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RRBS (Reduced Representation Bisulfite Sequencing) of Egr1-/- and Tet1-/- mouse frontal cortex

ABSTRACT: We performed methylome profiling for mouse frontal cortex tissues derived from 6~8 week old Egr1-/- and Tet1-/- mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE108762 | GEO | 2019/07/25

REPOSITORIES: GEO

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RRBS (Reduced Representation Bisulfite Sequencing) of Egr1-/- and Tet1-/- mouse frontal cortex

Project description:RRBS (Reduced Representation Bisulfite Sequencing) of Egr1-/- and Tet1-/- mouse frontal cortex

| PRJNA428509 | ENA

RNA-seq of Egr1-/- and Tet1-/- mouse frontal cortex

Project description:We performed transcriptome profiling for frontal cortex tissues derived from 6~8 week old Egr1-/- and Tet1-/- mice.

2019-07-25 | GSE108750 | GEO

RNA-seq of Egr1-/- and Tet1-/- mouse frontal cortex

Project description:RNA-seq of Egr1-/- and Tet1-/- mouse frontal cortex

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Egr1 Recruits Tet1 to Shape the Brain Methylome during Early Postnatal Development

Project description:Early growth response gene-1 (Egr1) is a critical transcription factor involved in many important biological processes, including neuronal plasticity and memory formation. With a rapid increase in expression during the first few weeks after birth, Egr1 controls the selection, maturation and functional integration of newborn neurons. The regulation of Egr1-mediated gene expression has been shown to be under methylation control. However, Egr1 target sites and their epigenetic regulation in the nervous system remains largely unknown. In this study, we performed ChIP-seq for EGR1 in mouse frontal cortex and identified a large number of EGR1 binding sites with their cell-type specific methylation patterns established during postnatal frontal cortex development. More specifically, the CpG dinucleotides within these EGR1 binding sites become hypo-methylated in mature neurons but remain heavily methylated in glia. We further demonstrated that EGR1 recruits a DNA demethylase TET1 to remove DNA methylation at EGR1 binding sites and activate downstream genes. In addition, we found that the frontal cortexes from knockout mice with the loss of Egr1 or Tet1 share strikingly similar profiles in both gene expression and DNA methylation. In summary, our study reveals Egr1 as a key mediator for gene-environment interactions shaping brain methylome together with Tet1 during early postnatal development and provides an important new insight into how early life experience may shape the brain methylome. This SuperSeries is composed of the SubSeries listed below.

2019-07-25 | GSE108768 | GEO

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

Project description: Not available

| S-EPMC3413387 | biostudies-literature

High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS).

Project description: Not available

| S-EPMC5065634 | biostudies-literature

Genome-wide maps of TET1 binding in mouse frontal cortex

Project description:With anti-TET1 immunoprecipitated chromatin from mouse frontal cortices, we generated TET1 binding maps with 4496 high-confidence peaks and approximately 90% of TET1 peaks were within intergenic regions.

2019-07-25 | GSE124671 | GEO

RRBS (Reduced Representation Bisulfite Sequencing) of HL60

Project description:We exploited the methylation genome-scale screening RRBS to correlate the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci. Out of 15275 non ambiguous gene loci identified by DNMT1 RIP-Seq, 9436 loci were covered by RRBS. These 9436 loci were clustered according to the fold of specific DNMT1 library peaks enrichment (defined as the ratio of the sum of the area under the curve of specific DNMT1 library peaks covering the gene loci). Genes were then stratified by the expression profile ultimately leading to the epitranscriptome map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile. Relationship between DNMT1-RNA interactions, DNA methylation and gene expression

2012-12-01 | E-GEOD-32168 | biostudies-arrayexpress

RRBS (Reduced Representation Bisulfite Sequencing) of HL60

2012-12-01 | GSE32168 | GEO

Reduced Representation Bisulfite Sequencing of HUES8 WT and HUES8 TET1/2/3 TKO hESCs

Project description:The TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish due to challenges of distinguishing global versus locus-specific effects. Here we show that TET1/2/3 triple knockout (TKO) human embryonic stem cells (hESCs) exhibit preferential hypermethylation at bivalent promoters without corresponding gene expression changes in undifferentiated hESCs. In the absence of the TET proteins, abnormal accumulation of DNMT3B at bivalent promoters results in hypermethylation and impaired gene activation upon differentiation. Broadly, the competitive balance between the TET proteins and de novo methyltransferases at bivalent promoters could facilitate rapid changes of their methylation state to either activate or silence transcription in a cell-lineage and gene dependent manner.

2017-12-01 | GSE89724 | GEO

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