GEO series

Af-CUT&Tag: A Sensitive and Antibody-Free Chromatin Profiling Method Using Genetically Encoded Tags and High-Affinity Binders Fused to Tn5

GSE283706 Homo sapiens; Mus musculus Genome binding/occupancy profiling by high throughput sequencing 65 samples Submitted 2024/12/15 Platform GPL34290Platform GPL34284

Summary

Conventional chromatin profiling techniques are often limited by antibody availability and performance. Here, we introduce Af-CUT&Tag, a target antibody-free method that overcomes these limitations by using CRISPR-integrated peptide tags (HiBiT/ALFA-tag) recognized by engineered binders (LgBiT/NbALFA) fused to a Tn5 transposase. Af-CUT&Tag eliminates dependence on traditional target antibodies, achieving robust specificity and sensitivity with as few as 500 cells. It provides high-quality chromatin profiles, with improved signal-to-noise ratios and library quality compared with conventional antibody-based counterparts, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration revealed dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g., Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a powerful tool for studying gene regulation in development, disease, and regeneration. Keywords: Antibody-Free CUT&Tag; Chromatin Binding; Epigenetic Profiling; Peptide-binder; Single-cell analysis

Published in

Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5

Wang X, Deng X, Qiu L et al. · Nature communications 2026 · PMID 41547832 · doi:10.1038/s41467-026-68454-9

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Direct links to NCBI, no account and no request form: the whole study as GSE283706_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 65 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA1195075 and SRA study SRP549873. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41547832) ↗

Study design

33 conditions, each sampled once — no replicated groups

SW480 cell,KI-RPB1-HiBiT,anti-RPB1(CUT&Tag), ×2 SW480 cell,KI-RPB1-HiBiT,LgBiT-Tn5(Af-CUT&Tag… ×2 SW480 cell,KI-RPB1-HiBiT,Nano-Tn5(nano-CUT&Ta… ×2 SW480 cell,KI-CTCT-HiBiT,nano-Tn5_anti-CTCF(n… ×2 SW480 cell,KI-CTCF-ALFA,NbALFA-Tn5(Af-CUT&Tag… ×2 SW480 cell,KI-CTCF-HiBiT,LgBiT-Tn5(Af-CUT&Tag… ×2 DLD-1 cell,KI-RPB1-ALFA-tag,NbALFA-Tn5(Af-CUT… ×2

Read from the first 40 of 65 sample titles: 33 distinct titles with little repetition. Check it against the sample list below before relying on it.

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