This gene is a member of the nesprin family of genes, that encode KASH (Klarsicht, Anc-1, Syne Homology) domain-containing proteins. In addition to the KASH domain, this protein also contains a coiled-coil and leucine zipper region, a spectrin repeat, and a kinesin-1 binding region. This protein localizes to the outer nuclear membrane, and is part of the linker of nucleoskeleton and cytoskeleton (LINC) complex in the nuclear envelope. LINC complexes are formed by SUN (Sad1, UNC-84)-KASH pairs, and are thought to mechanically couple nuclear components to the cytoskeleton. Mutations in this gene have been associated with progressive high-frequency hearing loss. The absence of this protein in mice also caused hearing loss, and changes in hair cell morphology in the ears. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
Transcription factors with Perturb-seq knockdown data for SYNE4. 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 = SYNE4 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 SYNE4, 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 |
|---|---|---|---|---|
| chr19:35,716,025–35,718,811 | 291.1 kb | Distal (>10kb) Multiome | 1018 | |
| chr19:35,740,083–35,741,430 | 268.0 kb | Distal (>10kb) Multiome | 829 | |
| chr19:35,744,481–35,746,086 | 263.5 kb | Distal (>10kb) Multiome | 679 | |
| chr19:35,748,170–35,749,017 | 260.4 kb | Distal (>10kb) Multiome | 749 | |
| chr19:35,757,432–35,758,657 | 250.7 kb | Distal (>10kb) Multiome | 851 | |
| chr19:35,767,601–35,768,256 | 240.8 kb | Distal (>10kb) Multiome | 276 | |
| chr19:35,775,066–35,776,063 | 233.3 kb | Distal (>10kb) Multiome | 474 | |
| chr19:35,784,357–35,785,306 | 224.1 kb | Distal (>10kb) Multiome | 183 | |
| chr19:35,860,621–35,861,651 | 147.5 kb | Distal (>10kb) Multiome | 299 | |
| chr19:35,868,369–35,868,860 | 140.3 kb | Distal (>10kb) Multiome | 320 | |
| chr19:35,869,343–35,870,482 | 138.8 kb | Distal (>10kb) Multiome | 492 | |
| chr19:35,899,240–35,900,760 | 109.1 kb | Distal (>10kb) Multiome | 751 | |
| chr19:35,931,342–35,932,167 | 77.1 kb | Distal (>10kb) Multiome | 835 | |
| chr19:35,936,083–35,936,704 | 72.4 kb | Distal (>10kb) Multiome | 417 | |
| chr19:35,986,945–35,987,622 | 21.6 kb | Distal (>10kb) Multiome | 363 | |
| chr19:35,994,796–35,995,940 | 13.6 kb | Distal (>10kb) Multiome | 897 | |
| chr19:36,008,519–36,009,006 | at TSS | At TSS | 427 | |
| chr19:36,009,229–36,009,633 | 416 bp | At TSS | 237 | |
| chr19:36,013,972–36,014,810 | 5.6 kb | Proximal (<10kb) Multiome | 623 | |
| chr19:36,032,424–36,033,187 | 24.0 kb | Distal (>10kb) Multiome | 179 | |
| chr19:36,053,782–36,055,591 | 45.7 kb | Distal (>10kb) Multiome | 1026 | |
| chr19:36,113,981–36,116,196 | 106.6 kb | Distal (>10kb) Multiome | 1052 | |
| chr19:36,127,575–36,128,707 | 119.2 kb | Distal (>10kb) Multiome | 942 | |
| chr19:36,139,425–36,141,811 | 131.1 kb | Distal (>10kb) Multiome | 1037 | |
| chr19:36,214,162–36,215,543 | 206.0 kb | Distal (>10kb) Multiome | 1008 | |
| chr19:36,245,106–36,245,849 | 236.7 kb | Distal (>10kb) Multiome | 153 |
Genomic view of the SYNE4 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.