Tight junctions represent one mode of cell-to-cell adhesion in epithelial or endothelial cell sheets, forming continuous seals around cells and serving as a physical barrier to prevent solutes and water from passing freely through the paracellular space. These junctions are comprised of sets of continuous networking strands in the outwardly facing cytoplasmic leaflet, with complementary grooves in the inwardly facing extracytoplasmic leaflet. This gene encodes a component of tight junction strands, which is a member of the claudin family. The protein is an integral membrane protein and is one of the entry cofactors for hepatitis C virus. The gene methylation may be involved in esophageal tumorigenesis. This gene is adjacent to another family member CLDN9 on chromosome 16.[provided by RefSeq, Aug 2010]
Transcription factors with Perturb-seq knockdown data for CLDN6. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = CLDN6 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CLDN6, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr16:2,720,741–2,721,896 | 296.9 kb | Distal (>10kb) Multiome | 758 | |
| chr16:2,751,637–2,753,398 | 265.7 kb | Distal (>10kb) Multiome | 1074 | |
| chr16:2,776,766–2,778,256 | 240.8 kb | Distal (>10kb) Multiome | 828 | |
| chr16:2,867,958–2,868,665 | 149.8 kb | Distal (>10kb) Multiome | 960 | |
| chr16:2,882,042–2,883,813 | 135.2 kb | Distal (>10kb) Multiome | 838 | |
| chr16:2,904,002–2,906,321 | 113.9 kb | Distal (>10kb) Multiome | 994 | |
| chr16:2,911,480–2,912,624 | 106.3 kb | Distal (>10kb) Multiome | 784 | |
| chr16:2,963,159–2,965,475 | 54.2 kb | Distal (>10kb) Multiome | 628 | |
| chr16:2,968,641–2,970,561 | 49.0 kb | Distal (>10kb) Multiome | 1039 | |
| chr16:2,979,651–2,981,140 | 37.7 kb | Distal (>10kb) Multiome | 795 | |
| chr16:2,981,390–2,982,257 | 36.4 kb | Distal (>10kb) Multiome | 460 | |
| chr16:3,003,612–3,004,589 | 14.1 kb | Distal (>10kb) Multiome | 652 | |
| chr16:3,007,583–3,008,956 | 9.7 kb | Proximal (<10kb) Multiome | 514 | |
| chr16:3,009,722–3,010,376 | 8.1 kb | Proximal (<10kb) Multiome | 395 | |
| chr16:3,017,242–3,018,799 | 3 bp | At TSS Multiome | 451 | |
| chr16:3,019,969–3,022,268 | 2.1 kb | Proximal (<10kb) Multiome | 963 | |
| chr16:3,022,369–3,022,785 | 4.2 kb | Proximal (<10kb) | 440 | |
| chr16:3,022,890–3,024,532 | 6.0 kb | Proximal (<10kb) Multiome | 933 | |
| chr16:3,027,854–3,029,038 | 10.2 kb | Distal (>10kb) Multiome | 546 | |
| chr16:3,036,222–3,037,148 | 18.7 kb | Distal (>10kb) Multiome | 256 | |
| chr16:3,045,413–3,047,408 | 28.0 kb | Distal (>10kb) Multiome | 510 | |
| chr16:3,058,226–3,060,102 | 41.2 kb | Distal (>10kb) Multiome | 769 | |
| chr16:3,098,550–3,100,475 | 82.1 kb | Distal (>10kb) Multiome | 454 | |
| chr16:3,106,146–3,106,906 | 88.5 kb | Distal (>10kb) Multiome | 851 | |
| chr16:3,123,818–3,124,940 | 106.2 kb | Distal (>10kb) Multiome | 800 | |
| chr16:3,134,425–3,135,445 | 116.8 kb | Distal (>10kb) Multiome | 752 | |
| chr16:3,149,357–3,151,137 | 132.5 kb | Distal (>10kb) Multiome | 975 | |
| chr16:3,152,009–3,153,129 | 134.6 kb | Distal (>10kb) Multiome | 889 | |
| chr16:3,156,990–3,157,742 | 139.2 kb | Distal (>10kb) Multiome | 680 | |
| chr16:3,158,260–3,159,345 | 140.7 kb | Distal (>10kb) Multiome | 764 | |
| chr16:3,171,474–3,172,591 | 154.0 kb | Distal (>10kb) Multiome | 574 | |
| chr16:3,174,125–3,174,566 | 156.1 kb | Distal (>10kb) Multiome | 371 | |
| chr16:3,175,429–3,175,953 | 157.5 kb | Distal (>10kb) Multiome | 483 | |
| chr16:3,182,514–3,183,488 | 164.7 kb | Distal (>10kb) Multiome | 690 | |
| chr16:3,187,874–3,189,822 | 171.3 kb | Distal (>10kb) Multiome | 679 | |
| chr16:3,191,282–3,192,194 | 173.6 kb | Distal (>10kb) Multiome | 509 | |
| chr16:3,234,780–3,235,610 | 217.1 kb | Distal (>10kb) Multiome | 845 | |
| chr16:3,263,988–3,264,941 | 246.4 kb | Distal (>10kb) Multiome | 923 | |
| chr16:3,282,413–3,283,892 | 264.9 kb | Distal (>10kb) Multiome | 964 | |
| chr16:3,305,073–3,306,009 | 287.3 kb | Distal (>10kb) Multiome | 681 |
Genomic view of the CLDN6 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.