Application and prospects of CRISPR/Cas9-based methods to trace defined genomic sequences in living and fixed plant cells

  • Solmaz Khosravi
  • Takayoshi Ishii
  • Steven Dreissig
  • Andreas HoubenEmail author


The 3D organization of chromatin plays an important role in genome stability and many other pivotal biological programs. Therefore, the establishment of imaging methods, which enable us to study the dynamics of chromatin in living cells, is necessary. Although primary live cell imaging methods were a breakthrough, there is a need to develop more specific labeling techniques. With the discovery of programmable DNA binding proteins, such zinc finger proteins (ZFP), transcription activator-like effectors (TALE), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), a major leap forward was made. Here, we review the applications and potential of fluorescent repressor-operator systems, programmable DNA binding proteins with an emphasis on CRISPR-based chromatin imaging in living and fixed cells, and their potential application in plant science.


chromatin dynamics CRISPR/Cas9 FISH live cell imaging RGEN-ISL telomere 



Bimolecular fluorescence complementation


Centromere specific histone H3


Clustered regularly interspaced short palindromic repeats


CRISPR-associated protein 9


Cysteine cysteine-histidine histidine


crisper RNA


dead Cas9




Fluorescence in situ hybridization


Fluorescent repressor operator system


Green fluorescent protein


guide RNA


Live-cell fluorescent in situ hybridization


Neisseria meningitides


Transcription activator-like effector


Protospacer adjacent motif


PUF binding site


Pumilio/fem-3 mRNA binding factor


RNA-guided endonuclease-in situ labeling


Repeat variable di-residue


Single-chain variable fragment antibody


GCN4 peptide binding single-chain variable fragment antibody


Streptococcus pyogenes


Streptococcus thermophilus


single guide RNA


Trans-activating RNA


Zinc finger proteins


Funding information

Cytogenetic research in the author’s laboratory has been supported by Deutsche Forschungsgemeinschaft (DFG) grant HO1779/28-1.


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)SeelandGermany
  2. 2.Arid Land Research Center (ALRC)Tottori UniversityTottoriJapan
  3. 3.Institute of Agricultural and Nutritional SciencesMartin Luther University Halle-WittenbergHalleGermany

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