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Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (Bisulfite-Seq)

ABSTRACT: Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (Bisulfite-Seq)

PROVIDER: PRJNA576509 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10247788_1.fastq.gz	Fastqsanger.gz
	SRR10247788_2.fastq.gz	Fastqsanger.gz
	SRR10247789_1.fastq.gz	Fastqsanger.gz
	SRR10247789_2.fastq.gz	Fastqsanger.gz
	SRR10247790_1.fastq.gz	Fastqsanger.gz

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Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (Bisulfite-Seq)

Project description:The genomes of mammalian neurons contain uniquely high levels of non-CG DNA methylation that can be bound by the Rett syndrome protein, MeCP2, to regulate gene expression. How patterns of non-CG methylation at genes are established and the mechanism by which this methylation works with MeCP2 to control gene expression is unclear. Here we find that genes repressed by MeCP2 are found within regions of high non-CG methylation that are defined by domains of chromatin folding. Rather than working directly at transcriptional start sites to regulate these genes, MeCP2 represses enhancer elements that are enriched for methylated cytosines occurring in the CA or CG context. Enhancers repressed by MeCP2 are found within genes that are upregulated upon loss of the protein, providing a regulatory logic for how disruption of MeCP2 can lead to wide-spread changes in gene expression. Hence, we have found that DNA topology can shape non-CG DNA methylation across the genome to dictate MeCP2-mediated enhancer regulation in the brain.

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Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (RNA-Seq)

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Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (ChIP-Seq)

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Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression

Project description:Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression

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Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (ChIP-Seq)

Project description:Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (ChIP-Seq)

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Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (RNA-Seq)

Project description:Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (RNA-Seq)

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Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression

Project description:This SuperSeries is composed of the SubSeries listed below.

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Whole genome bisulfite sequencing of adult hypothalamus male mouse brain

Project description: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.

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Transcription in Mecp2 null and Cfp1 null cells

Project description:The dinucleotide sequence 5'CG acts as a signalling module that can influence the epigenome and modulate chromosome function. CG exists in three chemically distinct forms that differ due to the modification status of the cytosine base: unmethylated, methylated or hydroxymethylated. The Cfp1 protein binds to unmethylated CG clusters in vivo and is required for the coincident trimethylation of lysine 4 in histone H3 by the Setd1 complex. On the other hand, the methyl-CG binding protein MeCP2 can direct deacetylation of histones. These findings align with evidence that nonmethylated CpG islands mark promoters, whereas CG methylation leads to gene silencing. Interfering with Cfp1 or Mecp2 function will therefore impact chromatin structure, possibly resulting in alteration of transcription. 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/ Abstract: This project aims to assess effects of Cfp1- and Mecp2-deficiency on transcription using RNA-seq of nascent RNA. This involves in vitro run-on transcription with isolated nuclei using BrU as a substrate to permit purification of nascent RNA. This technique shows where active polymerases are loaded on chromatin, unlike conventional RNA-seq, which only detects stable cytoplasmic RNAs.

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