TFE3
transcription factor binding to IGHM enhancer 3 | TFEA, bHLHe33

This gene encodes a basic helix-loop-helix domain-containing transcription factor that binds MUE3-type E-box sequences in the promoter of genes. The encoded protein promotes the expression of genes downstream of transforming growth factor beta (TGF-beta) signaling. This gene may be involved in chromosomal translocations in renal cell carcinomas and other cancers, resulting in the production of fusion proteins. Translocation partners include PRCC (papillary renal cell carcinoma), NONO (non-POU domain containing, octamer-binding), and ASPSCR1 (alveolar soft part sarcoma chromosome region, candidate 1), among other genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

Biological processes 41 terms
DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)chromatin (GO:0000785)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)humoral immune response (GO:0006959)humoral immune response (GO:0006959)lysosomal membrane (GO:0005765)lysosomal membrane (GO:0005765)lysosome organization (GO:0007040)negative regulation of cold-induced thermogenesis (GO:0120163)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of brown fat cell differentiation (GO:0090336)positive regulation of cell adhesion (GO:0045785)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)protein dimerization activity (GO:0046983)regulation of DNA-templated transcription (GO:0006355)regulation of osteoclast differentiation (GO:0045670)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific double-stranded DNA binding (GO:1990837)transcription cis-regulatory region binding (GO:0000976)
Expression (TPM)
TFE3 — as a Regulated Gene

TFs regulating TFE3 0 TFs

Transcription factors with Perturb-seq knockdown data for TFE3. 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 = TFE3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to TFE3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of TFE3, 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
chrX:48,801,126–48,802,845 241.5 kb Distal (>10kb) Multiome 734
chrX:48,891,080–48,891,988 151.7 kb Distal (>10kb) Multiome 525
chrX:48,897,163–48,898,345 145.5 kb Distal (>10kb) Multiome 672
chrX:48,911,574–48,912,414 131.4 kb Distal (>10kb) Multiome 671
chrX:48,917,179–48,917,999 126.0 kb Distal (>10kb) Multiome 468
chrX:48,918,412–48,919,792 124.3 kb Distal (>10kb) Multiome 693
chrX:48,957,469–48,959,105 85.1 kb Distal (>10kb) Multiome 722
chrX:49,001,538–49,002,676 41.0 kb Distal (>10kb) Multiome 540
chrX:49,039,840–49,040,493 3.3 kb Proximal (<10kb) Multiome 436
chrX:49,042,954–49,044,182 220 bp At TSS Multiome 664
chrX:49,053,328–49,054,050 10.3 kb Distal (>10kb) Multiome 403
chrX:49,071,863–49,072,612 28.7 kb Distal (>10kb) Multiome 107
chrX:49,073,903–49,074,451 30.7 kb Distal (>10kb) Multiome 464
chrX:49,100,885–49,101,855 57.9 kb Distal (>10kb) Multiome 562
chrX:49,155,633–49,156,658 112.8 kb Distal (>10kb) Multiome 524
chrX:49,163,555–49,164,377 120.6 kb Distal (>10kb) Multiome 485
chrX:49,166,140–49,166,713 123.1 kb Distal (>10kb) Multiome 416
chrX:49,184,219–49,185,254 141.1 kb Distal (>10kb) Multiome 389
chrX:49,186,113–49,186,660 143.1 kb Distal (>10kb) Multiome 589
chrX:49,190,730–49,191,899 147.8 kb Distal (>10kb) Multiome 636
chrX:49,199,793–49,200,448 156.8 kb Distal (>10kb) Multiome 806
chrX:49,230,792–49,231,268 187.6 kb Distal (>10kb) Multiome 221
chrX:49,268,786–49,270,236 226.0 kb Distal (>10kb) Multiome 603

Genome Browser

Genomic view of the TFE3 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.

chrX:48,791,126 – 49,280,236
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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