4 CUT&RUN and CUT&Tag applications to inspire your research in 2025
CUT&RUN and CUT&Tag are powerful chromatin mapping tools driving innovative research. Over the years, we have written comprehensive blog posts comparing these methods, detailed their advantages over ChIP-seq, and developed a robust Tech Support Center to help scientists optimize their experiments. But one of the best ways to truly appreciate the power of these assays is to explore how other researchers are using them. In this blog, we’ll highlight four exciting CUT&RUN and CUT&Tag applications from the literature to inspire your next breakthrough.
With an ever-growing number of citations, EpiCypher’s CUTANA™ CUT&RUN and CUT&Tag kits have become indispensable for researchers tackling complex questions in gene regulation, development, and disease. In 2024, CUT&RUN and CUT&Tag were pivotal in uncovering groundbreaking insights across immunology, developmental biology, and disease mechanisms, paving the way for more exciting applications in 2025. Below, we spotlight four studies that highlight how these technologies are driving innovation in chromatin mapping, from T-cell immunotherapies to epigenetic regulation in livestock, and beyond.
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EZH2 inhibition enhances T cell immunotherapies by inducing lymphoma immunogenicity and improving T cell function
Isshiki et al. Cancer Cell, 2024. PMID: 39642889
Chromatin mapping assay: CUT&RUN
EpiCypher Products: CUTANA™ ChIC/CUT&RUN Kit (14-1048)
Cell types: Mouse primary germinal center (GC) B cells; mouse T follicular lymphoma (TFL) cells; patient-derived xenograft (PDX) model of EZB-DLBCL
Target: H3K27me3
Background: CAR T-cell therapies have revolutionized blood cancer treatment, but durable remission remains a challenge for many patients. Lymphoma patients with mutations in the H3K27 methyltransferase EZH2 often experience poor outcomes following CAR T-cell therapy, suggesting an important role for epigenetics in therapy success.
Description: In this study, Isshiki et al. demonstrated that pretreatment with the EZH2 inhibitor Tazemetostat significantly improved CAR T-cell efficacy in mouse and patient-derived lymphoma models. Key findings included:
- Enhanced T-cell recruitment to lymphoma cells.
- Reduced T-cell exhaustion.
- Increased memory T-cell populations.
Together, these findings indicate that EZH2 inhibitors and CAR T-cell therapies can work synergistically to combat remission-resistant lymphoma.
CUT&RUN Application: The team used CUTANA™ CUT&RUN to measure H3K27me3 levels, as a direct readout of EZH2 activity. Tazemetostat treatment resulted in a significant reduction of H3K27me3, directly linking EZH2 inhibition to changes in T-cell behavior.
Future Impact:This study highlights how epigenetic modulation can enhance immunotherapies and sets the stage for new approaches to improve CAR T-cell therapy for treatment-resistant cancers.
Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development
Innis & Cabot. Cancer Cell, 2024. PMID: 38773546
Chromatin mapping assay: CUT&RUN
EpiCypher Products: CUTANA™ ChIC/CUT&RUN Kit (14-1048), H3K4me3 antibody (13-0041), BRG1/SMARCA4 antibody (13-2002), and IgG antibody (13-0042)
Cell types: Porcine trophectoderm (Ptr2) and porcine fetal fibroblasts (PFF)
Targets: H3K4me3, BRG1/SMARCA4, H3K27ac, H3K27me3
Background: Pigs are important agricultural animals as well as valuable models for studying human development and disease. However, the role of the epigenome in porcine development remains largely unexplored.
Description: Innis and Cabot used CUT&RUN to map the chromatin landscape in two porcine cell types: trophectoderm cells, which give rise to the placenta, and fetal fibroblasts, representing mid-gestation somatic cells. Key findings included:
- Identification of 10 chromatin states, including promoters, enhancers, and repressed regions.
- Broad H3K4me3 enrichment linked to lineage-specific developmental genes.
These results provide a foundation for understanding how chromatin structure drives development in pigs and how these insights might translate to human biology.
CUT&RUN Application: CUT&RUN allowed the researchers to efficiently profile histone modifications in porcine samples, revealing patterns consistent with findings in human and other model organisms.
Future Impact: This work sets the stage for using pigs as models for developmental studies and identifying biomarkers for breeding, health, and disease in agricultural settings.
Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver
Lou et al. Nature Communications, 2024. PMID: 39198388
Chromatin mapping assay: CUT&RUN
EpiCypher Products: CUTANA™ ChIC/CUT&RUN Kit (14-1048), CUTANA™ CUT&RUN Library Prep Kit (14-1001), and H3K4me3 antibody (13-0041)
Cell types: Toxoplasma gondii tachyzoite cultures maintained in immortalized human foreskin fibroblasts (HFFs)
Target: Ty-tagged AP2XIII-8
Background: Toxoplasma gondii, the parasite responsible for toxoplasmosis, undergoes a complex lytic cycle that involves budding, extensive cytoskeletal rearrangements, and waves of transcriptional changes. Understanding how chromatin regulates this cycle could reveal new therapeutic targets and provide potential insights for other infectious diseases.
Description: Lou et al. combined single-cell RNA-seq and ATAC-seq to map the transcriptomic and epigenomic landscape of the T. gondii lytic cycle, respectively. This work identified AP2XII-8 as a key regulator of T. gondii cycle transitions, highlighting the power of integrating different genomics tools to study complex biological processes.
CUT&RUN Application: CUT&RUN enabled precise mapping of AP2XII-8, confirming its role in T. gondii lytic cycle regulation.
Future Impact:This study advances our understanding of T. gondii pathogenicity and opens novel avenues for therapeutic interventions to disrupt T. gondii replication and reduce its virulence.
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Nucleation and spreading maintain Polycomb domains every cell cycle
Veronezi & Ramachandran. Cell Reports, 2024. PMID: 38607915
Chromatin mapping assay: CUT&Tag
EpiCypher Products: CUTANA™ pAG-Tn5 (15-1017) and anti-rabbit secondary antibody (13-0047)
Cell type: E14 mouse embryonic stem cells (mESCs)
Target: H3K27me3
Background: Polycomb domains, marked by H3K27me3, play a critical role in regulating gene repression during development. After DNA replication, these domains must be reestablished to preserve cell identity, but the mechanisms behind this process are still debated.
Drawing from studies of de novo Polycomb domain formation, two general mechanisms have been proposed:
- Nucleation: H3K27me3 is generated at specific DNA sequences, often referred to as Polycomb response elements.
- Spreading: Existing H3K27me3 acts as a docking station, enabling adjacent chromatin regions to acquire the same modification.
While spreading is believed to be crucial for forming large Polycomb domains, the relative contribution of nucleation and spreading to restoring H3K27me3 after DNA replication remains unclear.
Description: Veronezi and Ramachandran developed an innovative method, CUT&Flow, combining CUT&Tag with FACS to analyze H3K27me3 dynamics during cell division in mouse embryonic stem cells. Their key findings included:
- Nucleation sites form early after replication and are independent of preexisting H3K27me3.
- Both nucleation and spreading mechanisms are essential for reestablishing Polycomb domains after cell division.
This study provides valuable insights into how cells preserve epigenetic memory through successive divisions, a fundamental process in development.
CUT&RUN Application: Using CUT&Tag, the researchers achieved high-resolution mapping of H3K27me3 deposition across different stages of the cell cycle, illuminating the interplay between nucleation and spreading in reestablishing Polycomb domains.
Future Impact: This research deepens our understanding of epigenetic regulation and could inform studies on developmental disorders and diseases associated with Polycomb dysfunction.
How can we help with your CUT&RUN and CUT&Tag applications?
Every experiment can have pain points. At EpiCypher, our Tech Support Team is dedicated to helping you resolve these problems quickly and efficiently, so you can get back to your research. Answers to our most common questions are on our Tech Support Center, and include FAQs on:
- Sample prep
- Antibody selection and validation
- How our SNAP-CUTANA™ Spike-ins work
- Data analysis
Ready to transform your chromatin mapping experiments? Browse our latest CUT&RUN and CUT&Tag products and reach out to our expert support team today!