CUT&Tag for efficient epigenomic profiling of small samples and single cells

TLDR

Chromatin features are critical for gene regulation, and mapping them in small samples at high resolution is essential for a complete understanding. The study introduces CUT&Tag, an enzyme‑tethering strategy that generates efficient high‑resolution sequencing libraries for profiling diverse chromatin components. CUT&Tag uses antibody‑guided protein A‑Tn5 transposase to produce high‑resolution fragment libraries with low background, enabling a one‑day, single‑tube workflow from live cells to sequencing‑ready libraries. The method was validated by profiling histone modifications, RNA Polymerase II, and transcription factors in low‑cell‑number and single‑cell samples.

Abstract

Abstract Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells.