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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE210345 | GEO | 2026/08/02

REPOSITORIES: GEO

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Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track contains chromatin interaction data from the University of Washington ENCODE group generated using 5C (Chromatin Conformation Capture Carbon Copy). The 5C method is used here to define short and long-range range interactions between transcription start sites (TSS) and DNaseI hypersensitive sites (DHS) or other genomic features. The 5C method is summarized below. Transcription factors bind to promoter-associated proteins, bringing the associated DNA sequences in close proximity to each other. Cross linking the DNA and proteins immobilizes these interactions and thus maintains their close proximity. Cleavage of the sample with restriction endonuclease followed by ligation results in hybrid molecules where a fragment with a regulatory element is physically associated with a fragment containing a TSS. The interactions are then detected by oligonucleotide-dependent, ligation-mediated assays, where one set of primers is complementary to the end of fragments with a TSS and the second set of primers are complementary to fragments with a feature. Primers are designed to the forward strand of the feature and the reverse strand of the TSS so that ligation only occurs between TSS and feature, not between different features. Specific interactions are detected by massively parallel sequencing. The data in this track comprises two different experiment types focusing on targeted regions: Gene-targeted project: Analysis of DNase I hypersensitive sites reveals many genes where there are multiple sites restricted to the cell type where a protein is observed to be expressed. These sites potentially identify regulatory sites for the gene. This set of experiments attempts to observe interactions between these DHS sites and transcription starts in 25 regions selected based on genes expressed in GM06990 (B-lymphocyte), BJ (foreskin fibroblast), HepG2 (liver cancer cell line), or SK-N-SH_RA (neuroblastoma cell line, SKNSH, differentiated with retinoic acid). Myc project: Genome wide association studies have identified SNPs linked to prostate, colon, and breast cancer in the gene desert region upstream of the myc gene. 5C of HindIII fragments interacting with those containing refSeq txStarts in this region were performed in 5 cell types: GM12878 (B-lymphocyte), CaCo2 (colon cancer cell line), LNCaP (prostate cancer cell line), MCF7 (breast cancer cell line), and K562 (erythroleukemia cell line). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

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

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