GLI2

GLI family zinc finger 2 | HPE9, THP1, THP2

This gene encodes a protein which belongs to the C2H2-type zinc finger protein subclass of the Gli family. Members of this subclass are characterized as transcription factors which bind DNA through zinc finger motifs. These motifs contain conserved H-C links. Gli family zinc finger proteins are mediators of Sonic hedgehog (Shh) signaling and they are implicated as potent oncogenes in the embryonal carcinoma cell. The protein encoded by this gene localizes to the cytoplasm and activates patched Drosophila homolog (PTCH) gene expression. It is also thought to play a role during embryogenesis. The encoded protein is associated with several phenotypes- Greig cephalopolysyndactyly syndrome, Pallister-Hall syndrome, preaxial polydactyly type IV, postaxial polydactyly types A1 and B. [provided by RefSeq, Jul 2008]

Member of: DE-8 DE-8.4 Developmental clusters: GC1

Biological processes 72 terms

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)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)anatomical structure morphogenesis (GO:0009653)axon guidance (GO:0007411)branching morphogenesis of an epithelial tube (GO:0048754)cellular response to virus (GO:0098586)centrosome (GO:0005813)cerebellar cortex morphogenesis (GO:0021696)ciliary basal body (GO:0036064)ciliary base (GO:0097546)ciliary base (GO:0097546)ciliary tip (GO:0097542)ciliary tip (GO:0097542)cilium (GO:0005929)cilium (GO:0005929)cytoplasm (GO:0005737)cytosol (GO:0005829)developmental growth (GO:0048589)double-stranded DNA binding (GO:0003690)embryonic digestive tract development (GO:0048566)epidermal cell differentiation (GO:0009913)floor plate formation (GO:0021508)hair follicle morphogenesis (GO:0031069)heart development (GO:0007507)hindbrain development (GO:0030902)hindgut morphogenesis (GO:0007442)kidney development (GO:0001822)lung development (GO:0030324)mammary gland development (GO:0030879)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription by RNA polymerase II (GO:0000122)neuron development (GO:0048666)non-motile cilium (GO:0097730)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)odontogenesis of dentin-containing tooth (GO:0042475)osteoblast development (GO:0002076)osteoblast differentiation (GO:0001649)pattern specification process (GO:0007389)pituitary gland development (GO:0021983)positive regulation of DNA replication (GO:0045740)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of T cell differentiation in thymus (GO:0033089)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)promoter-specific chromatin binding (GO:1990841)protein binding (GO:0005515)proximal/distal pattern formation (GO:0009954)regulation of gene expression (GO:0010468)regulation of transcription by RNA polymerase II (GO:0006357)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)skeletal system development (GO:0001501)smoothened signaling pathway (GO:0007224)smoothened signaling pathway (GO:0007224)smoothened signaling pathway (GO:0007224)spinal cord dorsal/ventral patterning (GO:0021513)spinal cord ventral commissure morphogenesis (GO:0021965)tube development (GO:0035295)ventral midline development (GO:0007418)ventral spinal cord development (GO:0021517)zinc ion binding (GO:0008270)

Expression (TPM)

TFs regulating GLI2 0 TFs

Transcription factors with Perturb-seq knockdown data for GLI2. 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 = GLI2 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 GLI2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of GLI2, 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
chr2:120,441,791–120,443,631	292.7 kb	Distal (>10kb) Multiome	511
chr2:120,465,595–120,466,904	269.6 kb	Distal (>10kb) Multiome	829
chr2:120,552,937–120,553,500	182.7 kb	Distal (>10kb) Multiome	583
chr2:120,564,474–120,565,342	171.1 kb	Distal (>10kb) Multiome	467
chr2:120,586,914–120,587,807	148.5 kb	Distal (>10kb) Multiome	147
chr2:120,654,402–120,654,894	81.3 kb	Distal (>10kb) Multiome	139
chr2:120,695,462–120,696,173	40.0 kb	Distal (>10kb) Multiome	393
chr2:120,709,378–120,710,130	26.1 kb	Distal (>10kb) Multiome	157
chr2:120,735,239–120,738,237	6 bp	At TSS Multiome	508
chr2:120,740,786–120,742,359	5.1 kb	Proximal (<10kb) Multiome	305
chr2:120,786,141–120,786,851	50.7 kb	Distal (>10kb) Multiome	86
chr2:120,938,028–120,938,489	202.5 kb	Distal (>10kb) Multiome	198
chr2:121,018,712–121,019,319	283.1 kb	Distal (>10kb) Multiome	208

Genome Browser

Genomic view of the GLI2 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.