The EpiNext™ CUT&LUNCH (Cleavage Under Target and Liberate Unique Nucleic Complex Homogeneously) Assay Kit provides a rapid and efficient method for studying in vivo DNA-protein interactions. It integrates all the benefits of ChIP and CUT&RUN while effectively addressing their limitations. The CUT&LUNCH assay has the following advantages and features:
Click for full image
CUT&LUNCH outperforms CUT&RUN. Peak scores are plotted in the bar graph for 100,000 MCF-7 cells using the CUT&LUNCH assay kit, followed by NGS for histone H3K4me3. CUT&LUNCH shows lower background noise and narrower peaks.
CUT&LUNCH histone marker peak profiles are consistent with ENCODE ChIP-seq profiles. Peak scores are plotted for 0.1 million MCF-7 cells.
Target protein/DNA enrichment using the EpiNext™ CUT&LUNCH Assay Kit. Non-immune IgG used as a negative control.
CUT&LUNCH has higher enrichment of signals in the target regions. FRiP for CUT&LUNCH is 1.7-fold higher than for CUT&RUN.
Enrichment of histone or transcription factor (TF)-complexed DNA in vivo, followed by qPCR and/or next-generation sequencing, offers an advantageous tool for studying genome-wide protein-DNA interactions. The major method commonly used to achieve this goal is chromatin immunoprecipitation followed by sequencing (ChIP-seq). This method includes highly specific ChIP-exo and ChIP-nexus. These two assays provide high-resolution mapping. However, the major limitation of these assays is that they need a large amount of input material, cells, or tissue to produce a strong enough signal over background noise. CUT&RUN (Cleavage Under Target & Release Under Nuclease) was developed for mapping protein-DNA interaction with limited biological materials, which requires much less sample amount and also significantly improved mapping resolution. However, a considerable drawback of this assay is non-specific cleavage by antibody un-coupled pAG-MNase, significantly limiting the specificity of the CUT&RUN use for most transcription factors in different species and cell/tissue types. In addition, the original CUT&RUN has complicated steps and needs to optimize assay conditions, which is still time-consuming.
Starting materials can include various mammalian cell samples such as culture cells from a flask or plate, primary cells, or rare cell populations isolated from blood, body fluid, fresh/frozen tissues, and specific cells sorted from entire cell populations and embryonic cells, etc. The amount of cells can be 2 x 103 to 5 x 105 cells per reaction. For optimal preparation, the cell input amount should be 2 x 105, although the results for modified histones can be obtained with as few as 500 cells.
Cart (0)
