ArticleNucleic acids research2018
CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 58 citations in OpenAlex.
- Acidic transcription factors position the genome at nuclear speckles through transcription-dependent and -independent mechanisms.Molecular cell · 2026Article
- CRISPR-Cas-based live cell imaging of genome dynamics.Nature reviews. Genetics · 2026Review
- NIPBL-mediated 3D genome folding translates enhancer priming into gene activation and safeguards lineage fidelity during embryonic transitions.bioRxiv : the preprint server for biology · 2025Article
- Visualizing genetic information flow in space and time.Science China. Life sciences · 2025Review
- RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imaging.Science (New York, N.Y.) · 2025Article
- Article
- Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility.Science advances · 2023Article
- SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells.Nature communications · 2023Article
- iSMOD: an integrative browser for image-based single-cell multi-omics data.Nucleic acids research · 2023Article
- Single-molecule tracking (SMT): a window into live-cell transcription biochemistry.Biochemical Society transactions · 2023Article
- Live cell imaging of DNA and RNA with fluorescent signal amplification and background reduction techniques.Frontiers in cell and developmental biology · 2023Review
- Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells.Nature communications · 2022Article
- Review
- A guide for single-particle chromatin tracking in live cell nuclei.Cell biology international · 2022Review
- Fluorescent labeling of genomic loci inCell reports methods · 2022Article
- Design of a synthesis-friendly hypoxia-responsive promoter for cell-based therapeutics.Engineering in life sciences · 2021Article
- The solid and liquid states of chromatin.Epigenetics & chromatin · 2021Review
- Mammalian DNA Replication Timing.Cold Spring Harbor perspectives in biology · 2021Review
- Physical Nature of Chromatin in the Nucleus.Cold Spring Harbor perspectives in biology · 2021Review
- p53 mediates target gene association with nuclear speckles for amplified RNA expression.Molecular cell · 2021Article
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
Abstract
Nuclear organization has an important role in determining genome function; however, it is not clear how spatiotemporal organization of the genome relates to functionality. To elucidate this relationship, a method for tracking any locus of interest is desirable. Recently clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) or transcription activator-like effectors were adapted for imaging endogenous loci; however, they are mostly limited to visualization of repetitive regions. Here, we report an efficient and scalable method named SHACKTeR (Short Homology and CRISPR/Cas9-mediated Knock-in of a TetO Repeat) for live cell imaging of specific chromosomal regions without the need for a pre-existing repetitive sequence. SHACKTeR requires only two modifications to the genome: CRISPR/Cas9-mediated knock-in of an optimized TetO repeat and its visualization by TetR-EGFP expression. Our simplified knock-in protocol, utilizing short homology arms integrated by polymerase chain reaction, was successful at labeling 10 different loci in HCT116 cells. We also showed the feasibility of knock-in into lamina-associated, heterochromatin regions, demonstrating that these regions prefer non-homologous end joining for knock-in. Using SHACKTeR, we were able to observe DNA replication at a specific locus by long-term live cell imaging. We anticipate the general applicability and scalability of our method will enhance causative analyses between gene function and compartmentalization in a high-throughput manner.
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