CRISPR-mediated multiplexed live cell imaging of nonrepetitive genomic loci with one guide RNA per locus

Patricia A. Clow, Menghan Du, Nathaniel Jillette, Aziz Taghbalout, Jacqueline J. Zhu () and Albert W. Cheng ()
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Patricia A. Clow: The Jackson Laboratory for Genomic Medicine
Menghan Du: The Jackson Laboratory for Genomic Medicine
Nathaniel Jillette: The Jackson Laboratory for Genomic Medicine
Aziz Taghbalout: The Jackson Laboratory for Genomic Medicine
Jacqueline J. Zhu: The Jackson Laboratory for Genomic Medicine
Albert W. Cheng: The Jackson Laboratory for Genomic Medicine

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: Abstract Three-dimensional (3D) structures of the genome are dynamic, heterogeneous and functionally important. Live cell imaging has become the leading method for chromatin dynamics tracking. However, existing CRISPR- and TALE-based genomic labeling techniques have been hampered by laborious protocols and are ineffective in labeling non-repetitive sequences. Here, we report a versatile CRISPR/Casilio-based imaging method that allows for a nonrepetitive genomic locus to be labeled using one guide RNA. We construct Casilio dual-color probes to visualize the dynamic interactions of DNA elements in single live cells in the presence or absence of the cohesin subunit RAD21. Using a three-color palette, we track the dynamic 3D locations of multiple reference points along a chromatin loop. Casilio imaging reveals intercellular heterogeneity and interallelic asynchrony in chromatin interaction dynamics, underscoring the importance of studying genome structures in 4D.

Date: 2022
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DOI: 10.1038/s41467-022-29343-z

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