Cut&tag: a powerful epigenetic tool for chromatin profiling

Figures & data

Figure 1. Schematic of scCuT&Tag applied to cultured cells and tissues in different species. Cells or nuclei suspension are isolated from cell culture, mice tissues, human tissues and plant tissues. These cells or nuclei are subjected to antibody incubation, pA-Tn5 binding and tagmentation, then they are combined with nanowell, 10× Genomics or split-pool system to distinguish cellular identity.

Figure 2. Multifactorial CUT&Tag strategies. (left) CUT&Tag 2 for 1 involves the use of two antibodies against H3K27me3 (heterochromatin marks) and Ser5P-RNAPII (active chromatin marks). This approach follows the same workflow as regular CUT&Tag, except for mixing two antibodies into the cells. The difference in fragment size and feature breadth (broad domains for H3K27me3 and narrow peak of Ser5P-RNAPII) are used together to calculate the deconvolution of two signals. (middle) in MuTi-Tag approach, each antibody is pre-incubated with the barcoded pA-Tn5, thus marking several different histone modifications and TFs in the same experiment. (right) nano-CUT&Tag is the use of nanobodies, single-chain antibodies directly fused to Tn5, where higher efficiency can be obtained without protein A.

Figure 3. The principle of CUT&Tag and CUT&Tag variants. In the CUT&Tag experiment, the primary antibody recognizes the target protein and then mediates the binding of the secondary antibody and the protein A/G-Tn5 fusion protein. Tn5 can precisely target and cleave the DNA sequence near the target protein in the presence of Mg²⁺. Simultaneously, the sequencing adapters will be inserted into both ends of DNA fragments by Tn5. For tissue section, spatial-CUT&Tag and MERFISH can be conducted. For cell suspension, CUT&Tag and CUT&Tag variants can be performed.

Table 1. CUT&Tag and CUT&Tag variants.

Technique	Antibody	Feature	Simultaneous profiling multiple proteins	Minimal cell number	Single cell detection	Spatial single-cell detection	Ref
CUT&Tag	Primary, secondary	Tn5-Protein A fusion	NO	1–60	YES	YES	[10]
scCUT&Tag	Primary, secondary	Single-cell resolution	NO	1	YES	YES	[10], [54], [61], [62]
TIP seq	Primary, secondary	T7 transcription based scCUT &Tag	NO	1	YES	Likely
CUT&Tag 2 in 1	Primary, secondary	Bulk and single-cell deconvolution CUT&Tag	YES	1	YES	Likely	[70]
multi-CUT&Tag	Primary, secondary	Multifactorial bulk and single-cell CUT&Tag	YES	1	YES	Likely	[71]
MulTI-Tag	Primary, secondary	Multifactorial bulk and single-cell CUT&Tag	YES	1	YES	Likely	[72]
NanoCUT&Tag	Primary, nanobody	Multifactorial single-chain antibodies fused to Tn5	YES	1	YES	Likely	[73], [74]

Table 2. The combinations of CUT&Tag with other omics.

Technique	Antibody	Feature	Simultaneous profiling multiple proteins	Minimal cell number	Single cell detection	Spatial single-cell detection	Ref
CoTECH	Primary, secondary	Joint scCUT &Tag and scRNA-seq	NO	1	YES	Likely	[65]
Paired-Tag	Primary, secondary	Joint scCUT &Tag and scRNA-seq	NO	1	YES	Likely	[67]
scCUT&Tag-pro	Primary, secondary	Joint scCUT &Tag and abundance of surface proteins	NO	1	YES	Likely	[68]
CUT&Tag-BS	Primary, secondary	CUT&Tag with bisulphite sequencing	NO	4000	NO	NO	[69]
Spatial-CUT&Tag	Primary, secondary	NGS based Spatial-CUT&Tag	NO	1	YES	YES	[75]
epigenomic MERFISH	Primary, secondary	Multiplexed imaging based Spatial-CUT&Tag	NO	1	YES	YES	[76]

Data availability statement

Data sharing is not applicable to this article as no new data were created or analysed in this study.