Alpha-synuclein is a member of the synuclein family, which also includes beta- and gamma-synuclein. Synucleins are abundantly expressed in the brain and alpha- and beta-synuclein inhibit phospholipase D2 selectively. SNCA may serve to integrate presynaptic signaling and membrane trafficking. Defects in SNCA have been implicated in the pathogenesis of Parkinson disease. SNCA peptides are a major component of amyloid plaques in the brains of patients with Alzheimer's disease. Alternatively spliced transcripts encoding different isoforms have been identified for this gene. [provided by RefSeq, Feb 2016]
Transcription factors with Perturb-seq knockdown data for SNCA. 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 = SNCA 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 SNCA, 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 |
|---|---|---|---|---|
| chr4:89,609,404–89,610,571 | 227.1 kb | Distal (>10kb) Multiome | 122 | |
| chr4:89,640,712–89,641,562 | 195.9 kb | Distal (>10kb) Multiome | 327 | |
| chr4:89,836,019–89,838,409 | 76 bp | At TSS Multiome | 559 | |
| chr4:89,897,965–89,898,867 | 61.3 kb | Distal (>10kb) Multiome | 241 | |
| chr4:90,126,585–90,128,847 | 290.2 kb | Distal (>10kb) Multiome | 613 |
Genomic view of the SNCA 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.