With the rapid advancement of genomics and epigenetics, two novel immunology approaches, CUT&RUN and CUT&Tag, have emerged for chromatin profiling. These methods address many of the limitations and drawbacks of classical chromatin mapping techniques, such as ChIP-seq (Chromatin Immunoprecipitation Sequencing).
Here are some tips to help you choose between CUT&RUN and CUT&Tag for your experimental design.
Cell number
CUT&RUN requires more cells than CUT&Tag, typically 500,000 cells per reaction compared to 100,000 nuclei per reaction. CUT&Tag is better for low cell numbers or when speed is important.
Compatibility
CUT&RUN is more compatible with diverse cell types, fixation conditions, and targets. CUT&Tag is reliable for mapping histone PTMs, but not recommended for chromatin-associated proteins.
Ease of use
CUT&RUN is a good choice for beginners because it's reliable and requires few optimization steps. CUT&Tag is an expert-level assay.
Assay speed
CUT&RUN requires traditional library prep steps, making it about one day longer than CUT&Tag.
Background noise
Both CUT&RUN and CUT&Tag have low background noise levels.
Here are some additional tips for using CUT&RUN and CUT&Tag:
Use native (unfixed) cells or nuclei.
Include positive and negative control antibodies in every experiment.
For labile histone PTMs, lightly cross-linking cell samples may improve assay performance.
The quality of antibody is crucial to CUT&RUN. Antibodies with low enrichment efficiency and/or specificity generate low yields and poor sequencing results.