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The 3D architecture of gene regulation in the distal convoluted tubule

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE210346 | GEO | 2026/08/02

REPOSITORIES: GEO

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Distal convoluted tubule.

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The 3D architecture of gene regulation in the distal convoluted tubule (RNA-Seq)

Project description:Cell-type specific gene expression patterns are essential for kidney function. This is governed by binding of polymerases and transcription (co)-factors to regulatory DNA elements that can either be located close to their target genes or at great genomic distances from their target genes. Therefore, the 3D structure of the genome is an essential factor in cell-type specific gene transcription. Here, we generated a chromosome conformation capture (Hi-C) map in a distal convoluted tubule (DCT) cell line with a 5kb resolution. To study the role of the 3D genome in transcriptional regulation in the DCT the Hi-C data was integrated with chromatin accessibility (ATAC-seq), gene expression (RNA-seq) and histone mark ChIP-seq data of the same cell line. Our analysis uncovered the basis of 3D genome characteristics in the DCT. Similar to other studies, promoter connectivity correlated with gene expression levels of the participating genes. As proof of principle, we studied the importance of long-range chromatin interactions in transcriptional regulation mediated by transcription factor HNF1β. Our analysis revealed that HNF1β controls the expression of housekeeping genes primarily by binding to promoters in close proximity of the transcription start site (TSS) of the gene, while the expression of developmental genes is regulated by both promoters and distal enhancers. Moreover, by employing a CRISPR/Cas9 enhancer mutant, we demonstrated that Caveolin-1 expression is regulated by an HNF1β-bound enhancer ~95kb from the TSS of the gene. In conclusion, we describe the first Hi-C map in a DCT cell line and demonstrate that the 3D architecture of the genome controls specificity of HNF1β-mediated gene transcription.

2026-08-02 | GSE210345 | GEO

The 3D architecture of gene regulation in the distal convoluted tubule

Project description:The 3D architecture of gene regulation in the distal convoluted tubule

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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description: Not available

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