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

Author

Listed:
  • Patricia A. Clow

    (The Jackson Laboratory for Genomic Medicine)

  • Menghan Du

    (The Jackson Laboratory for Genomic Medicine
    University of Connecticut Health Center)

  • 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
    Arizona State University)

  • Albert W. Cheng

    (The Jackson Laboratory for Genomic Medicine
    University of Connecticut Health Center
    Arizona State University
    The Jackson Laboratory Cancer Center)

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.

Suggested Citation

  • Patricia A. Clow & Menghan Du & Nathaniel Jillette & Aziz Taghbalout & Jacqueline J. Zhu & Albert W. Cheng, 2022. "CRISPR-mediated multiplexed live cell imaging of nonrepetitive genomic loci with one guide RNA per locus," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29343-z
    DOI: 10.1038/s41467-022-29343-z
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    References listed on IDEAS

    as
    1. Aziz Taghbalout & Menghan Du & Nathaniel Jillette & Wojciech Rosikiewicz & Abhijit Rath & Christopher D. Heinen & Sheng Li & Albert W. Cheng, 2019. "Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    2. Melissa J. Fullwood & Mei Hui Liu & You Fu Pan & Jun Liu & Han Xu & Yusoff Bin Mohamed & Yuriy L. Orlov & Stoyan Velkov & Andrea Ho & Poh Huay Mei & Elaine G. Y. Chew & Phillips Yao Hui Huang & Willem, 2009. "An oestrogen-receptor-α-bound human chromatin interactome," Nature, Nature, vol. 462(7269), pages 58-64, November.
    3. Peiwu Qin & Mahmut Parlak & Cem Kuscu & Jigar Bandaria & Mustafa Mir & Karol Szlachta & Ritambhara Singh & Xavier Darzacq & Ahmet Yildiz & Mazhar Adli, 2017. "Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9," Nature Communications, Nature, vol. 8(1), pages 1-10, April.
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    1. Qin Peng & Ziliang Huang & Kun Sun & Yahan Liu & Chi Woo Yoon & Reed E. S. Harrison & Danielle L. Schmitt & Linshan Zhu & Yiqian Wu & Ipek Tasan & Huimin Zhao & Jin Zhang & Sheng Zhong & Shu Chien & Y, 2022. "Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Yanan Li & Yonghua Wu & Ru Xu & Jialing Guo & Fenglei Quan & Yongyuan Zhang & Di Huang & Yiran Pei & Hua Gao & Wei Liu & Junjie Liu & Zhenzhong Zhang & Ruijie Deng & Jinjin Shi & Kaixiang Zhang, 2023. "In vivo imaging of mitochondrial DNA mutations using an integrated nano Cas12a sensor," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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