Rett syndrome-causing MECP2 mutations severely impact key cellular and molecular features of human astrocytes
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ABSTRACT:
PROVIDER: PRJNA772970 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16497780_1.fastq.gz | Fastqsanger.gz | |||
| SRR16497780_2.fastq.gz | Fastqsanger.gz | |||
| SRR16497781_1.fastq.gz | Fastqsanger.gz | |||
| SRR16497781_2.fastq.gz | Fastqsanger.gz | |||
| SRR16497782_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goal of this RNA sequencing (RNA-seq) study is to identify aberrations in the astrocyte transcriptional landscape caused by R270X mutation in MECP2. Methods: mRNA-seq analysis was performed on total RNA extracted from human embryonic stem cell (ESCs)-derived wild-type (WT) and MECP2-R270X mutant astrocytes. The R270X mutation was inserted into ESCs (line H1) via CRISPR/Cas9 technology. Samples were generated in triplicates, sequenced by Illumina NovaSeq 6000 Sequencing System. Raw reads were first trimmed for 10 bases at the 5’end to remove reads with biased nucleotide (ACGT) distribution. Trimmed reads were then aligned to the Homo sapiens genome (GRCh38p12, GENCODE, primary assembly), using STAR aligner. Differential gene expression (DEG) analyses on the read counts were performed using DESeq2. Genes with sum of read counts across all samples with less 10 were filtered out from analysis. Results: Our RNA-seq analysis showed that 1,621 genes were dysregulated in mutant astrocytes (fold-change >1.5 or <2/3; padj < 0.05, average reads count >10 in at least one genotype)
2024-02-15 | GSE185726 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE24285: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome (mm8 chromosomal tiling arrays) GSE24286: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome (mm8 promoter tiling arrays) GSE24320: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome (high-throughput small RNA sequencing) Refer to individual Series
2010-09-29 | E-GEOD-24329 | biostudies-arrayexpress
Project description:Mutations in the gene encoding the transcriptional modulator methyl-CpG binding protein 2 (MeCP2) are responsible for the neurodevelopmental disorder Rett syndrome that is one of the most frequent sources of intellectual disability in women. It has been shown that mutant astrocytes contribute to neuronal defects, probably as a result of aberrant secretion of soluble factor(s). Based on the hypothesis that this irregular secretion of soluble factor is the result of abnormal transcription of those factors, we have compared the gene expression profiles of wild type and mutant astrocytes from Mecp2 308/y mice by using Affymetrix mouse 2.0 microarrays. P0 newborns from pregnant Mecp2 308/+ heterozygous mice were used for the preparation of dissociated cortical astrocyte cultures. Four wild-type and four mutant confluent astrocytes cultures were used for total RNA extraction with the Qiagen RNeasy kit (Qiagen, Courtaboeuf, France) as described by the manufacturer. The gene expression profiles of wild type and mutant astrocytes from Mecp2 308/y mice have been assayed by using Affymetrix mouse 2.0 microarrays.
2015-01-01 | E-GEOD-56709 | biostudies-arrayexpress
Project description:Rett syndrome is a human intellectual disability disorder that is associated with mutations in the X-linked MECP2 gene. Theepigenetic reader MeCP2 binds to methylated cytosines on the DNA and regulates chromatin organization. We have shownpreviously that MECP2 Rett syndrome missense mutations are impaired in chromatin binding and heterochromatinreorganization. Here, we performed a proteomics analysis of post-translational modifications of MeCP2 isolated from adult mousebrain. We show that MeCP2 carries various post-translational modifications, among them phosphorylation on S80 and S421, whichlead to minor changes in either heterochromatin binding kinetics or clustering. We found that MeCP2 is (di)methylated on severalarginines and that this modification alters heterochromatin organization. Interestingly, we identified the Rett syndrome mutationsite R106 as a dimethylation site. In addition, co-expression of protein arginine methyltransferases 1 and 6 lead to a decrease ofheterochromatin clustering. Altogether, we identified and validated novel modifications of MeCP2 in the brain and show that thesecan modulate its ability to bind as well as reorganize heterochromatin, which may play a role in the pathology of Rett syndrome.
2022-10-15 | PXD033696 | Pride
Project description:Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heterozygous mutations of MECP2. Reactivation of the silent wild-type MECP2 allele on the inactive X chromosome (Xi) represents a promising therapeutic opportunity for female RTT patients. Here, we applied a multiplex epigenome editing approach to reactivate MECP2 on Xi. Demethylation of the MECP2 promoter by dCas9-Tet1 with target sgRNA reactivated MECP2 on Xi in RTT hESCs without detectable off-target effects at the transcriptome level. Neurons derived from methylation edited RTT hESCs reversed the smaller soma size and electrophysiological abnormalities. Insulation of the methylation edited MECP2 locus in RTT neurons by dCpf1-CTCF with target crRNA stabilized MECP2 reactivation and rescued the RTT-related neuronal defects, providing a proof-of-concept study for multiplex epigenome editing to treat RTT.
2023-09-01 | GSE214549 | GEO
Project description:Wide phenotypic spectrum of human stem cell-derived excitatory neurons with Rett syndrome-associated MECP2 mutations
2022-10-31 | GSE148435 | GEO
Project description:Disruption of the MECP2 gene leads to Rett syndrome (RTT), a severe neurological disorder with features of autism. MECP2 encodes a methyl-DNA-binding protein that is proposed to function as a transcriptional repressor, but, despite numerous studies examining neuronal gene expression in MeCP2 mutants, no coherent model has emerged for how MeCP2 regulates transcription. Here we identify a genome-wide length-dependent increase in the expression of long genes in neurons lacking MeCP2. This gene misregulation occurs in human RTT brains and correlates with onset and severity of phenotypes in Mecp2 mutant mice, suggesting that the disruption of long gene expression contributes to RTT pathology. We present evidence that MeCP2 represses long genes by binding to brain-enriched, methylated CA dinucleotides within genes and show that loss of methylated CA in the brain recapitulates gene expression defects observed in MeCP2 mutants. We find that long genes encode proteins with neuronal functions, and overlap substantially with genes that have been implicated in autism and Fragile X syndrome. Reversing the overexpression of long genes in neurons lacking MeCP2 can improve some RTT-associated cellular deficits. These findings suggest that a function of MeCP2 in the mammalian brain is to temper the expression of genes in a length-dependent manner, and that mutations in MeCP2 and possibly other autism genes may cause neurological dysfunction by disrupting the expression of long genes in the brain.
2015-03-12 | GSE60074 | GEO
Project description:Rett syndrome (RTT; OMIM#312750) is a rare devastating neurodevelopmental disorder that represents the most common genetic cause of severe intellectual disability in girls. Mutations in the X-linked methyl-CpG-binding protein 2 (MECP2) gene have been reported in over 95% cases of classical forms of RTT. Although initial studies supported a role for MeCP2 exclusively in neurons, recent data indicate a function also in astrocytes, which emerged as critical players involved in RTT pathogenesis through non-cell autonomous effects. Indeed, Mecp2 knock-out (KO) astrocytes cannot properly support neuronal maturation of wilt-type (WT) neurons and our data demonstrated a detrimental effect also on synaptogenesis and synaptic maintainence. Nevertheless, the molecular mechanisms by which RTT astrocytes can impact on neuronal health remains unknown. In comparison to previous studies exploring the transcriptomic and proteomic profiles of KO astrocytes per se, we used an indirect strategy to unveil the molecular mechanisms responsible for their negative action on neurons. We thus analysed the molecular pathways deregulated in WT neurons cultivated under the influence of KO (n=8) versus WT (n=7) astrocytes, in a transwell-based co-culture system, that allows the exchange of paracrine signals preventing cell-to-cell contact. Astrocytes were seeded on transwell inserts and transferred on neurons at Div0; the co-cultures were maintained until Div14. WT cortical neurons cultivated alone were also included (n=5).
2024-02-19 | E-MTAB-12393 | biostudies-arrayexpress
Project description:Rett syndrome (RTT, OMIM 312750) is a severe X-linked neurodevelopmental disorder linked to heterozygous de novo mutations in the MECP2 gene. MECP2 encodes methyl-CpG-binding protein 2 (MeCP2), which represses gene transcription by binding to 5-methylcytosine residues in symmetrically positioned CpG dinucleotides. The disorder is almost exclusively diagnosed in females, because males affected by the disease usually die perinatally due to severe encephalopathy. Direct MeCP2 target genes underlying the neuropathogenesis of RTT remain largely unknown.
2007-11-02 | E-GEOD-6955 | biostudies-arrayexpress
Project description:Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heterozygous mutations of MECP2. Reactivation of the silent wild-type MECP2 allele on the inactive X chromosome (Xi) represents a promising therapeutic opportunity for female RTT patients. Here, we applied a multiplex epigenome editing approach to reactivate MECP2 on Xi. Demethylation of the MECP2 promoter by dCas9-Tet1 with target sgRNA reactivated MECP2 on Xi in RTT hESCs without detectable off-target effects at the transcriptome level. Neurons derived from methylation edited RTT hESCs reversed the smaller soma size and electrophysiological abnormalities. Insulation of the methylation edited MECP2 locus in RTT neurons by dCpf1-CTCF with target crRNA stabilized MECP2 reactivation and rescued the RTT-related neuronal defects, providing a proof-of-concept study for multiplex epigenome editing to treat RTT.
2023-09-01 | GSE214547 | GEO