Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 expression through 3D chromatin Architecture

ABSTRACT: lncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 expression through 3D chromatin Architecture

PROVIDER: PRJNA551451 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9608420_1.fastq.gz	Fastqsanger.gz
	SRR9608420_2.fastq.gz	Fastqsanger.gz
	SRR9608430_1.fastq.gz	Fastqsanger.gz
	SRR9608430_2.fastq.gz	Fastqsanger.gz
	SRR9608440_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 88

Similar Datasets

lncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 expression through 3D chromatin Architecture

Project description:Both three-dimensional chromatin architecture and long non-coding RNAs (lncRNAs) play essential roles in pluripotency maintenance. However, whether lncRNAs are involved in organizing 3D chromatin structure remains largely unexplored. Here, we identified 39 lncRNAs bound by Klf4, a pluripotency factor mediating long-range chromatin interactions. Among these 39 Klf4-bound lncRNAs, we further investigated the function of 5430416N02Rik. 4C-seq and capture-C experiments revealed that the 5430416N02Rik promoter is a chromatin interaction hub, and 5430416N02Rik RNA functions to facilitate chromatin interactions with the 5430416N02Rik promoter. Knockout of 5430416N02Rik reduces the proliferation rate of embryonic stem cells (ESCs). Moreover, compared to deletion of the gene body alone, deleting both the promoter and the gene body of 5430416N02Rik causes a more severe proliferation defect and a more profound impact on the transcriptome. The reduced proliferation of 5430416N02Rik knockout ESCs is mainly due to the down-regulation of Mid1 transcription, the activation of which requires the inter-chromosomal interaction between Mid1 and 5430416N02Rik loci. In summary, our data demonstrated that lncRNA 5430416N02Rik maintains the proliferation of ESCs by activating the expression of Mid1 through its function of mediating chromatin interaction.

2019-09-02 | GSE133435 | GEO

Comparative 3D Genome Architecture in Vertebrates

Project description:Comparative 3D Genome Architecture in Vertebrates

| PRJNA704983 | ENA

lncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 Expression through 3D Chromatin Architecture.

Project description:Both 3D chromatin architecture and long non-coding RNAs (lncRNAs) play essential roles in pluripotency maintenance. However, whether lncRNAs are involved in organizing 3D chromatin structure remains largely unexplored. We identified 39 lncRNAs bound by Klf4, among which we further revealed the 5430416N02Rik promoter is a chromatin interaction hub. Knockout of the 5430416N02Rik locus reduces the proliferation rate of embryonic stem cells (ESCs). Moreover, deleting both the promoter and the gene body of 5430416N02Rik causes a more severe proliferation defect and has a more profound impact on the transcriptome than deleting the gene body alone. The reduced proliferation of the 5430416N02Rik locus knockout ESCs is mainly due to the downregulation of Mid1, the expression of which requires the inter-chromosomal interaction between Mid1 and 5430416N02Rik loci. In summary, our data demonstrated that the lncRNA 5430416N02Rik gene locus maintains the fast proliferation of ESCs by activating the expression of Mid1 through chromatin interaction.

| S-EPMC7066321 | biostudies-literature

Cross-talk between enhancers, structural elements and activating transcription factors maintains the 3D architecture and expression of the CFTR gene.

Project description:Here we examine the mechanisms by which multiple cis-regulatory elements (CREs) at the CFTR locus coordinate its expression in intestinal epithelial cells. Using CRISPR/Cas9 to remove CREs, individually and in tandem, followed by assays of gene expression and higher-order chromatin structure (4C-seq), we reveal the cross-talk and dependency of two cell-specific intronic enhancers. The results also suggest an internal monitoring mechanism at the locus whereby alternative enhancers may be recruited when the normal sites are lost. Of note, activating transcription factors such as FOXA2 may contribute to this mechanism. Also, by deleting the 5' topologically-associating domain (TAD) boundary, we illustrate its relative contribution to normal mechanisms of CFTR gene expression and 3D gene architecture.

2024-10-17 | GSE186272 | GEO

Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

Project description:Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.

2022-04-12 | GSE167580 | GEO

Comparative 3D Genome Architecture in Vertebrates (Hi-C)

2022-04-12 | GSE167579 | GEO

Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

Project description:Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

| PRJNA704985 | ENA

Comparative 3D Genome Architecture in Vertebrates (Hi-C)

Project description:Comparative 3D Genome Architecture in Vertebrates (Hi-C)

| PRJNA704984 | ENA

Cross-talk between enhancers, structural elements and activating transcription factors maintains the 3D architecture and expression of the CFTR gene.

Project description:Cross-talk between enhancers, structural elements and activating transcription factors maintains the 3D architecture and expression of the CFTR gene.

| PRJNA773098 | ENA

Memory-induced 3D chromatin architecture in Huntington's disease (HD) mice [4C-seq]

Project description:Evaluation of the effect of procedural memory using the double-H maze (DH) on striatal 3D chromatin architecture in HD R6/1 mice

2022-10-06 | GSE157076 | GEO

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