Biology subjects

Selfridge, J.

Publications and source records attributed to Selfridge, J..

7 recordsLinked to original sources

bioRxiv2026

FMR1 gene therapy restores activity-driven inhibition and prevents audiogenic seizures in Fmr1-/y mice

Fragile X syndrome (FXS) is a neurodevelopmental disorder associated with auditory hypersensitivity, circuit hyperexcitability, and seizures. Whether re-expression of the FMR1 gene and encoded Fragile X Messenger Ribonucleoprotein (FMRP) can restore sensory circuit dysfunction remains unclear. Here, we show that a viral AAV-FMR1 vector rescues audiogenic seizures in the Fmr1-/y mouse model after both neonatal and adult delivery, indicating that auditory circuit dysfunction remains reversible. Local re-expression in the inferior colliculus (IC) is sufficient to reduce seizure susceptibility, identifying this region as a key site of FMRP-dependent circuit regulation. In the IC, Translating Ribosome Affinity Purification and RNA-seq (TRAP-seq) profiling reveals impaired induction of sound-evoked translation programs in Fmr1-/y neurons, including those regulated by transcription factor Npas4. AAV-FMR1 restores a WT-like molecular response and normalizes unbalanced sound-evoked activation of VGLUT2+ excitatory neurons over VGAT+ inhibitory neurons in Fmr1-/y IC. Together, these findings indicate altered translation of Npas4 in response to sound impairs recruitment of inhibition in the Fmr1-/y IC, and this can be reversed with AAV-FMR1 administration. Moreover, the rescue of seizures after adult administration of AAV-FMR1 supports a gene therapy approach for FXS. HighlightsO_LITRAP-seq reveals impaired activity-driven translation in Fmr1-/y inferior colliculus (IC) C_LIO_LIDeficient Npas4 induction reduces evoked inhibition in Fmr1-/y IC C_LIO_LIAAV9-FMR1 gene therapy normalizes translation and excitatory/inhibitory balance in Fmr1-/y IC C_LIO_LIAAV9-FMR1 gene therapy prevents audiogenic seizures in Fmr1-/y mice when administered neonatally or in adulthood C_LI

neuroscience↗

bioRxiv2025

Pervasive binding of the stem cell transcription factor SALL4 shapes the chromatin landscape

Mechanistic understanding of how gene activity is regulated has focussed on the roles of transcription factors at promoters and enhancers, whereas mechanisms capable of globally fine-tuning gene expression through dispersed binding across large genomic regions have received less attention. Here we provide evidence that the essential stem cell transcription factor SALL4 modulates gene expression according to DNA base composition by reading the frequency of its AT-rich target motifs. Using an acute depletion strategy, we establish that SALL4-repressed genes localise to AT-rich genomic domains with high levels of dispersed SALL4 occupancy. While SALL4 is localised within peaks and distributed broadly across the genome, explainable machine learning revealed that its occupancy across the gene body is a strong predictor of transcriptional output. We observed rapid increases in chromatin accessibility and histone acetylation independent of transcriptional activity, suggesting that SALL4 primarily acts upon chromatin, while transcriptional changes are secondary. Accordingly, preventing SALL4 from recruiting the histone deacetylase and nucleosome remodelling corepressor NuRD mimicked a Sall4-null phenotype in stem cells and animal models. Our findings reveal that SALL4s interpretation of DNA sequence optimises the global epigenome and transcriptome, a process integral to maintaining the stem cell gene expression programme.

genomics↗

bioRxiv2025

Brain Mecp2 Gene Dosage and Gene Therapy Shape Multi-Omic Signatures and Biomarkers in Rett Syndrome

Rett syndrome (RTT) is a neurodevelopmental disorder caused by MECP2 mutations. Like other genetic neurodevelopmental disorders, it lacks protein biomarkers to evaluate disease and therapeutic outcomes. We present a strategy to define putative biomarkers of MeCP2 dysfunction in brain with potential to delineate mechanisms and monitor therapeutic interventions. This strategy relies on a library of proteins responsive to Mecp2 gene dosage and correlated with molecular and clinical outcomes after AAV9-mediated MECP2 gene therapy in Mecp2-KO mice. Gene rescue restored MeCP2 in brain, improved clinical phenotypes, and reverted transcriptome and proteome abnormalities. We identified 327 shared proteins among 1852 cortical and hippocampal proteins responsive to Mecp2/MECP2. Of these, 119 also displayed Mecp2/MECP2-dependent transcript changes. Both the Mecp2-responsive proteome and transcript-protein pairs were enriched in synaptic and metabolic pathways, including central carbon and NAD+ metabolism. We used this therapy-responsive protein library to guide selection of candidate cerebrospinal fluid (CSF) biomarkers in RTT. CSF composition from neurotypical and RTT groups was analyzed using ultrasensitive nucleic acid-based multiplexed ELISA. Twenty-eight proteins were altered in RTT, nine overlapping with Mecp2 dosage- and therapy-sensitive proteins. Multivariate regression linked several candidates to Mecp2/MeCP2 abundance and phenotypic improvement in mice. This paradigm provides a rigorous molecular systems-level framework integrating genetics, preclinical gene therapy, and clinical metrics to define robust cross-species putative biomarkers and possible mechanisms in RTT, with potential applicability to other neurodevelopmental disorders. One Sentence SummaryGenetic Identification of cross-species biomarkers and mechanisms in Rett Syndrome

neuroscience↗

bioRxiv2020

Neuronal non-CG methylation is an essential target for MeCP2 function

SUMMARYDNA methylation is implicated in neuronal biology via the protein MeCP2, mutation of which causes Rett syndrome. MeCP2 recruits the NCOR1/2 corepressor complexes to methylated cytosine in the CG dinucleotide, but also to non-CG methylation, which is abundant specifically in neuronal genomes. To test the biological significance of its dual binding specificity, we replaced the MeCP2 DNA binding domain with an orthologous domain whose specificity is restricted to mCG motifs. Knock-in mice expressing the domain-swap protein displayed severe Rett syndrome-like phenotypes, demonstrating that interaction with sites of non-CG methylation, specifically the mCAC trinucleotide, is critical for normal brain function. The results support the notion that the delayed onset of Rett syndrome is due to the late accumulation of both mCAC and its reader MeCP2. Intriguingly, genes dysregulated in both Mecp2-null and domain-swap mice are implicated in other neurological disorders, potentially highlighting targets of particular relevance to the Rett syndrome phenotype.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2020

SALL4 controls cell fate in response to DNA base composition

SO_SCPLOWUMMARYC_SCPLOWMammalian genomes contain long domains with distinct average compositions of A/T versus G/C base pairs. In a screen for proteins that might interpret base composition by binding to AT-rich motifs, we identified the stem cell factor SALL4 which contains multiple zinc-fingers. Mutation of the domain responsible for AT binding drastically reduced SALL4 genome occupancy and prematurely up-regulated genes in proportion to their AT content. Inactivation of this single AT-binding zinc-finger cluster mimicked defects seen in Sall4-null cells, including precocious differentiation of embryonic stem cells and embryonic lethality in mice. In contrast, deletion of two other zinc-finger clusters was phenotypically neutral. Our data indicate that loss of pluripotency is triggered by down-regulation of SALL4, leading to de-repression of a set of AT-rich genes that promotes neuronal differentiation. We conclude that base composition is not merely a passive by-product of genome evolution, but constitutes a signal that aids control of cell fate. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/179481v2_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1ec4eb9org.highwire.dtl.DTLVardef@1246a36org.highwire.dtl.DTLVardef@1b9134dorg.highwire.dtl.DTLVardef@1a24904_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2018

A mutation-led search for novel functional domains in MeCP2

Most missense mutations causing Rett syndrome affect domains of MeCP2 that have been shown to either bind methylated DNA or interact with a transcriptional co-repressor complex. Several mutations, however, including the C-terminal truncations that account for ~10% of cases, fall outside these characterised domains. We studied the molecular consequences of four of these \"non-canonical\" mutations in cultured neurons and mice to see if they reveal additional essential domains without affecting known properties of MeCP2. The results show that the mutations partially or strongly deplete the protein and also in some cases interfere with co-repressor recruitment. These mutations therefore impact the activity of known functional domains and do not invoke new molecular causes of Rett syndrome. The finding that a stable C-terminal truncation does not compromise MeCP2 function raises the possibility that small molecules which stabilise these mutant proteins may be of therapeutic value.

molecular biology↗

bioRxiv2016

Domains of methylated CAC and CG target MeCP2 to tune transcription in the brain

Mutations in the gene encoding the methyl-CG binding protein MeCP2 cause neurological disorders including Rett syndrome. The di-nucleotide methyl-CG (mCG) is the canonical MeCP2 DNA recognition sequence, but additional targets including non-methylated sequences have been reported. Here we use brain-specific depletion of DNA methyltransferase to show that DNA methylation is the primary determinant of MeCP2 binding in mouse brain. In vitro and in vivo analyses reveal that MeCP2 binding to non-CG methylated sites in brain is largely confined to the tri-nucleotide sequence mCAC. Structural modeling suggests that mCG and mCAC may be interchangeable as minimal structural perturbation of MeCP2 accompanies binding. MeCP2 binding to chromosomal DNA in mouse brain is proportional to mCG + mCAC density and defines domains within which transcription is sensitive to MeCP2 occupancy. The results suggest that MeCP2 interprets patterns of mCAC and mCG in the brain to negatively modulate transcription of genes critical for neuronal function.

molecular biology↗