TCF4

transcription factor 4 | E2-2, ITF2, SEF2-1B, bHLHb19

This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor. The encoded protein recognizes an Ephrussi-box ('E-box') binding site ('CANNTG') - a motif first identified in immunoglobulin enhancers. This gene is broadly expressed, and may play an important role in nervous system development. Defects in this gene are a cause of Pitt-Hopkins syndrome. In addition, an intronic CTG repeat normally numbering 10-37 repeat units can expand to >50 repeat units and cause Fuchs endothelial corneal dystrophy. Multiple alternatively spliced transcript variants that encode different proteins have been described. [provided by RefSeq, Jul 2016]

Member of: DE-9 DE-9.2 Developmental clusters: GC3

Biological processes 48 terms

DNA binding (GO:0003677)DNA binding (GO:0003677)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)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)E-box binding (GO:0070888)E-box binding (GO:0070888)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)TFIIB-class transcription factor binding (GO:0001093)TFIIB-class transcription factor binding (GO:0001093)beta-catenin-TCF complex (GO:1990907)beta-catenin-TCF7L2 complex (GO:0070369)chromatin (GO:0000785)chromatin (GO:0000785)chromatin (GO:0000785)chromatin binding (GO:0003682)identical protein binding (GO:0042802)identical protein binding (GO:0042802)negative regulation of DNA-templated transcription (GO:0045892)nucleoplasm (GO:0005654)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 neuron differentiation (GO:0045666)positive regulation of neuron differentiation (GO:0045666)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)protein heterodimerization activity (GO:0046982)protein heterodimerization activity (GO:0046982)protein-DNA complex assembly (GO:0065004)protein-DNA complex assembly (GO:0065004)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific double-stranded DNA binding (GO:1990837)transcription corepressor activity (GO:0003714)transcription regulator complex (GO:0005667)transcription regulator complex (GO:0005667)transcription regulator complex (GO:0005667)

Expression (TPM)

TFs regulating TCF4 0 TFs

Transcription factors with Perturb-seq knockdown data for TCF4. 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 = TCF4 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

Rows:

Elements linked to TCF4

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of TCF4, 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.

Element	Dist. to TSS	Link type	TFs
chr18:55,040,317–55,041,192	549.1 kb	Distal (>10kb) Multiome	104
chr18:55,321,567–55,322,018	at TSS	At TSS	344
chr18:55,322,133–55,322,873	267.4 kb	Distal (>10kb) Multiome	382
chr18:55,438,990–55,439,594	150.6 kb	Distal (>10kb) Multiome	111
chr18:55,466,657–55,467,846	122.8 kb	Distal (>10kb) Multiome	159
chr18:55,572,972–55,573,887	16.3 kb	Distal (>10kb) Multiome	122
chr18:55,582,376–55,582,628	3.5 kb	Proximal (<10kb)	116
chr18:55,587,477–55,588,617	1.7 kb	Proximal (<10kb) Multiome	353
chr18:55,589,695–55,590,485	74 bp	At TSS Multiome	572
chr18:55,747,941–55,749,345	158.7 kb	Distal (>10kb) Multiome	394
chr18:56,637,964–56,639,090	1048.8 kb	Distal (>10kb) Multiome HiCAR	800
chr18:56,650,881–56,651,893	1061.5 kb	Distal (>10kb) Multiome HiCAR	834

Genome Browser

Genomic view of the TCF4 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.