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Extra-coding RNAs regulate neuronal DNA methylation and long-term memory formation [MBD-seq]

ABSTRACT: This dataset contains whole-genome MBD (methylbinding domain) sequencing results from cortical neuronal cultures and serves as the basis for characterization of DNA methylation profiles from neuronal systems.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE64987 | GEO | 2016/05/31

SECONDARY ACCESSION(S): PRJNA272629

REPOSITORIES: GEO

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Extra-coding RNAs regulate neuronal DNA methylation and long-term memory formation [MBD-seq]

Project description:This dataset contains whole-genome MBD (methylbinding domain) sequencing results from cortical neuronal cultures and serves as the basis for characterization of DNA methylation profiles from neuronal systems. This experiment contains three sequencing datasets from 2 biological samples. Two datasets originate from samples that underwent MBD-capture prior to whole-genome sequencing. A third dataset contains non-MBD-captured genomic DNA as a control.

2016-05-31 | E-GEOD-64987 | biostudies-arrayexpress

Extra-coding RNAs regulate neuronal DNA methylation and long-term memory formation [RNA-seq]

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Extra-coding RNAs regulate neuronal DNA methylation and long-term memory formation [RNA-seq]

Project description:This dataset contains whole-genome RNA sequencing results from cortical neuronal cultures and serves as the basis for characterization of extra-coding RNA species from neuronal systems. This experiment contains six biological samples, each of which underwent PolyA+ and PolyA- RNA-seq. Samples were either unstimulated (i.e., treated with media alone; samples V1 and V2), stimulated with 25mM potassium chloride for 1hr (K1, K2) or inactivated with tetrodotoxin for 1hr (T1, T2). Datasets were obtained using RNA-seq from PolyA+ fractions or PolyA- fractions of RNA. PolyA- fractions are denoted "ec". Thus, 12 samples are listed here due to the difference in RNA library preparation.

2016-05-31 | E-GEOD-64902 | biostudies-arrayexpress

Extra-coding RNAs regulate neuronal DNA methylation dynamics

Project description:Extra-coding RNAs regulate neuronal DNA methylation dynamics

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Extra-coding RNAs regulate neuronal DNA methylation dynamics.

Project description:Epigenetic mechanisms such as DNA methylation are essential regulators of the function and information storage capacity of neurons. DNA methylation is highly dynamic in the developing and adult brain, and is actively regulated by neuronal activity and behavioural experiences. However, it is presently unclear how methylation status at individual genes is targeted for modification. Here, we report that extra-coding RNAs (ecRNAs) interact with DNA methyltransferases and regulate neuronal DNA methylation. Expression of ecRNA species is associated with gene promoter hypomethylation, is altered by neuronal activity, and is overrepresented at genes involved in neuronal function. Knockdown of the Fos ecRNA locus results in gene hypermethylation and mRNA silencing, and hippocampal expression of Fos ecRNA is required for long-term fear memory formation in rats. These results suggest that ecRNAs are fundamental regulators of DNA methylation patterns in neuronal systems, and reveal a promising avenue for therapeutic targeting in neuropsychiatric disease states.

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Extra-coding RNAs regulate neuronal DNA methylation dynamics

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-05-31 | E-GEOD-64988 | biostudies-arrayexpress

Extra-coding RNAs regulate neuronal DNA methylation dynamics

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

2016-05-31 | GSE64988 | GEO

Pantoea sp. MBD-2R isolate:MBD-2R

Project description:Pantoea sp. MBD-2R isolate:MBD-2R Genome sequencing

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MBD-seq of GBP Muscle samples

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Methylation-dependent and -independent genomic targeting principles of the MBD protein family

Project description:In order to gain insight into DNA methylation readout, we have established a controlled strategy for profiling genomic targeting of chromatin-interacting factors in vivo. With this approach we determined binding preferences for the methyl-CpG binding domain (MBD) family of proteins, including disease relevant mutants, deletions and isoforms. In vivo binding of MBD proteins occurs as a linear function of local methylation density, and is dependent on functional MBD domain – methyl-CpG interactions. This directs specificity of MBD proteins to methylated, CpG dense and inactive regulatory regions. In contrast, binding to unmethylated sites is MBD protein specific and mediated via alternative domains or protein-protein interactions. The latter is observed for NuRD complex-mediated MBD2 tethering to a subset of unmethylated, tissue-specific regulatory regions, similar to MBD3. These functional binding maps reveal methylation-dependent and -independent binding modes determined by distinct protein domains and revise current models of DNA methylation readout through MBD proteins.

2013-04-01 | GSE39610 | GEO

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