Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

3D chromatin organization involving MEIS1 factor in the cis-regulatory landscape of GJB2

ABSTRACT: 3D chromatin organization involving MEIS1 factor in the cis-regulatory landscape of GJB2

PROVIDER: PRJNA830351 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18850355.fastq.gz	Fastqsanger.gz
	SRR18850356.fastq.gz	Fastqsanger.gz
	SRR18850357.fastq.gz	Fastqsanger.gz
	SRR18850358.fastq.gz	Fastqsanger.gz
	SRR18850359.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

3D chromatin organization involving MEIS1 factor in the cis-regulatory landscape of GJB2

Project description:To study GJB2 gene regulation, we used Circular Chromosome Conformation Capture technique (4C) to analyse chromatin interactions inside DFNB1 locus.

2022-07-13 | GSE201205 | GEO

Characterization of GJB2 cis-regulatory elements in the DFNB1 locus

Project description:Although most disease-causing variants are within coding region of genes, it is now well established that cis-acting regulatory sequences, depending on 3D-chromatin organization, are required for temporal and spatial control of gene expression. Disruptions of such regulatory elements and/or chromatin conformation are likely to play a critical role in human genetic disease. Hence, recurrent monoallelic cases of the most common hereditary type of nonsyndromic hearing loss (i.e. DFNB1) carrying out only one identified pathogenic allele, led to strongly suggest the presence of uncharacterized distal cis-acting elements in the missing allele. Herewith, we study the spatial organization of a large DFNB1 locus encompassing the gap junction protein beta 2 (GJB2) gene, the most frequently mutated gene in this inherited hearing loss, with the chromosome conformation capture carbon copy technology (5C). By combining this approach with functional activity reporter assays and mapping of CCCTC-binding factor (CTCF) along the DFNB1 locus by quantitative real-time PCR chromatin immunoprecipitation, we identify a novel set of cooperating GJB2 cis-acting elements and propose a DFNB1 three-dimensional looping regulation model. A loop chromatin forming, allows bringing closer enhancers to the GJB2 promoter, but also avoids GJB2 silencing with an enhancer-blocking insulator activity.

2020-03-26 | GSE128881 | GEO

3D Chromatin Organization Involving MEIS1 Factor in the <i>cis</i>-Regulatory Landscape of <i>GJB2</i>.

Project description:The human genome is covered by 8% of candidate cis-regulatory elements. The identification of distal acting regulatory elements and an understanding of their action are crucial to determining their key role in gene expression. Disruptions of such regulatory elements and/or chromatin conformation are likely to play a critical role in human genetic diseases. Non-syndromic hearing loss (i.e., DFNB1) is mostly due to GJB2 (Gap Junction Beta 2) variations and DFNB1 large deletions. Although several GJB2 cis-regulatory elements (CREs) have been described, GJB2 gene regulation remains not well understood. We investigated the endogenous effect of these CREs with CRISPR (clustered regularly interspaced short palindromic repeats) disruptions and observed GJB2 expression. To decipher the GJB2 regulatory landscape, we used the 4C-seq technique and defined new chromatin contacts inside the DFNB1 locus, which permit DNA loops and long-range regulation. Moreover, through ChIP-PCR, we determined the involvement of the MEIS1 transcription factor in GJB2 expression. Taken together, the results of our study enable us to describe the 3D DFNB1 regulatory landscape.

| S-EPMC9266880 | biostudies-literature

Characterization of GJB2 cis-regulatory elements in the DFNB1 locus

Project description:Characterization of GJB2 cis-regulatory elements in the DFNB1 locus

| PRJNA529209 | ENA

The pathogenesis of common Gjb2 mutation associated with human hereditary deafness in mice

Project description:Mutations in GJB2 (Gap junction protein beta 2) are the most common genetic cause of non-syndromic hereditary deafness in humans, especially the 35delG and 235delC mutations. Owing to the homozygous-lethal of Gjb2 mutation in mice, there are currently no perfect mouse models carrying Gjb2 mutation to mimic human hereditary deafness and unveil the pathogenesis. Here, we first constructed heterozygous mutant mice, Gjb2+/35delG and Gjb2+/235delC, through androgenic haploid embryonic stem cells (AG-haESCs) mediated semi-cloning technology, which showed normal hearing function at P28. Furthermore, a homozygous mutant mouse model, Gjb235delG/35delG, was generated via enhanced tetraploid embryo complementation, which exhibited profound hearing loss like human patients at P14. Mechanism analysis showed that Gjb2 35delG disrupts the formation of intercellular gap junction channel and tunnel of Corti, and hair cell mechanotransduction, rather than the development of hair cells. Collectively, our study provides ideal mouse models for understanding the pathogenic mechanism and opens up a new avenue for investigating the treatment for DFNB1A-related hereditary deafness.

2023-05-12 | GSE215106 | GEO

Gene expression and functional analysis of GJB2 mutated HaCaT cell lines [G130V]

Project description:Vohwinkel syndrome, VS (OMIM#124500), a rare autosomal dominant genetic disease, with less than 50 reported cases in the literature. Although clinical symptoms of VS are complex, which are caused by GJB2 mutation is more typical. To explore related differential genes and signaling pathways of Vohwinkel syndrome (VS) caused by mutations of GJB2. Human Gene Expression Array of the GJB2-VS mutated (G130V) HaCaT cell lines and identified distinct classes of up- and down- regulated genes during this process.

2023-09-30 | GSE200384 | GEO

Gene expression and functional analysis of GJB2 mutated HaCaT cell lines [D66H]

Project description:Vohwinkel syndrome, VS (OMIM#124500), a rare autosomal dominant genetic disease, with less than 50 reported cases in the literature. Although clinical symptoms of VS are complex, which are caused by GJB2 mutation is more typical. To explore related differential genes and signaling pathways of Vohwinkel syndrome (VS) caused by mutations of GJB2. Human Gene Expression Array of two types of GJB2-VS mutated (G130V and D66H) HaCaT cell lines and identified distinct classes of up- and down- regulated genes during this process.

2023-09-30 | GSE200386 | GEO

Meis1 genomics

Project description:Meis1 function in leukemogenesis

| PRJEB50012 | ENA

Cell-specific delivery of GJB2 restores auditory function in mouse models of DFNB1 deafness and mediates appropriate expression in NHP cochlea

Project description:Mutations in the GJB2 gene cause DFNB1, the most common hereditary hearing loss. GJB2 is expressed by cochlear epithelial cells and fibrocytes, but not by sensory hair cells or neurons. Attempts to treat DFNB1 mouse models with gene therapy have not substantially restored function, as inappropriate expression in hair cells and neurons might compromise their electrical activity. Here, we use ATAC-seq to identify candidate gene regulatory elements (GREs) that can drive cell-type-specific expression of GJB2. HA-tagged GJB2, delivered to a conditional knockout mouse with AAV vectors carrying GREs, is expressed by the appropriate cells, prevents degeneration, and rescues hearing by only 10–20 dB. In a Gjb2 partial knockdown model, a vector lacking HA prevents degeneration and completely restores hearing. In cynomolgus monkey cochleas, human GJB2.HA delivered with similar vectors is located in the appropriate cell types and causes little or no compromise of hearing sensitivity. Together, these findings suggest that GRE-mediated expression of GJB2 can prevent hearing loss in DFNB1 patients.

2025-10-21 | GSE308613 | GEO

RNA-seq of human glioblastoma (GBM) cell lines treated with shRNA against GJB2, SCN9A, or non-targeted controls

Project description:Ion channels and related proteins of the ion permeome (IP) are common drug targets; however, their roles in cancer remain understudied. We performed a computational, pan-cancer analysis of druggable IP genes to prioritise targets for therapeutic and biomarker development. Two candidate biomarkers in glioblastoma (GBM), GJB2 and SCN9A, associated with poor prognosis in multiple datasets, as well as inter- and intratumoral heterogeneity and malignant cell types. We used shRNA to knock down GJB2 (G5) and SCN9A (S3) in patient-derived GBM cells (729) in triplicates and performed whole transcriptome sequencing to profile the transcriptome-wide changes. Pathway enrichment identified neural projection and proliferation pathways were significantly dysregulated in GJB2 and SCN9A GBM cell line knockdowns compared to non-targeted shRNA controls (Scr). Our study underlines altered bioelectrical signalling as a cancer hallmark and provides a catalogue of IP genes for functional experiments and therapy development.

2023-09-29 | E-MTAB-12859 | biostudies-arrayexpress

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