Learn about CUT&RUN - a low cell number alternative to ChIP-qPCR and ChIP-seq to analyze protein-DNA interaction in chromatin.
The development of methods that enable mapping of protein-DNA interactions, such as chromatin-immunoprecipitation (ChIP) and ChIP-seq, have led to a growing awareness that aberrant epigenetic regulation drives a wide variety of human diseases. Cleavage Under Target & Release Using Nuclease (CUT&RUN) is a new technology that can be used for chromatin profiling.
CUT&RUN is an in vivo method that uses a target-specific primary antibody and a Protein A-Protein G-Micrococcal Nuclease (pAG-MNase) to isolate specific protein-DNA complexes1,2,3. It only takes 1 to 2 days to get from cell to DNA and can be automated for maximal throughput and reproducibility4.
To isolate the protein-DNA complex of interest, cells are first harvested and bound to Concanavalin A-coated magnetic beads to simplify cell handling and minimize cell loss during subsequent washes. Cell membranes are permeabilized with digitonin to facilitate the entry of the primary antibody into the nuclei, where it binds to the histone, transcription factor, or cofactor of interest. The pAG domain of the pAG-MNase fusion protein then binds to the primary antibody heavy chain, targeting the enzyme to the chromatin region of interest. The addition of Ca2+ activates the pAG-MNase to initiate DNA digestion. This allows the cleaved chromatin complex to diffuse away from the genomic chromatin, out of the nuclei, and into the sample supernatant, where it can be collected using either a DNA spin column or phenol/chloroform extraction followed by ethanol precipitation.
|Low sample requirement||Only 100K cells needed|
|Fast time to results||1 to 2 days from cell to DNA|
|Sequencing cost savings||Only 3 to 5 million high-quality reads required|
|Target versatility||Generate sequencing and/or qPCR data for histones, histone modifications, transcription factors, and cofactors|
|Antibody versatility||Compatible with rabbit and mouse antibodies|
|Reproducible results||Spike in control DNA to normalize signal between samples|
|Avoid “crosslinking” artifacts||An in vivo method performed using native chromatin|
Save time by only culturing 100K cells to look at protein-DNA interactions and/or get epigenetic information for low abundance cell types.
Save on the time it takes to enrich for the target chromatin. Spend just 1 to 2 days to get from cells to DNA.
The relatively low background means you can distinguish your signal from genomic background noise with a lower sequencing depth. Sequencing data can be obtained with just 3 to 5 million high-quality reads, reducing your sequencing costs significantly. An added bonus? The method’s low background also makes it possible to profile low-signal genomic features.
Purified, enriched DNA can be used for sequencing and/or qPCR experiments to investigate histones, histone modifications, transcription factors, and cofactors.
CUT&RUN Assay Kit #86652 works as well as ChIP-qPCR and ChIP-seq when studying histone modifications and only requires 100,000 cells.
CUT&RUN and ChIP assays were performed with HCT 116 cells (1x105 cells for CUT&RUN, 4x106 cells for ChIP) and Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9751 or Rabbit (DA1E) mAb IgG XP® Isotype Control (CUT&RUN) #66362, using the CUT&RUN Assay Kit #86652 (left panel) or the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 (right panel). The enriched DNA was quantified by real-time PCR using the SimpleChIP® Universal qPCR Master Mix #88989, and SimpleChIP® Human GAPDH Exon 1 Primers #5516, and SimpleChIP® Human α Satellite Repeat Primers #4486. The amount of immunoprecipitated DNA in each sample is represented as the signal relative to the total amount of input chromatin, which is equivalent to 1.
CUT&RUN Assay Kit #86652 works as well as ChIP-qPCR and ChIP-seq when studying transcription factor DNA-protein interactions and only requires 100,000 cells.
CUT&RUN and ChIP assays were performed with HCT 116 cells (1x105 cells for CUT&RUN, 4x106 cells for ChIP) and CTCF (D31H2) XP® Rabbit mAb #3418 or Rabbit (DA1E) mAb IgG XP® Isotype Control (CUT&RUN) #66362, using the CUT&RUN Assay Kit #86652 (left panel) or the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005 (right panel). The enriched DNA was quantified by real-time PCR using the SimpleChIP® Universal qPCR Master Mix #88989 and human c-Myc promoter primers, SimpleChIP® Human H19/Igf2 ICR Primers #5172, and SimpleChIP® Human α Satellite Repeat Primers #4486. The amount of immunoprecipitated DNA in each sample is represented as the signal relative to the total amount of input chromatin, which is equivalent to 1.
CUT&RUN Assay Kit #86652 works as well as ChIP-qPCR and ChIP-seq when studying cofactor DNA-protein interactions and only requires 100,000 cells.
pAG-MNase binds to both mouse and rabbit antibodies, increasing the catalog of antibodies compatible with CUT&RUN assays.
Spike in heterologous DNA to normalize your data to improve your experimental reproducibility. Normalize between samples within a given experiment or different experiments.
CUT&RUN works with native chromatin and doesn’t require crosslinking or immunoprecipitation, which can lead to “crosslinking artifacts.”
CST offers flexible solutions for your CUT&RUN assays, whether you’re just starting to explore epigenetics in your research or you are an expert. All you need to provide is a primary antibody against your protein of interest. CST provides everything else in a simple-to-order kit that contains all the buffers and reagents you need, along with a detailed protocol. Or just order the pAG-MNase and spike-in DNA if you prefer.
|86652||CUT&RUN Assay Kit|
|40366||CUT&RUN pAG-MNase and Spike-in DNA|
|14209||DNA Purification Buffers and Spin Columns (ChIP, CUT&RUN)|
|88989||SimpleChIP® Universal qPCR Master Mix|
|56795||SimpleChIP® ChIP-seq DNA Library Prep Kit for Illumina®|
|47538||SimpleChiP® ChIP-seq Multiplex Oligos for Illumina® (Dual Index Primers)|
|29580||SimpleChIP® ChIP-seq Multiplex Oligos for Illumina® (Single Index Primers)|
|14654||12-Tube Magnetic Separation Rack|
|7017||6-Tube Magnetic Separation Rack|