This gene encodes a member of the nerve growth factor family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protein. Binding of this protein to its cognate receptor promotes neuronal survival in the adult brain. Expression of this gene is reduced in Alzheimer's, Parkinson's, and Huntington's disease patients. This gene may play a role in the regulation of the stress response and in the biology of mood disorders. [provided by RefSeq, Nov 2015]
Transcription factors with Perturb-seq knockdown data for BDNF. 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 = BDNF 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 BDNF, 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 |
|---|---|---|---|---|
| chr11:27,443,724–27,444,393 | 256.6 kb | Distal (>10kb) Multiome | 91 | |
| chr11:27,444,522–27,445,324 | 255.4 kb | Distal (>10kb) Multiome | 199 | |
| chr11:27,471,035–27,473,509 | 227.7 kb | Distal (>10kb) Multiome | 780 | |
| chr11:27,506,080–27,507,386 | 193.7 kb | Distal (>10kb) Multiome | 861 | |
| chr11:27,628,672–27,629,755 | 71.2 kb | Distal (>10kb) Multiome | 92 | |
| chr11:27,634,338–27,635,109 | 65.7 kb | Distal (>10kb) Multiome | 115 | |
| chr11:27,696,533–27,696,669 | 3.8 kb | Proximal (<10kb) | 21 | |
| chr11:27,698,739–27,701,728 | 302 bp | At TSS Multiome | 518 | |
| chr11:27,705,790–27,706,183 | 5.3 kb | Proximal (<10kb) | 112 | |
| chr11:27,718,043–27,719,845 | 18.3 kb | Distal (>10kb) Multiome | 477 | |
| chr11:27,720,144–27,720,769 | 1.3 kb | Proximal (<10kb) | 306 | |
| chr11:27,721,736–27,723,344 | 22.3 kb | Distal (>10kb) Multiome | 381 | |
| chr11:27,795,831–27,797,062 | 96.0 kb | Distal (>10kb) Multiome | 361 |
Genomic view of the BDNF 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.