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Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories

ABSTRACT: Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories

PROVIDER: PRJNA994099 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25248900_1.fastq.gz	Fastqsanger.gz
	SRR25248900_2.fastq.gz	Fastqsanger.gz
	SRR25248901_1.fastq.gz	Fastqsanger.gz
	SRR25248901_2.fastq.gz	Fastqsanger.gz
	SRR25248902_1.fastq.gz	Fastqsanger.gz

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Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories [ChIP-seq]

Project description:Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories [ChIP-seq]

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Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories (scRNA-Seq)

Project description:Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories (scRNA-Seq)

| PRJNA1001298 | ENA

Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories

Project description:To examine the transcriptomic alteration by SETD1A deficiency, combining CRISPR/CAS9 genome editing and 3-Dimentional Cell Culture technology, we generated organoid models of the developing human cerebral cortex derived from isogenic human induced pluripotent stem cells (hiPSCs) modified to carry a SETD1A LoF schizophrenia risk mutation. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and mutant cortical neurons at DIV70.

2025-04-17 | GSE237165 | GEO

Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories [ChIP-seq]

Project description:To examine the genomic alteration by SETD1A deficiency, combining CRISPR/CAS9 genome editing and 3-Dimentional Cell Culture technology, we generated organoid models of the developing human cerebral cortex derived from isogenic human induced pluripotent stem cells (hiPSCs) modified to carry a SETD1A LoF schizophrenia risk mutation. We then performed genomic profiling analysis using data obtained from CUT&Tag of WT and mutant cortical neurons at DIV70.

2025-04-17 | GSE237297 | GEO

Neurodevelopmental Genomics: Trajectories of Complex Phenotypes

Project description:Neurodevelopmental Genomics: Trajectories of Complex Phenotypes

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Developmental disruption to the cortical transcriptome and synaptosome in a model of SETD1A loss-of-function

Project description:Large-scale genomic studies of schizophrenia implicate genes involved in the epigenetic regulation of transcription by histone methylation and genes encoding components of the synapse. However, the interactions between these pathways in conferring risk to psychiatric illness are unknown. Loss-of-function (LoF) mutations in the gene encoding histone methyltransferase, SETD1A, confer substantial risk to schizophrenia. Among several roles, SETD1A is thought to be involved in the development and function of neuronal circuits. Here, we employed a multi-omics approach to study the effects of heterozygous Setd1a LoF on gene expression and synaptic composition in mouse cortex across five developmental timepoints from embryonic day 14 to postnatal day 70. Using RNA sequencing, we observed that Setd1a LoF resulted in the consistent downregulation of genes enriched for mitochondrial pathways. This effect extended to the synaptosome, in which we found age-specific disruption to both mitochondrial and synaptic proteins. Using large-scale patient genomics data, we observed no enrichment for genetic association with schizophrenia within differentially expressed transcripts or proteins, suggesting they derive from a distinct mechanism of risk from that implicated by genomic studies. This study highlights biological pathways through which SETD1A loss-of-function may confer risk to schizophrenia. Further work is required to determine whether the effects observed in this model reflect human pathology.

2022-05-26 | PXD032742 | Pride

Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories (scRNA-Seq)

Project description:To dissect, in more detail, cell population alterations and examine in situ genotypic differences in transcriptomic and regulatory profiles during neurogenesis and neuronal differentiation, we used single cell RNA sequencing (scRNA-seq) to profile cell type composition and molecular signatures of FOs derived from mutant and control iPSC lines at DIV70

2025-04-17 | GSE239864 | GEO

Developmental disruption to the cortical transcriptome and synaptosome in a model of SETD1A loss-of-function

Project description:We employed a multi-omics approach to study the effects of heterozygous Setd1a LoF on gene expression and synaptic composition in mouse cortex across five developmental timepoints from embryonic day 14 to postnatal day 70. Using RNA sequencing, we observed that Setd1a LoF resulted in the consistent downregulation of genes enriched for mitochondrial pathways. This effect extended to the synaptosome, in which we found age-specific disruption to both mitochondrial and synaptic proteins.

2022-05-02 | GSE199428 | GEO

DNA methylation in frontal cortex of Setd1a haploinsufficient mice

Project description:SETD1A, a histone methyltransferase, is implicated in schizophrenia through rare loss-of-function mutations. While SETD1A regulates gene expression via histone H3K4 methylation, its influence on broader epigenetic dysregulation remains incompletely understood. We explored the hypothesis that SETD1A haploinsufficiency contributes to neurodevelopmental disruptions associated with schizophrenia risk via alterations in DNA methylation. We profiled DNA methylation in the frontal cortex of Setd1a+/- mice across prenatal and postnatal development using Illumina Mouse Methylation arrays. Differentially methylated positions and regions were identified, and their functional relevance examined through gene and biological annotation. We integrated these findings with transcriptomic and proteomics datasets, and assessed mitochondrial complex I activity to explore potential downstream functional effects. Setd1a haploinsufficiency resulted in widespread hypomethylation of genes related to ribosomal function and RNA processing that persisted across all developmental stages. Setd1a-targeted promoter regions and noncoding small nucleolar RNAs (snoRNAs) were also enriched for differentially methylated sites. Despite the downregulation of mitochondrial gene expression, the same genes were not differentially methylated and complex I activity in Setd1a+/- mice did not differ significantly from controls. Genes overlapping hypomethylated regions were enriched for common genetic associations with schizophrenia. Our findings suggest that SETD1A haploinsufficiency disrupts the epigenetic regulation of ribosomal pathways. These results provide insight into an alternative mechanism through which genetic variation in SETD1A influences developmental and synaptic plasticity, contributing to schizophrenia pathophysiology.

2025-04-22 | GSE295008 | GEO

Methylomic trajectories across human

Project description:Dynamic changes to the epigenome mediate key neurobiological and cognitive processes in the central nervous system, and also play a role in transcriptional regulation during brain development. Although the importance of DNA methylation in brain development is highlighted by the neurodevelopmental deficits associated with mutations in genes including methyl-CpG binding protein 2 (MECP2), our knowledge about the specific methylomic trajectories associated with human neurodevelopment is extremely limited. Here we report an analysis of genome-wide patterns of DNA methylation in 179 human fetal cortex samples. Bisulphite converted DNA from 179 human brain samples was hybridized to the Illumina 450K Human Methylation Beadchip.

2014-12-19 | E-GEOD-58885 | biostudies-arrayexpress

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