Visualizing looping of two endogenous genomic loci using synthetic zinc‐finger proteins with anti‐FLAG and anti‐HA frankenbodies in living cells

  title={Visualizing looping of two endogenous genomic loci using synthetic zinc‐finger proteins with anti‐FLAG and anti‐HA frankenbodies in living cells},
  author={Yang Liu and Ning Zhao and Masato T. Kanemaki and Yotaro Yamamoto and Yoshifusa Sadamura and Yuma Ito and Makio Tokunaga and Timothy J. Stasevich and Hiroshi Kimura},
  journal={Genes to Cells},
  pages={905 - 926}
In eukaryotic nuclei, chromatin loops mediated through cohesin are critical structures that regulate gene expression and DNA replication. Here we demonstrate a new method to visualize endogenous genomic loci using synthetic zinc-finger proteins harboring repeat epitope tags (ZF probes) for signal amplification via binding of tag-specific intracellular antibodies, or frankenbodies, fused with fluorescent proteins. We achieve this in two steps. First, we develop an anti-FLAG frankenbody that can… 


Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins
This work constructed several polydactyl zinc finger (PZF) DNA-binding domains aimed to recognize specific DNA sequences in Arabidopsis and mouse and fused these with GFP, demonstrating that live cell imaging of specificDNA sequences can be achieved with artificial zinc finger proteins in different organisms.
Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF.
It is speculated that evidence for R BRi-dependent loops may provide a molecular mechanism for establishing cell-specific CTCF loops, potentially regulated by RNA(s) or other RBRi-interacting partners.
Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells
The different approaches for generating the desired custom ZFNs with high sequence-specificity and affinity are explored and the potential of ZFN-mediated gene targeting for ‘directed mutagenesis’ and targeted ‘gene editing’ of the plant and mammalian genome is discussed.
Visualization of specific DNA sequences in living mouse embryonic stem cells with a programmable fluorescent CRISPR/Cas system
The prokaryotic CRISPR/Cas adaptive immunity system is repurposed to specifically detect endogenous genomic loci in mouse embryonic stem cells and opens new perspectives to study functional nuclear architecture.
Neutralizing the function of a β-globin–associated cis-regulatory DNA element using an artificial zinc finger DNA-binding domain
This study designed and functionally characterized an artificial DNA-binding domain that neutralizes the function of a cis-regulatory DNA element associated with adult β-globin gene expression and demonstrated that artificialDNA-binding proteins lacking effector domains are useful tools for studying and modulating thefunction of cis-Regulatory DNA elements.
A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation.
Genetically encoded system to track histone modification in vivo
A genetically encoded system for tracking histone modifications by generating fluorescent modification-specific intracellular antibodies (mintbodies) that can be expressed in vivo is developed and lays the foundation for epigenetic analysis in vivo.
Protospacer Adjacent Motif (PAM)-Distal Sequences Engage CRISPR Cas9 DNA Target Cleavage
In vitro analysis of target site recognition revealed that interactions between the 5′ end of the guide and PAM-distal target sequences are necessary to efficiently engage Cas9 nucleolytic activity, providing an explanation for why off-target editing is significantly lower than expected from ChIP-seq data.