bioRxiv : the preprint server for biologyJul 10, 2026

Key proteins control how heparan sulfate is modified and binds to other molecules, found using CRISPR activation screens

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Updated Jul 14, 2026

Abstract

Genome-wide CRISPR activation screens identified syndecan-1 as a key enhancer of antithrombin binding to heparan sulfate.

Heparan sulfate proteoglycans are crucial for various biological processes through their interactions with extracellular ligands.
Different sulfation patterns on heparan sulfate chains dictate the specificity of ligand interactions.
Proteoglycan core proteins were revealed as significant regulators of heparan sulfate function.
Syndecan-1 significantly enhanced binding of antithrombin compared to other syndecan family members.
Increased levels of heparan sulfate were associated with the upregulation of syndecan family members, but only syndecan-1 improved antithrombin binding.
Syndecan-1-associated heparan sulfate chains showed higher 6-O-sulfation and were more effective substrates for specific sulfotransferases.

Simplified

Heparan sulfate proteoglycans (HSPGs) are essential cell surface and extracellular matrix glycoconjugates that mediate diverse biological processes through interactions between their heparan sulfate (HS) chains and extracellular ligands. While HS sulfation patterning is known to dictate ligand specificity, how cells control HS assembly to regulate these interactions remains incompletely understood. To systematically identify genetic modifiers of HS-protein interactions, we performed genome-wide CRISPR activation (CRISPRa) screens in HEK293T cells using binding of antithrombin (AT), which selectively recognizes 3- O -sulfated HS motifs, or the N -sulfation-specific antibody 10E4 as functional readouts. Strikingly, the screens revealed proteoglycan core proteins as key modulators of HS function. In particular, syndecan-1 (SDC1) emerged as a preferential enhancer of AT binding compared to other syndecan family members. Targeted upregulation of syndecan family members increased total HS levels, but only SDC1 enhanced AT binding. Structural and enzymatic analyses demonstrated that SDC1-associated HS chains contain elevated 6- O -sulfation and serve as superior substrates for 3- O -sulfotransferases relative to SDC2-associated HS chains. Additionally, SDC1 exhibited slower cell surface recovery, which was blocked by cycloheximide treatment, consistent with extended trafficking and biosynthetic processing. Overall, these findings indicate that proteoglycan core protein identity influences HS sulfation patterning and ligand-binding specificity and trafficking kinetics may contribute to core protein-dependent regulation of HS modification.

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Key proteins control how heparan sulfate is modified and binds to other molecules, found using CRISPR activation screens

Abstract

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