NHLH2

nescient helix-loop-helix 2 | NSCL2, bHLHa34, HEN2

Enables RNA polymerase II-specific DNA-binding transcription factor binding activity and sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within with a positive effect on apoptotic process; hypothalamus gonadotrophin-releasing hormone neuron development; and peripheral nervous system development. Predicted to act upstream of or within several processes, including cell migration in hindbrain; male gonad development; and male mating behavior. Predicted to be located in chromatin. Predicted to be part of transcription regulator complex. Implicated in hypogonadotropic hypogonadism. [provided by Alliance of Genome Resources, Apr 2025]

Biological processes 24 terms

DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)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)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629)central nervous system development (GO:0007417)central nervous system development (GO:0007417)chromatin (GO:0000785)chromatin (GO:0000785)nucleus (GO:0005634)nucleus (GO:0005634)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 transcription by RNA polymerase II (GO:0006357)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific double-stranded DNA binding (GO:1990837)sequence-specific double-stranded DNA binding (GO:1990837)transcription coactivator binding (GO:0001223)transcription regulator complex (GO:0005667)

Expression (TPM)

TFs regulating NHLH2 0 TFs

Transcription factors with Perturb-seq knockdown data for NHLH2. 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 = NHLH2 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 NHLH2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NHLH2, 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
chr1:115,593,347–115,594,339	247.0 kb	Distal (>10kb) Multiome	81
chr1:115,641,554–115,643,092	198.9 kb	Distal (>10kb) Multiome	748
chr1:115,649,832–115,650,363	190.6 kb	Distal (>10kb) Multiome	246
chr1:115,771,492–115,772,197	68.8 kb	Distal (>10kb) Multiome	355
chr1:115,828,121–115,829,682	12.0 kb	Distal (>10kb) Multiome	408
chr1:115,833,914–115,834,099	6.6 kb	Proximal (<10kb)	33
chr1:115,837,650–115,839,828	2.8 kb	Proximal (<10kb) Multiome	304
chr1:115,840,598–115,840,885	at TSS	At TSS	36
chr1:115,924,342–115,925,363	84.1 kb	Distal (>10kb) Multiome	172
chr1:115,975,977–115,977,205	135.8 kb	Distal (>10kb) Multiome	536
chr1:116,138,890–116,139,376	298.5 kb	Distal (>10kb) Multiome	625

Genome Browser

Genomic view of the NHLH2 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.