Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1015710 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26044615_1.fastq.gz | Fastqsanger.gz | |||
| SRR26044615_2.fastq.gz | Fastqsanger.gz | |||
| SRR26044616_1.fastq.gz | Fastqsanger.gz | |||
| SRR26044616_2.fastq.gz | Fastqsanger.gz | |||
| SRR26044617_1.fastq.gz | Fastqsanger.gz |
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Project description:ett Syndrome is a neurological disorder caused by mutation in the MeCP2 gene encoding protein, which is a component of chromatin. The neurological spectrum of Rett Syndrome suggests that this protein plays an important role in the nervous system. Limitations of in vivo studies such as the accumulation of indirect effects have impeded understanding of direct consequences of the loss of MeCP2. Thus, it is important to develop simplified models of Rett Syndrome to create the disease in a dish. This can be achieved for instance by differentiating human neuronal progenitors, which carry various MeCP2 mutations, into a homogeneous neuronal population and analyze alterations in the chromatin states such as methylation, hydroxymethylation, histone modifications and changes in transcription. Protocol: LUHMES cell line of human neural progenitors was differentiated into neurons for 9 days in presence of defined medium. At the end of differentiation, neuronal genomic DNA was extracted using Qiagen DNeasy kit and bisulfite-treated. Adaptors were ligated to purified DNA and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-01-31 | E-ERAD-112 | biostudies-arrayexpress
Project description:Cockayne syndrome is an inherited premature aging syndrome associated with developmental and neurological disorders. Mutations in the genomic locus encoding CSB are associated with 80% Cockayne syndrome cases. CSB is invovled in relieving UV-induced and oxidative stree. To gain more insights into the fucntion of CSB under these stress, we use ChIP-seq to determine the genomic localization of CSB 1 hour after UV irradiation and menadione treatment.
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Project description:We elucidate a neurological syndrome affecting both the PNS and CNS defined by CLP1 mutations that impair tRNA splicing Identification and biochemical characterization of mutant CLP1 in human patients
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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. MeCP2 ChIP-seq from the forebrain and cerebellum of wild-type mice.
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Project description:Mutations in the MECP2 gene cause the profound neurological disorder Rett syndrome. MeCP2 protein is an epigenetic reader that recruits the NCOR1/2 corepressor complexes to methylated cytosine in its canonical CG setting, but also to methylated CA motifs, which are abundant in neurons but rare in other cell types. In this study we set out to test the biological significance of this non-canonical mode of DNA binding. To achieve this, we replaced the endogenous MeCP2 DNA binding domain with that of MBD2, which only binds mCG. Knock-in mice expressing the hybrid “MM2” protein created by this domain-swap displayed severe Rett syndrome-like phenotypes. This indicates that binding to mCA, specifically the mCAC trinucleotide, is critical for normal brain function and it offers a plausible explanation for the delayed onset of Rett syndrome, due to the coincident late accumulation of mCAC and its cognate interpreter, MeCP2. We show that the small subset of genes aberrantly expressed in both Mecp2-null and MM2 mice is strikingly enriched for genes implicated in neurological disorders, highlighting targets with potential relevance to the Rett syndrome phenotype
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