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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

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			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

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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

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

Gene expression profiles upon Meis1 knockout in Hoxa9/Meis1-induced AML

Project description:Meis1 is found cooperatively activated with Hoxa7/a9 in AML, and it indeed promotes leukemogenic activities of Hoxa9. It is important to identify downstream target genes of Meis1 to understand its cooperative activity with Hoxa9 in leukemogenesis. We used microarrays to detail the global programme of gene expression upon Meis1 knockout. Murine primary bone marrow cells of the Rosa26-Cre-ERT2 knock-in mouse were transformed by retroviral transduction of Hoxa9 and floxed Meis1. The immortalized bone marrow cells were treated with 2 μM of 4-hydroxytamoxifen to delete Meis1 cDNA. Gene expression profiles were compared between the original Hoxa9/Meis1-expressing cells and Meis1 deleted (Hoxa9 only) cells.

2015-01-01 | E-GEOD-50645 | biostudies-arrayexpress

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