HSPG2
heparan sulfate proteoglycan 2 | PRCAN, perlecan, SJS1

This gene encodes the perlecan protein, which consists of a core protein to which three long chains of glycosaminoglycans (heparan sulfate or chondroitin sulfate) are attached. The perlecan protein is a large multidomain proteoglycan that binds to and cross-links many extracellular matrix components and cell-surface molecules. It has been shown that this protein interacts with laminin, prolargin, collagen type IV, FGFBP1, FBLN2, FGF7 and transthyretin, etc., and it plays essential roles in multiple biological activities. Perlecan is a key component of the vascular extracellular matrix, where it helps to maintain the endothelial barrier function. It is a potent inhibitor of smooth muscle cell proliferation and is thus thought to help maintain vascular homeostasis. It can also promote growth factor (e.g., FGF2) activity and thus stimulate endothelial growth and re-generation. It is a major component of basement membranes, where it is involved in the stabilization of other molecules as well as being involved with glomerular permeability to macromolecules and cell adhesion. Mutations in this gene cause Schwartz-Jampel syndrome type 1, Silverman-Handmaker type of dyssegmental dysplasia, and tardive dyskinesia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

Member of: DE-4 DE-4.24 Developmental clusters: GC6
Biological processes 41 terms
Golgi lumen (GO:0005796)Golgi lumen (GO:0005796)amyloid-beta binding (GO:0001540)basement membrane (GO:0005604)basement membrane (GO:0005604)brain development (GO:0007420)brain development (GO:0007420)calcium ion binding (GO:0005509)cell differentiation (GO:0030154)cell differentiation (GO:0030154)circulatory system development (GO:0072359)circulatory system development (GO:0072359)extracellular exosome (GO:0070062)extracellular matrix (GO:0031012)extracellular matrix (GO:0031012)extracellular matrix (GO:0031012)extracellular matrix structural constituent conferring compression resistance (GO:0030021)extracellular matrix structural constituent conferring compression resistance (GO:0030021)extracellular region (GO:0005576)extracellular region (GO:0005576)extracellular region (GO:0005576)focal adhesion (GO:0005925)gel phase of basement membrane (GO:0140148)inflammatory response (GO:0006954)integrin binding (GO:0005178)lipid metabolic process (GO:0006629)low-density lipoprotein particle receptor binding (GO:0050750)lysosomal lumen (GO:0043202)microfibril (GO:0001527)molecular adaptor activity (GO:0060090)negative regulation of amyloid fibril formation (GO:1905907)negative regulation of angiogenesis (GO:0016525)negative regulation of neuron apoptotic process (GO:0043524)negative regulation of synaptic transmission, cholinergic (GO:0032223)neuromuscular junction (GO:0031594)neuron projection (GO:0043005)plasma membrane (GO:0005886)plasma membrane protein complex (GO:0098797)protein binding (GO:0005515)protein localization to synapse (GO:0035418)receptor-mediated endocytosis (GO:0006898)
Expression (TPM)
HSPG2 — as a Regulated Gene

TFs regulating HSPG2 0 TFs

Transcription factors with Perturb-seq knockdown data for HSPG2. 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 = HSPG2 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 HSPG2

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of HSPG2, 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
chr1:21,638,784–21,640,464 297.5 kb Distal (>10kb) Multiome 542
chr1:21,651,625–21,652,424 285.4 kb Distal (>10kb) Multiome 367
chr1:21,659,145–21,659,637 277.9 kb Distal (>10kb) Multiome 960
chr1:21,668,987–21,670,050 267.8 kb Distal (>10kb) Multiome 743
chr1:21,782,310–21,784,177 153.9 kb Distal (>10kb) Multiome 1096
chr1:21,814,299–21,814,932 122.7 kb Distal (>10kb) Multiome 227
chr1:21,922,465–21,923,180 14.5 kb Distal (>10kb) Multiome 263
chr1:21,933,771–21,934,095 3.2 kb Proximal (<10kb) 267
chr1:21,936,519–21,938,007 117 bp At TSS Multiome 630
chr1:21,944,503–21,944,715 7.2 kb Proximal (<10kb) 94
chr1:22,024,858–22,026,137 88.2 kb Distal (>10kb) Multiome 937
chr1:22,052,314–22,053,858 115.4 kb Distal (>10kb) Multiome 912
chr1:22,142,284–22,143,888 206.0 kb Distal (>10kb) Multiome 298
chr1:22,154,320–22,155,232 217.5 kb Distal (>10kb) Multiome 103

Genome Browser

Genomic view of the HSPG2 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.

chr1:21,628,784 – 22,165,232
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq