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6.5 - 270 kDa 범위를 커버하는 3가지 컬러 밴드를 포함하며,
최대 100%까지의 transfer 효과를 개런티하는 Prestained protein ladder를 소개합니다.



  • ChIP-Seq은 타겟단백질이 결합된 크로마틴 부위를 침전시켜 농축하고 그 시퀀스를 NGS로 분석하는 기술입니다. 그러나 ChIP-Seq은 세포의 양이 적은 샘플의 경우 DNA를 얻기 힘들고, 노이즈 백그라운드가 높다는 한계를 갖고 있습니다. 이에 반해 CUT&RUN 시퀀싱은 온전한 세포로부터 타겟 단백질만을 잘라내는 방식으로, ChIP-Seq에 비해 적은 수의 cell 로도 분석이 가능하고, 시간이 단축되며, signal to noise ratio가 월등히 향상되어 Chromatin NGS에 효과적으로 이용될 수 있는 툴 입니다. 
  • 다양한 DNA-Interacting protein 타겟에 적용할 수 있습니다. (histone PTMs, chromatin-interacting proteins including transcription factors, epigenetic enzymes, epigenetic reader proteins, chromatin remodeling proteins)




  • CUT&RUN (Cleavage Under Targets & Release Using Nuclease)에 의한 genomic mapping은 Histone 변형 및 Protein-DNA 상호 작용을 분석하고, 결합부위의 유전자를 규명하기 위해 이용됩니다.
  • Intact cell이나 핵내에 타겟에 대한 항체를 반응 시킨 후, Proteins A and/or G to Micrococcal Nuclease (pAG-MNase)가 in situ에서 항체가 결합된 chromatin만 선택적으로 자르는 특성을 이용하여 타겟만을 특이적으로 절단하므로 백그라운드가 감소됩니다.
  • ChIP-seq 실험에 비해 훨씬 적은 시간과 비용으로 고해상도로 히스톤 PTM 및 염색질 상호 작용 단백질을 매핑합니다. (데이터까지 4일 소요)
  • 적은양의 샘플(5,000개-500,000개 세포), 적은양의 sequencing reads로도 고품질의 시퀀싱 데이터를 얻을 수 있습니다.
  • 세포, 핵, 동결세포, 조직, 면역세포, crosslinked material등 다양한 시료에 따른 최적의 상세한 샘플 준비 프로토콜을 제공합니다. 
  • 4가지의 CUTANA H3K4 MetStat Spike-in Controls을 제공하여 실험 결과 및 troubleshooting시 실험의 정확도를 입증합니다. 

CUTANA H3K4 MetStat Spike-in Controls


1. lectin-coated 된 magnetic bead (concanavalin A (ConA) beads)에 cell을 고정하고 permeabilization화 합니다.
2. 크로마틴 타겟(ex: 히스톤 PTM 또는 크로마틴/DNA 결합 단백질)에 대한 항체를 반응시킵니다.
3. CUTANA pAG-MNase를 처리하여 타겟 nucleosome을 잘라냅니다.
4. CaCl2+를 넣으면 nucleosome complex가 유리됩니다.
5. nucleosome complex로부터 DNA를 추출 및 정제하여 sequencing library를 준비합니다.
6. NGS를 진행합니다.


Day 1) CUTANA™ CUT&RUN Kit을 이용하여 nucleosome complex를 얻습니다.
Day 2) DNA를 추출하고 NGS를 위한 library를 준비합니다. 
Day 3) NGS 시퀀싱을 진행합니다. 
Day 4) 데이터를 분석합니다.

cut&run workflow

Kit의 구성 

  • ConA Beads (21-1401)
  • SA Beads (21-1402)
  • Bead Activation Buffer (21-1001)
  • Pre-Wash Buffer (21-1002)
  • Stop Buffer (21-1003)
  • 5% Digitonin (21-1004) 
  • 1 M Spermidine (21-1005)
  • pAG-MNase (15-1016) 
  • H3K4me3 Positive Control Antibody (13-0041k)
  • Rabbit IgG Negative Control Antibody (13-0042k)
  • E. coli Spike-in DNA (18-1401)
  • CUTANA H3K4 MetStat Spike-in Controls (19-1006,19-1321,19-1334,19-1316)
  • 8-strip Tubes (10-0009k)
  • DNA Cleanup Columns (10-0010)
  • DNA Collection Tubes (10-0011) 
  • 0.5 M EDTA (21-1006)
  • 100 mM Calcium Chloride (21-1007)
  • DNA Binding Buffer (21-1008)
  • DNA Wash Buffer (21-1009)
  • DNA Elution Buffer (21-1010)

참고 데이터

1. CUTANA CUT&RUN은 S/N를 향상시키고 sequencing depth를 줄여줍니다. 

A representative 350 kb region of an H3K4me1 profile in K-562 cells, generated using CUT&RUN (yellow panels), native ChIP-seq (blue panels), or crosslinked ChIP-seq (green panels). All  data were generated by EpiCypher and are expressed as reads per million (RPM). Color-coded gradient (to left) represents S/N ratios determined by genome wide analysis (bamFingerprint data, not shown).

2. CUTANA CUT&RUN는 적은수의 cell로도 high quality data를 얻을 수 있습니다. 


In CUTANA CUT&RUN K-562 cell titration experiments, data quality is largely indistinguishable from 500,000 cells down to 5,000 cells. Genome tracks show representative regions from cell titration experiments for a variety of different targets, including a euchromatin-associated histone PTM (H3K4me3, left), heterochromatin-associated PTM (H3K27me3, middle) and a chromatin binding protein (BRD4, right).

함께 이용하는 제품

ChIP-seq vs. CUT&RUN vs. CUT&Tag 비교

*CUT&Tag has been applied for single-cell chromatin analysis in the literature. However, the recommended input for CUTANA™ CUT&Tag assays is 10,000 to 100,000 cells.

주요 사용 논문

Skene and Henikoff. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6, e21856 (2017). (PMID: 28079019)

In 2017, Steven Henikoff’s lab at the Fred Hutchinson Cancer Research Center published their first paper describing CUT&RUN. This in situ chromatin mapping assay builds on ChIC technology from Ulrich Laemmli’s group, using a protein A-fused micrococcal nuclease (pA-MNase) to selectively cleave antibody-bound chromatin loci in intact cells and nuclei. Skene et al. describes the assay and uses it to profile several transcription factors in yeast and human nuclei. Head-to-head comparisons with ChIP-seq assays further highlights the enhanced sensitivity, improved signal : noise, and reduced sequencing requirement of CUT&RUN vs. leading assays.

Meers et al. Improved CUT&RUN chromatin profiling tools. eLife 8, e46314 (2019). (PMID: 31232687)

This 2019 paper from the Henikoff lab reports the development of a novel protein A-protein G fused micrococcal nuclease (pAG-MNase), for use in CUT&RUN. pAG-MNase expands antibody species compatibility in CUT&RUN assays and forms the basis for EpiCypher’s CUTANA CUT&RUN technology. This paper also describes the use of E. coli DNA for assay calibration and a modified MNase digestion strategy for improved yield with minimal background, representing significant breakthroughs for CUT&RUN assays.

Yusufova et al. Histone H1 Loss drives lymphoma by disrupting 3D chromatin architecture. Nature AOP (2020). (PMID: 33299181)

Linker histone H1 proteins are important components of chromatin structure and are frequently mutated in B-cell lymphoma, but their role in cancer development has been unclear. Here, Yusufova et al. establish H1 as a bona fide tumor suppressor protein, demonstrating that H1 mutations alter chromatin structure to support re-expression of developmental genes and subsequent cancer development. EpiCypher’s use of CUTANA CUT&RUN technology to examine changes in H3K9me2 and H3K9me3 was key to uncovering this complex mechanism.

Wilson et al. ARID1A mutations promote P300-dependent endometrial invasion through super-enhancer hyperacetylation. Cell Rep. 33, 108366 (2020). (PMID: 33176148)

ARID1A is a key subunit of the SWI/SNF chromatin remodeling complex and is commonly mutated in severe forms of endometriosis; however, its function is not well defined. Here, Wilson et al. show that ARID1A co-localizes with and represses the p300 lysine acetyltransferase. Mutation of ARID1A results in increased H2K27ac at super-enhancers and supports invasive endometrial growth. To profile H3K27ac at super-enhancers, Wilson et al. applied EpiCypher’s CUTANA pAG-MNase for ultra-sensitive CUT&RUN assays.

Stengel et al. Definition of a small core transcriptional circuit regulated by AML1-ETO. Mol Cell AOP (2020). (PMID: 33382982)

Chromosomal translocations in cancer can result in fusions of transcription factors to other protein domains, altering gene expression to drive oncogenesis. In acute myeloid leukemia (AML), the most common fusion protein is AML-ETO, combining the DNA binding domain of AML/RUNX1 to the transcriptional corepressor ETO. Here, Stengel et al. performed a comprehensive analysis of AML-ETO function, utilizing PRO-seq, CRISPR-based mutagenesis, and EpiCypher CUT&RUN technology to define AML-ETO targets and downstream effects.


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