CUT&RUN and CUT&Tag are prominent innovations in the study of protein/DNA interactions, designed to address the limitations of the popular ChIP-seq technique, namely: cross-linking artifacts that can induce epitope masking and false-positive signals; random shearing of extracted chromatin resulting in immunoprecipitated DNA fragments of varying length (typically several hundred base pairs long) and thus poor resolution of interaction sites; and the large amount of starting material required to produce strong enough signals over background noise.
By simultaneously tethering protein-bound primary antibody and enzymatically cleaving chromatin near the protein/DNA binding region, in situ within live cells or isolated nuclei, the CUT&RUN and CUT&Tag methods eliminate interference from cross-linking and yield shorter-length DNA fragments, allowing for reduced background signals. CUT&Tag has the added feature of combining cleavage and library preparation into a single step via NGS adapter-loaded fusion protein.
A diagram illustrating how EpigenTek's CUT&RUN-Fast method cleaves near a protein-bound primary antibody for minimal interference leading to reduced background signals.
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Despite these advantages, enzymatic over-digestion of DNA, high costs, and lengthy protocol times are still problematic for CUT&RUN and CUT&Tag. Accordingly, EpiGentek has developed two new assays, the EpiNext™ CUT&RUN Fast Kit and the EpiNext™ cTIP (CUT&Tag In-Place)-Sequencing Kit. These improved approaches integrate the benefits of CUT&RUN and CUT&Tag with the fastest procedures in convenient all-in-one kits to rapidly, cost-effectively, and reliably identify true target protein-enriched regions. High-resolution mapping with minimal background is achievable from very low sample input amounts. Library DNA can be generated in just a few hours starting from as little as 500 cells or 100 ng of chromatin extract.
Kit Details
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EpiNext CUT&RUN Fast Kit For enrichment of specific DNA complexes with a protein from low input cells/chromatin identify or map in vivo protein-DNA interaction by NGS
Rapid: the procedure from cells to library DNA is less than 3 hours.
Low Input Materials: input cell amount can be as few as 500 cells, or chromatin amount can be as low as 0.1 µg.
Minimal Background: cleavage of unbound DNA sequences in the two (2) end of the target protein/DNA complex in situ enables the minimized immunocapture background, allowing the sequencing data analysis with <10 million reads.
Catalog #: P-2028
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EpiNext cTIP (CUT&Tag In-Place)-Sequencing Kit For enrichment of a protein-specific DNA complex from low input cells/chromatin and preparation of a library for NGS using Illumina platforms
Streamlined Procedure: the procedure from cells to library DNA is less than 5 hours.
Low Input Materials: the input cell amount can be as few as 500 cells or chromatin amount can be as low as 50 ng.
Minimal Background: cleavage of unbound DNA sequences in the two (2) end of the target protein/DNA complex in situ enables the minimized immunocapture background, allowing the sequencing data analysis with <10 million reads.
Additional Tagging Step: in-place tagging allows very short fragments (ex: < 70 bps) bound to transcription factors (TF) to be purified for library construction.
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