Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain
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PROVIDER: PRJNA227438 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA methylation plays critical roles in the nervous system and has been traditionally considered to be restricted to CpG dinucleotides in metazoan genomes. Here we show that the single-base resolution neuronal DNA methylome from the adult mouse dentate gyrus consists of both CpG (~75%) and CpH (~25%) methylation (H = A/C/T). Neuronal CpH methylation is conserved in human brains, enriched in low CpG-density regions, depleted at protein-DNA interaction sites, and anti-correlated with gene expression. Functionally, both mCpGs and mCpHs can repress transcription in vitro and are recognized by MeCP2 in vivo. Unlike most CpG methylation, CpH methylation is established de novo during neuronal maturation and requires DNMT3A for active maintenance in post-mitotic neurons. These characteristics of CpH methylation suggest a significantly expanded proportion of the neuronal genome under cytosine methylation regulation and provide a new framework for understanding the roles of this key epigenetic modification in neuronal identity, maturation, plasticity and neurological disorders.
2013-12-22 | GSE52330 | GEO
Project description:DNA methylation plays critical roles in the nervous system and has been traditionally considered to be restricted to CpG dinucleotides in metazoan genomes. Here we show that the single-base resolution neuronal DNA methylome from the adult mouse dentate gyrus consists of both CpG (~75%) and CpH (~25%) methylation (H = A/C/T). Neuronal CpH methylation is conserved in human brains, enriched in low CpG-density regions, depleted at protein-DNA interaction sites, and anti-correlated with gene expression. Functionally, both mCpGs and mCpHs can repress transcription in vitro and are recognized by MeCP2 in vivo. Unlike most CpG methylation, CpH methylation is established de novo during neuronal maturation and requires DNMT3A for active maintenance in post-mitotic neurons. These characteristics of CpH methylation suggest a significantly expanded proportion of the neuronal genome under cytosine methylation regulation and provide a new framework for understanding the roles of this key epigenetic modification in neuronal identity, maturation, plasticity and neurological disorders.
2013-12-22 | GSE52261 | GEO
Project description:DNA methylation plays critical roles in the nervous system and has been traditionally considered to be restricted to CpG dinucleotides in metazoan genomes. Here we show that the single-base resolution neuronal DNA methylome from the adult mouse dentate gyrus consists of both CpG (~75%) and CpH (~25%) methylation (H = A/C/T). Neuronal CpH methylation is conserved in human brains, enriched in low CpG-density regions, depleted at protein-DNA interaction sites, and anti-correlated with gene expression. Functionally, both mCpGs and mCpHs can repress transcription in vitro and are recognized by MeCP2 in vivo. Unlike most CpG methylation, CpH methylation is established de novo during neuronal maturation and requires DNMT3A for active maintenance in post-mitotic neurons. These characteristics of CpH methylation suggest a significantly expanded proportion of the neuronal genome under cytosine methylation regulation and provide a new framework for understanding the roles of this key epigenetic modification in neuronal identity, maturation, plasticity and neurological disorders. Three biological replicates (dentate gyrus samples from C57Black6 mice) were analyzed by mRNA-seq
2013-12-22 | E-GEOD-52261 | biostudies-arrayexpress
Project description:DNA methylation plays critical roles in the nervous system and has been traditionally considered to be restricted to CpG dinucleotides in metazoan genomes. Here we show that the single-base resolution neuronal DNA methylome from the adult mouse dentate gyrus consists of both CpG (~75%) and CpH (~25%) methylation (H = A/C/T). Neuronal CpH methylation is conserved in human brains, enriched in low CpG-density regions, depleted at protein-DNA interaction sites, and anti-correlated with gene expression. Functionally, both mCpGs and mCpHs can repress transcription in vitro and are recognized by MeCP2 in vivo. Unlike most CpG methylation, CpH methylation is established de novo during neuronal maturation and requires DNMT3A for active maintenance in post-mitotic neurons. These characteristics of CpH methylation suggest a significantly expanded proportion of the neuronal genome under cytosine methylation regulation and provide a new framework for understanding the roles of this key epigenetic modification in neuronal identity, maturation, plasticity and neurological disorders. Two biological replicates (dentate gyrus samples from C57Black6 mice) were analyzed in Bisulfite-seq.
2013-12-22 | E-GEOD-52330 | biostudies-arrayexpress
Project description:DNA methylation has critical roles in the nervous system and has been traditionally considered to be restricted to CpG dinucleotides in metazoan genomes. Here we show that the single base-resolution DNA methylome from adult mouse dentate neurons consists of both CpG (~75%) and CpH (~25%) methylation (H = A/C/T). Neuronal CpH methylation is conserved in human brains, enriched in regions of low CpG density, depleted at protein-DNA interaction sites and anticorrelated with gene expression. Functionally, both methylated CpGs (mCpGs) and mCpHs can repress transcription in vitro and are recognized by methyl-CpG binding protein 2 (MeCP2) in neurons in vivo. Unlike most CpG methylation, CpH methylation is established de novo during neuronal maturation and requires DNA methyltransferase 3A (DNMT3A) for active maintenance in postmitotic neurons. These characteristics of CpH methylation suggest that a substantially expanded proportion of the neuronal genome is under cytosine methylation regulation and provide a new foundation for understanding the role of this key epigenetic modification in the nervous system.
| S-EPMC3970219 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-12-22 | E-GEOD-52331 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2013-12-22 | GSE52331 | GEO
Project description:Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain (RNA-seq)
| PRJNA227308 | ENA
Project description:Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain (Bisulfite-seq)
| PRJNA227899 | ENA
Project description:Cytosine (C) modifications within CpG dyads are central regulatory elements of mammalian genomes. In addition to 5-methylcytosine (mC), genomes can also contain high levels of 5-hydroxymethylcytosine (hmC) that is read differently by nuclear proteins than mC. However, hmC can co-exist with C and mC in different combinations in the two strands of CpG dyads, and it is poorly understood, how these combinatorial marks differ in their protein interactomes and regulatory functions. To identify nuclear binding proteins, we employed DNA promoter probes with differentially modified CpG dyads in pulldown experiments. The datasets comprise three biological replicates of HEK293T nuclear proteins binding to a VEGFA promoter sequence with differentially modified CpG dyads. Each biological replicate contains five technical replicates per modified CpG dyad, resulting in a total of 15 replicates for C/C, mC/mC and hmC/mC, and 10 replicates for hmC/C and hmC/hmC.
2024-08-15 | MSV000095609 | MassIVE