Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Principles governing DNA methylation during neural lineage and subtype specification

ABSTRACT: DNA methylation, in concert with other epigenetic regulators, controls the accessibility of transcription factors to DNA. While comprehensively described in the development of neuronal progenitors, the role of DNA methylation/demethylation in neuronal lineage/subtype specification is not known. By profiling two distinct neuronal lineages, and five neuron subtypes in the hippocampus and striatum, we uncovered a set of five principles that govern DNA methylation dynamics in neurodevelopment. By dividing neurodevelopment to three alternating methylation and demethylation periods and applying the principles to each of these stages, we created a matrix that comprehensively describes the targets, genomic contexts, functional consequences and putative mechanisms of methylation/demethylation events. The overarching theme is that the developmental methylation program is remarkably similar in the hippocampal and striatal lineages, with significant divergence only occurring during subtype specification. Our matrix can be cross-referenced with disease-associated epigenetic changes to specify the possible events and underlying principles compromised in disease.

ORGANISM(S): Mus musculus

PROVIDER: GSE72700 | GEO | 2016/02/20

SECONDARY ACCESSION(S): PRJNA294687

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Principles governing DNA methylation during neural lineage and subtype specification

Project description:DNA methylation, in concert with other epigenetic regulators, controls the accessibility of transcription factors to DNA. While comprehensively described in the development of neuronal progenitors, the role of DNA methylation/demethylation in neuronal lineage/subtype specification is not known. By profiling two distinct neuronal lineages, and five neuron subtypes in the hippocampus and striatum, we uncovered a set of five principles that govern DNA methylation dynamics in neurodevelopment. By dividing neurodevelopment to three alternating methylation and demethylation periods and applying the principles to each of these stages, we created a matrix that comprehensively describes the targets, genomic contexts, functional consequences and putative mechanisms of methylation/demethylation events. The overarching theme is that the developmental methylation program is remarkably similar in the hippocampal and striatal lineages, with significant divergence only occurring during subtype specification. Our matrix can be cross-referenced with disease-associated epigenetic changes to specify the possible events and underlying principles compromised in disease. Compared tissue from C57BL6 male animals at differenent developmental timepoints and regions for differences in DNA methylation and RNA expression. Additionally Dnmt3a conditional knockdown mice were used to determine role of Dnmt3a during development.

2016-02-20 | E-GEOD-72700 | biostudies-arrayexpress

Mus musculus

Project description:Principles governing DNA methylation during neural lineage and subtype specification

| PRJNA294687 | ENA

Repression by PRDM13 is critical for generating precise neuronal identity (RNA-Seq)

Project description:The mechanisms that activate some genes while silencing others are critical to ensure precision in lineage specification as multipotent progenitors become restricted in cell fate. During neurodevelopment, these mechanisms are required to generate the wide variety of neuronal subtypes found in the nervous system. Here we report interactions between basic helix-loop-helix (bHLH) transcriptional activators and the transcriptional repressor PRDM13 that are critical for these processes during specification of dorsal spinal cord neurons. PRDM13 inhibits gene expression programs for the excitatory neuronal lineages in the dorsal neural tube while also suppressing a battery of genes that determine ventral neural tube fates including Olig1, Olig2 and Prdm12. PRDM13 does this via recruitment to chromatin by multiple neural bHLH factors to restrict gene expression in specific neuronal lineages. Together these findings highlight the function of PRDM13 in repressing bHLH transcriptional activators that together are required to achieve precise neuronal specification during development.

2017-08-04 | GSE90937 | GEO

Repression by PRDM13 is critical for generating precise neuronal identity (ChIP-Seq)

2017-08-04 | GSE90936 | GEO

Mus musculus

Project description:G9a influences neuronal subtype specification in striatum

| PRJNA237301 | ENA

PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations [RNA-seq]

Project description:The link between DNA methylation and neurodevelopmental disorders is well established. However, how DNA methylation is fine-tuned – ensuring precise gene expression and developmental fidelity – remains poorly understood. PROSER1, a known TET2 interactor, was recently linked to a severe neurodevelopmental disorder. Here, we demonstrate that PROSER1 interacts with all TET enzymes and stabilizes chromatin-bound TET-OGT-PROSER1-DBHS (TOPD) complexes, which regulate DNA demethylation and developmental gene expression. Surprisingly, we find that PROSER1 also sequesters TET enzymes, preventing widespread demethylation and transposable element de-repression. Our findings identify PROSER1 as a key factor which both positively and negatively regulates DNA demethylation essential for mammalian neurodevelopment.

2024-11-21 | GSE273516 | GEO

PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations [EM-seq]

2024-11-20 | GSE273515 | GEO

PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations [ChIP-seq]

2024-11-20 | GSE273514 | GEO

Dynamic epigenomic landscapes during early lineage specification in mouse embryos

Project description:In mammals, all somatic development originates from lineage segregation in early embryos. However, the dynamics of transcriptomes and epigenomes in concert with initial cell fate commitment remains poorly characterized. Here, we report comprehensive investigation of transcriptomes and base-resolution methylomes for early lineages in peri- and postimplantation mouse embryos. We found allele- and lineage-specific de novo methylation at CG and CH sites, leading to differential methylation between embryonic and extraembryonic lineages at promoters of lineage regulators, gene bodies, and DNA methylation valleys. By determining chromatin architecture using Hi-C across the same developmental period, we showed both global demethylation and remethylation in early development correlate with chromatin compartments. Dynamic local methylation is evident during gastrulation, which revealed maps of putative regulatory elements. Finally, we found that de novo methylation patterning does not strictly require implantation. These data unveiled dynamic transcriptomes, DNA methylomes, and 3D chromatin landscapes during the earliest mammalian lineage specification.

2017-12-05 | GSE76505 | GEO

5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging [mRNA profiling]

Project description:DNA methylation dynamics influence brain function and are altered in neurological disorders. 5-hydroxymethylcytosine (5-hmC), a DNA base derived from 5-methylcytosine (5mC) accounts for ~40% of modified cytosine in brain, and has been implicated in DNA methylation-related plasticity. Here we map 5-hmC genome-wide across three ages in mouse hippocampus and cerebellum, allowing assessment of its stability and dynamic regulation during postnatal neurodevelopment through adulthood. We find developmentally programmed acquisition of 5-hmC in neuronal cells. Epigenomic localization of 5-hmC-regulated regions reveals stable and dynamically modified loci during neurodevelopment and aging. By profiling 5-hmC in human cerebellum we establish conserved genomic features of 5-hmC. Finally, we implicate 5-hmC in neurodevelopmental disease by finding that its levels are inversely correlated with methyl-CpG-binding protein 2 (Mecp2) dosage, a protein encoded by a gene in which mutations cause Rett Syndrome. These data point toward critical roles for 5-hmC-mediated epigenetic modification in neurodevelopment and diseases. Gene expression data derived from P7 and 6wk mouse cerebellum used for determining expression outcomes associated with dynamic alterations in 5-hydroxymethylcytosine

2011-10-29 | E-GEOD-32187 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data