77 / 2026-04-05 20:12:17

CTCF aligns single-cell TAD-like domain boundaries and stabilizes long-range active chromatin clusters

CTCF,single cell 3D genome,single cell omics

CTCF is a key architectural protein in the 3D genome, yet how its loss reshapes chromatin structure and transcription at single-cell resolution remains unclear. Using HiRES, which jointly profiles chromatin contacts and RNA from the same nucleus, we examined genome-wide effects of CTCF depletion. TAD-like domains (TLDs) across single cells remained largely unchanged in number and size after CTCF loss, but their boundaries became more variable, and pseudobulk analyses revealed reduced interactions within A compartments. To characterize higher-order organization, we develop SALTAFinder to identify Spatially Aggregated Long-distance TLD Assemblies (SALTAs), defined as clusters of TLDs occupying shared 3D space within single cells. A subset of SALTAs is enriched for highly expressed genes and super-enhancers, and decreases in frequency upon CTCF depletion. This structural reorganization coincided with a global reduction in per-cell RNA output, as indicated by HiRES and orthogonal measurements. Together, these findings suggest CTCF contributes to the maintenance of transcriptional capacity in part by stabilizing long-range active chromatin clusters.