequins") as well as a mouse neural stem cell dataset from samples with a null mutation of the epigenetic regulator Smchd1 were analysed using a mix of long-read specific tools for preprocessing together with established short-read RNA-seq methods. We used limma-voom to perform differential gene expression analysis, and the novel FLAMES pipeline to perform isoform identification and quantification, followed by DRIMSeq and limma-diffSplice (with stageR) to perform differential transcript usage analysis. We compared results from the sequins dataset to the ground truth, and results of the mouse dataset to a previous short-read study on equivalent samples. Overall, our work shows that transcriptomic analysis of long-read nanopore data using short-read software and methods that are already in wide use can yield meaningful results.

bioinformatics↗

bioRxiv2019

Xmas ESC: A new female embryonic stem cell system that reveals the BAF complex as a key regulator of the establishment of X chromosome inactivation

Although female pluripotency significantly differs to male, complications with in vitro culture of female embryonic stem cells (ESC) have severely limited the use and study of these cells. We report a replenishable female ESC system, Xmas, that has enabled us to optimise a protocol for preserving the XX karyotype. Our protocol also improves male ESC fitness. We utilised our Xmas ESC system to screen for regulators of the female-specific process of X chromosome inactivation, revealing chromatin remodellers Smarcc1 and Smarca4 as key regulators of establishment of X inactivation. The remodellers create a nucleosome depleted region at gene promotors on the inactive X during exit from pluripotency, without which gene silencing fails. Our female ESC system provides a tractable model for XX ESC culture that will expedite study of female pluripotency and has enabled us to discover new features of the female-specific process of X inactivation.

cell biology↗

bioRxiv2018

Long-range chromatin interactions on the inactive X and at Hox clusters are regulated by the non-canonical SMC protein Smchd1.

The regulation of higher order chromatin structure is complex and dynamic; however we do not yet understand the full suite of mechanisms governing architecture. Here we reveal the non-canonical SMC protein Smchd1 as a novel regulator of long-range chromatin interactions, and add it to the canon of epigenetic proteins required for Hox gene regulation. The effect of losing Smchd1-dependent chromatin interactions has varying outcomes dependent on chromatin context. At autosomal targets transcriptionally sensitive to Smchd1 deletion, we find increased short-range interactions and ectopic enhancer activation. By contrast, the inactive X chromosome is transcriptionally refractive to Smchd1 ablation, despite chromosome-wide increases in short-range interactions. There we observe spreading of H3K27me3 domains into regions not normally decorated by this mark. Together these data suggest Smchd1 has the capacity to insulate the chromatin, thereby limiting access to other chromatin modifying proteins.

molecular biology↗