Two catalytically inactive dCas9 proteins are each fused to one half of a chemically induced dimerisation domain. A distinct sgRNA guides each dCas9 to a separate genomic anchor point, such as an enhancer and a promoter. When you add the small-molecule dimeriser, it bridges the two fusion domains. This brings the two dCas9-bound loci into proximity and forms an artificial chromatin loop. Short-term induction is reversible upon ABA washout. However, prolonged induction can stabilise an induced chromatin contact in a cell-context-dependent manner.
Epigenetics Research Tools
dCas9 Chromatin Looping Tools for 3D Genome Engineering
dCas9 chromatin looping tools for on-demand, small-molecule-inducible 3D genome engineering
A split dimeriser approach targets one catalytically dead Cas9 (dCas9) to each anchor locus. Adding the small-molecule inducer drives rapid heterodimerisation between the two dCas9-dimeriser fusion proteins, which physically bridges the two loci into a loop, letting you study how enhancer-promoter contact affects gene expression.
Lentivector-based delivery systems support stable expression of both dCas9-dimeriser constructs in suitable transducible cell types. This avoids the variability of transient transfection. The inducer agent is available as part of a complete kit with both lentivectors. You can also order it separately for experiments that need repeated or dose-escalating additions after you have established stable cell lines. You clone one target-specific gRNA into each of the two lentiviral dCas9 fusion vectors. One vector uses an SpCas9-compatible gRNA and the other an SaCas9-compatible gRNA. Positioning each dCas9 within a few kilobases of your intended anchor point maximises loop formation efficiency.
This system gives you reversible, locus-specific 3D genome engineering without nuclease-mediated cleavage or targeted sequence alteration at the selected genomic loci. This makes it suitable for studying causal relationships between chromatin architecture and transcriptional output.
Choosing the right dCas9 chromatin looping reagent configuration
- If you are setting up inducible chromatin looping for the first time and need all components: a complete dCas9 chromatin loop induction kit gives you both dCas9-dimeriser lentivectors and the small-molecule inducer agent in one package.
- If you have stable dCas9 cell lines established and only need the inducer: you can order the small-molecule inducer reagent separately, extending existing experiments without repurchasing the lentivector components.
- If your target loci require precise gRNA positioning for loop efficiency: Select gRNA target sites near the regulatory elements or genomic anchors of interest. The dimeriser bridge spans the distance between both bound dCas9 molecules.
- If you want to confirm loop formation before phenotypic analysis: pairing the inducible looping system with 3C or Hi-C on induced versus uninduced cells verifies contact frequency changes at the targeted loci before you measure downstream gene expression.
Parent category: epigenetics research kits
Applications
Enhancer-promoter contact studies
dCas9-based loop induction tethers an enhancer to your promoter for gene-expression measurement, separating looping from chromatin state changes.
Disease variant functional annotation
A loop directed to connect your non-coding GWAS variant to its putative target gene tests whether forced contact alters expression.
Phase separation and compartment studies
Defined loops, induced and monitored for co-localisation with condensates or histone marks, link organisation to phase-separated compartments.
Synthetic gene circuit control
Inducible looping built on CRISPR-Cas9 tools regulates promoter activity, bringing a synthetic insulator into contact with your engineered promoter.
Loop formation validation
Induced and uninduced samples paired with Hi-C or 3C library preparation confirm a rise in contact frequency at the targeted loci before your phenotypic analysis.
Temporal dynamics of loop formation and reversal
Adding or withdrawing the small-molecule inducer studies loop assembly and disassembly kinetics, and the transcriptional response over time.
Frequently asked questions
Chromosome conformation capture assays, including 3C, 4C, or Hi-C, are the standard methods. Verify an induced contact by comparing targeted, induced cells with appropriate uninduced and guide-control conditions using a suitable chromosome-conformation assay, such as locus-specific 3C.
Include uninduced controls and guide configurations that do not target the intended two loci. Confirm correct dCas9 targeting and compare induced with control conditions before attributing a transcriptional phenotype to loop formation. Run a 3C or RT-qPCR readout from each control set before you interpret phenotypic results.
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