Epigenomics
Decode non-sequence genetic modifications and explore how the environment shapes gene expression through these marks.
CUT&Tag
CUT&TAG (Cleavage Under Targets and Tagmentation), developed by Steven Henikoff's lab in 2019, is a revolutionary technique for genome-wide protein-DNA interaction maps. The gold-standard ChIP-seq needs millions of cells, risks crosslink bias, is lengthy and noisy. CUT&TAG performs in-situ immunotargeting and cleavage within cells, directly enriching target-bound DNA—offering extremely high signal-to-noise, minimal cells (as few as 60), speed and high resolution, becoming a new epigenetics tool.
Principle Introduction
CUT&TAG relies on protein A-Tn5 (pA-Tn5) tagmentation. Permeabilized nuclei are incubated with a primary antibody recognizing the target (TF, histone mark); pA-Tn5 binds the antibody Fc, navigating Tn5 to the binding site. Mg²⁺ activates Tn5 to cut nearby DNA and ligate adapters in situ. Cell lysis releases adapter-bearing fragments representing bound regions, then PCR and library prep.
Literature
Published in Nature Genetics, "Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia" used in-house automated CUT&Tag/CUT&RUN on KMT2A-rearranged leukemia, finding fusion proteins bind gene bodies and form dynamic bivalent chromatin (H3K4me3/H3K27me3) at promoters; single-cell CUT&Tag revealed this bivalence as intercellular chromatin heterogeneity explaining lineage plasticity between myeloid and lymphoid; fusion-partner type affected DOT1L/Menin recruitment, predicting inhibitor sensitivity—highlighting automated epigenomics in precision medicine.
Sample Requirements
≥200,000 cells/sample.
>300 mg.
young leaves ≥0.3 g/sample; seeds/roots/stems ≥0.5–1 g/sample.
Deliverables
Internal QC
fragment size, TSS enrichment, genome-wide coverage, sample correlation.
Standard analysis
peak calling and annotation, basic statistics, genomic feature annotation.
Functional enrichment
peak-linked genes, GO and KEGG.
Motif analysis
de novo discovery and known motif matching.
Advanced
multi-group comparison and differential peak analysis.
FAQ
1) Antibody dependence—relies on specificity/affinity. 2) Poor for hard-to-permeabilize samples (plant cells, fungi, some sections). 3) Quantification debate—peak height vs. binding may not be strictly linear; better for qualitative/semi-quantitative.
High background: over/under permeabilization, high antibody concentration, excess/free Tn5, purification contamination. No signal: failed/unsuitable antibody, inactive pA-Tn5, failed Mg²⁺ activation, failed PCR.
