Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of TET3 deletion on gene expression in ileum [RNA-seq]

ABSTRACT: Effects of TET3 deletion on gene expression in ileum [RNA-seq]

PROVIDER: PRJNA1009881 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25773501.fastq.gz	Fastqsanger.gz
	SRR25773502.fastq.gz	Fastqsanger.gz
	SRR25773503.fastq.gz	Fastqsanger.gz
	SRR25773504.fastq.gz	Fastqsanger.gz
	SRR25773505.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Effects of TET3 deletion on gene expression in ileum [RNA-seq]

Project description:Bulk RNA-seq show differential gene expression profile beween Wild type (WT) and Tet3 knockout (KO) in ileum. We identified genes involved in innate immune defense, anti-microbial response and growth signaling to be affected by TET3 deletion.

2023-09-04 | GSE241790 | GEO

Rest recruits neuronal Tet3 to induce chromatin remodeling and gene expression

Project description:Ten-eleven translocation (Tet) hydroxylases (Tet1-3) oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). In neurons increased 5hmC levels within gene bodies correlate positively with gene expression. The mechanisms controlling Tet activity and 5hmC levels are poorly understood. In particular, it is not known how the neuronal Tet3 isoform lacking a DNA binding domain is targeted to the DNA. To identify factors binding to Tet3 we screened for proteins that co-precipitate with Tet3 from mouse retina and identified the transcriptional repressor Rest as a highly enriched Tet3-specific interactor. Rest was able to enhance Tet3 hydroxylase activity after co-expression and overexpression of Tet3 activated transcription of Rest-target genes. Moreover, we found that Tet3 also interacts with Nsd3 and two other H3K36 methyltransferases and is able to induce H3K36 trimethylation. We propose a mechanism for transcriptional activation in neurons that involves Rest-guided targeting of Tet3 to the DNA for directed 5hmC-generation and Nsd3-mediated H3K36 trimethylation.

2015-04-02 | PXD001857 | Pride

Redirected nuclear glutamate dehydrogenase supplies Tet3 with a-ketoglutarate in neurons

Project description:Tet3 is an Fe2+-dependent enzyme that oxidizes genomic 5-methylcytosine to 5-hydroxymethylcytosine with the help of alpha-ketoglutarate and oxygen. It is the most abundant Tet enzyme in differentiated tissues including brain. Adult brain contains the highest 5-hydroxymethylcytosine levels. How alpha-ketoglutarate is made available for the oxidation of mC in brain cells and how the Tet activity is linked to neural activity are unsolved questions. Our experiments with full mouse brains show that Tet3 interacts in the nucleus directly with selected enzymes of the mitochondrial citric acid cycle. This leads to the formation of isocitrate. Tet3 also interacts with aspartate aminotransferase, which produces oxaloacetate. Although oxaloacetate and isocitrate are biosynthetic alpha-ketoglutarate precursors, they function as inhibitors of Tet3 and are needed to protect the reactive Fe2+ center from degrading DNA. The supply of Tet3 with alpha-ketoglutarate is established by a direct interaction of Tet3 with glutamate dehydrogenase (Glud1), which converts the neurotransmitter glutamate directly into alpha-ketoglutarate. This links Tet3 function to neural activity.

2021-05-10 | PXD004518 | Pride

Time course of gene expression signatures for Tet3 induced neurons

Project description:To further investigate the gene expression at different courses in MEFs and Tet3 induced neurons, we have employed whole genome microarray expression profiling as a discovery platform to identify the expression level of specific genes, such as neuronal specific genes, fibrobalst specific genes. The gene expression in mouse embryonic fibroblasts and Tet3 induced neurons at 1, 3, 5, 7 dpi.

2016-03-03 | E-GEOD-78841 | biostudies-arrayexpress

Gene expression profile of ileum, jejunum and colon

Project description:The gene expression of ileum, jejunum and colon.

2020-12-21 | GSE143342 | GEO

Effects of DECR1 deletion on cardiomyocytes

Project description:Effects of DECR1 deletion on cardiomyocytes

| PRJNA1332647 | ENA

Effect of TET3 expression on muscle insulin sensitivity

Project description:To gain a mechanistic insight into TET3-mediated regulation of muscle insulin sensitivity, we performed genome-wide expression profiling (RNA-seq) on RNA isolated from GAS muscles of muscle TET3 specific knockdown mice and WT littermates.

2023-12-05 | GSE224042 | GEO

The role of Tet3 in regulating gene expression in response to global synaptic activity changes

Project description:Counter to the long-held belief that DNA methylation of terminally differentiated cells is permanent and essentially immutable, post-mitotic neurons exhibit extensive DNA demethylation. The causal role of active DNA demethylation in neurons, however, is not known. Tet family proteins oxidize 5-methylcytosine to initiate active DNA demethylation through the base-excision repair pathway. Here, we show that synaptic activity bi-directionally regulates neuronal Tet3 expression. Functionally, knockdown of Tet or inhibition of base-excision repair in hippocampal neurons elevates excitatory glutamatergic synaptic transmission, whereas overexpressing Tet3 or Tet1 catalytic domain decreases it. Furthermore, dysregulation of Tet3 signalling prevents homeostatic synaptic plasticity. Mechanistically, Tet3 dictates neuronal surface GluR1 levels. RNA-seq analyses further revealed a pivotal role of Tet3 in regulating gene expression in response to global synaptic activity changes. Thus, Tet3 serves as a synaptic activity sensor to epigenetically regulate basic properties and meta-plasticity of neurons via active DNA demethylation.

2015-03-25 | GSE67245 | GEO

Effects of Nova1 Deletion on Gene Expression in Tissues and Cells

Project description:Effects of Nova1 Deletion on Gene Expression in Tissues and Cells

| PRJNA875480 | ENA

The effects of liver specific deletion of Dhcr7 on gene expression

Project description:The effects of liver specific deletion of Dhcr7 on gene expression

| PRJNA610810 | ENA