CUT&ID for 8 targets in HCT116 cells

ABSTRACT: Understanding how gene regulators bind DNA and interact with one another is essential for understanding gene expression, yet existing technologies typically measure either chromatin occupancy or protein–protein interactions in isolation, require high cell numbers, and/or depend on genetic engineering. Here, we develop CUT&ID, which simultaneously profiles DNA binding and proximal protein interactors of histone marks, transcription factors, and non-DNA-binding regulators without requiring crosslinking or tagging. CUT&ID is enabled by a fusion protein combining TurboID, protein A/G, and micrococcal nuclease, which drives sequential proximity biotinylation and targeted DNA cleavage from 1 million cells in a three-day workflow. Benchmarking against state-of-the-art methods demonstrated that CUT&ID achieves high signal-to-noise genomic profiles and robust interactor identification. For CTCF and SMARCA4, CUT&ID recovered peaks with strong motif enrichment and high overlap with ENCODE datasets, while proteomic profiling identified canonical interactors, including cohesin components and SWI/SNF complex members. Applying CUT&ID to a broader panel of gene regulators, including histone marks (H3K27ac), transcription factors (TCF7L2, JUN), and non-DNA-binding proteins (β-catenin, RAD21, HDAC1), revealed specific genomic landscapes and interaction networks, validating the method’s versatility. Together, these results establish CUT&ID as a powerful and broadly applicable technology for integrative mapping of gene regulator function.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Malignant Cell, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Anna Nordin  

LAB HEAD: Claudio Cantù

PROVIDER: PXD071610 | Pride | 2026-10-05

REPOSITORIES: Pride