CUT&Tag: A Technology for Protein-DNA Interaction Studies
Introduction
This kit optimizes the reagent components of the original CUT&Tag method, featuring exclusively designed elements such as a primary antibody binding enhancer and a DNA fragment release enhancer (1). It also improves experimental procedures, enhancing the ability to detect transcription factor binding profiles, making it particularly suitable for CUT&Tag experiments focusing on transcription factors.
Figure 1. CUT&Tag Technical schematic
Technical Principles
A defined antibody (e.g., anti-H3K27ac) is first bound in situ to its cognate chromatin protein. The complex is then tethered to an A–Tn5 transposase fusion protein. Activation of Tn5 cleavage restricts fragmentation to chromatin regions directly occupied by the antibody-targeted protein, yielding a high-resolution, low-background fragment library with high efficiency.
Applications
1.H3K27ac Function: Maps enhancer landscapes and identifies super-enhancers.
2.H3K4me3 Function: Marks activated promoter regions near transcription start sites (TSSs).
3.Histone Lactylation (Kla) Function: Enriched at gene promoters, linked to Warburg effect-associated processes (e.g., angiogenesis, hypoxia, macrophage polarization) and activation of related genes.
4.Histone Crotonylation (Kcr) Function: Correlates with active transcription and gene activation, regulating gene expression and gametogenesis. Also implicated in RNA splicing, protein synthesis/degradation, DNA replication/repair, endocytosis, and cell-cell junctions.
5.DNA G-Quadruplex (G4) Function: Localizes to gene promoters, 5'UTRs, and telomeres, modulating DNA replication, transcription, and genomic stability. G4 structures act as regulatory switches by blocking or facilitating transcription factor binding, with implications in cancer and neurodegenerative diseases.
6.Explores protein-DNA interactions to elucidate regulatory networks.
Advantages
1.Low cell input
2.Easy operation, all steps completed in one tube
3.High signal-to-noise ratio (low background), excellent reproducibility
Sample Types and Requirements
1. Limited to human, mouse, and rat cells, tissues, and total RNA; other species require evaluation.
2. Cells：2×10^5-5×10^5 cells/sample
Bioinformatic Analysis
1. Genome alignment analysis
2. Genome enrichment analysis
2.1 Basic information of enriched regions
2.2 Distribution characteristics of enriched regions
2.3 GO analysis of peak-associated genes
2.4 KEGG analysis of peak-associated genes
2.5 GO and KEGG analysis of differential peak-associated genes
3. Motif analysis of enriched regions
4. Super-Enhancer analysis (H3K27ac antibody, BRD4 antibody)
Figure 2. IGV peak plots
Demo
Figure 3. CUT&Tag QC
Figure 4. Epibiotek uses CUT&Tag to detect the read coverage map of histone modification H3K27me3, showing the CUT&Tag H3K27me3 peaks (second track) and comparing them with the literature data (first track)[1]
Figure 5. Epibiotek used CUT&Tag to detect the TSS distribution of H3K27me3 in the heat map (left column), and compared with the literature data (right column)[1]
Figure 6. Identification and analysis of enhancer and super-enhancer
Figure 7. Signal enrichment map of enhancer and super-enhancer
Figure 8. Figure of super-enhancer identification and quantity analysis
Figure 9. Prediction of super-enhancer binding transcription factors
Figure 10. Core transcription factor regulatory circuit（CRC）
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CUT&Tag technical service for Epibiotek
A variety of histone modification antibodies and transcription factor antibodies are available free of charge
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Epibiotek also provides ChIP-seq technical services
Figure 11. The heat map showed that H3K9la CUT&Tag sequencing signals were significantly enriched in TBD0220TR cells
Project Articles
1. Adv Sci：Histone H3K9 Lactylation Confers Temozolomide Resistance in Glioblastoma via LUC7L2-Mediated MLH1 Intron Retention (2)
The study combined techniques such as CUT&Tag, SLAM-seq and RNA-seq，not only shed light on the mechanism of lactylation in GBM TMZ resistance but also provide a potential combined therapeutic strategy for clinical GBM treatment.
Figure 12. Most of the enriched peaks of H3K9la upregulated in TBD0220TR cells were located in the promoter region
Figure 13. The IGV plot shows the H3K9la peak on the LUC7L2 promoter
Figure 14. CUT&Tag identified the SE driving gene ZFP36L1
2. Elife：Super-enhancer-driven ZFP36L1 promotes PD-L1 expression in infiltrative gastric cancer (3)
Using H3K27ac CUT&Tag sequencing, this study uncovered the super-enhancer (SE) heterogeneity between infiltrative and expansive gastric cancer (GC). A marked enrichment of the ZFP36L1 SE was observed in infiltrative tumors, and treatment with the SE inhibitors JQ1 and THZ1 confirmed that this element drives ZFP36L1 transcription. Mechanistically, SPI1, a key SE-bound transcription factor, cooperates with BRD4 to activate ZFP36L1 expression. ZFP36L1 in turn degrades HDAC3 mRNA, relieving its histone-deacetylase-mediated repression of the PD-L1 promoter and thereby promoting IFN-γ-induced PD-L1 up-regulation, which facilitates immune evasion.
References
[1] Kaya-Okur HS, Wu SJ, Codomo CA, et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun. 2019 Apr 29;10(1):1930.
[2] Yue Q, Wang Z, Shen Y, Lan Y, Zhong X, Luo X, Yang T, Zhang M, Zuo B, Zeng T, Lu J, Wang Y, Liu B, Guo H. Histone H3K9 Lactylation Confers Temozolomide Resistance in Glioblastoma via LUC7L2-Mediated MLH1 Intron Retention. Adv Sci (Weinh). 2024 May;11(19):e2309290. （EPIBIOTEK® Project Publications）
[3] Wei X, Liu J, Cheng J, et al. Super-enhancer-driven ZFP36L1 promotes PD-L1 expression in infiltrative gastric cancer. Elife. 2024;13:RP96445. Published 2024 Oct 7.
[4] Zhou J, Wang S, Nie D, et al. Super-enhancer landscape reveals leukemia stem cell reliance on X-box binding protein 1 as a therapeutic vulnerability. Sci Transl Med. 2021 Sep 22;13(612):eabh3462. （EPIBIOTEK® Project Publications）
[5] Huang Y, Wang X, Hu R, Pan G, Lin X. SOX2 regulates paclitaxel resistance of A549 non‑small cell lung cancer cells via promoting transcription of ClC‑3. Oncol Rep. 2022 Oct;48(4):181. （EPIBIOTEK® Project Publications）
[6] Yue Q, Wang Z, Shen Y, et al. Histone H3K9 Lactylation Confers Temozolomide Resistance in Glioblastoma via LUC7L2-Mediated MLH1 Intron Retention. Adv Sci (Weinh). 2024;11(19):e2309290. （EPIBIOTEK® Project Publications）