Abstract
Dynamic imaging of genomic loci is key for understanding gene regulation, but methods for imaging genomes, in particular non-repetitive DNAs, are limited. We developed CRISPRdelight, a DNA-labeling system based on endonuclease-deficient CRISPR–Cas12a (dCas12a), with an engineered CRISPR array to track DNA location and motion. CRISPRdelight enables robust imaging of all examined 12 non-repetitive genomic loci in different cell lines. We revealed the confined movement of the CCAT1 locus (chr8q24) at the nuclear periphery for repressed expression and active motion in the interior nucleus for transcription. We uncovered the selective repositioning of HSP gene loci to nuclear speckles, including a remarkable relocation of HSPH1 (chr13q12) for elevated transcription during stresses. Combining CRISPR–dCas12a and RNA aptamers allowed multiplex imaging of four types of satellite DNA loci with a single array, revealing their spatial proximity to the nucleolus-associated domain. CRISPRdelight is a user-friendly and robust system for imaging and tracking genomic dynamics and regulation.
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Data availability
The data supporting the findings of this study are available in the paper and its Supplementary Information and Source Data files. Raw imaging data are available at https://doi.org/10.17632/v9p8pm3fd7.1 (ref. 60). Source data are provided with this paper.
Code availability
No custom code was used for the analysis presented in this study. All imaging data were processed and analyzed using publicly available software packages including ImageJ, Icy and Imaris.
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Acknowledgements
We are grateful to H. Wu and other members of the Chen lab for reading the manuscript. We acknowledge the Wysocka lab at Stanford University for sharing the CARGO array plasmids and the L1 cell line and H. Cheng’s lab at CEMCS, CAS, for sharing the SRRM2 knock-in plasmids. We acknowledge Y.-X. He at SIPPE, CAS, and Y. Wang, Y.-H. Tu and X.-L. Liu from CEMCS, CAS, for support in microscopy and FACS. This study was supported by the National Key R&D Program of China (2021YFA1100203), the Strategic Priority Research Program of CAS (XDB0570000), CAS Project for Young Scientists in Basic Research (YSBR-009) and the National Natural Science Foundation of China (NSFC) (31821004) to L.-L.C. L.-L.C. acknowledges support from the Xplorer Prize and New Cornerstone Science Foundation (NCI202232).
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L.-L.C. conceived the project. Y.-X.L., Y.-H.M. and L.-Z.Y. designed and performed experiments with the help of B.-Q.G., X.-Q.L, Y.H. and L.-L.C.; Z.J.L., L.Y., H.W., L.-Z.Y. and L.-L.C. wrote the manuscript. L.-L.C. supervised the project.
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L.-L.C., Y.-H.M. and L.-Z.Y. are named as inventors on patents related to CRISPR-array-mediated imaging of non-repetitive and multiple genomic loci held by CAS Center for Excellence in Molecular Cell Science. The other authors declare no competing interests.
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Extended data
Extended Data Fig. 1 HyperdLbCas12a displays the most robust DNA imaging efficiency.
a, Schematic of dCas12a/dSpCas9-EGFP and crRNA/sgRNA expression elements. b, Whole nucleus fluorescence intensities of dLbCas12a variants in Fig. 1c showed the comparable expression levels of those proteins. c, Representative images of dLbCas12a variants used for Sat III labeling with different SatIII-targeting crRNAs in HeLa cells. d, HyperdLbCas12a achieved the most robust Sat I labeling at non-canonical PAM sites. e, Statistics of puncta numbers of Sat III labeled by dLbCas12a variants and crRNAs in c). f, Co-labeling of Sat I (left) and Sat III (right) using CRISPR-hyperdLbCas12a-EGFP (Green) and DNA FISH (Red) in HeLa cells. g, Statistics of puncta numbers of Sat I (up) and Sat III (down) labeled by CRISPR-hyperdLbCas12a and DNA FISH. h, Representative images of Sat I labeled by different dCas12a species and variants with associated crRNAs in HeLa cells. i, The SNR statistics of Sat I signal labeled by different dCas12a species and variants and crRNAs in h). P values are <0.0001, <0.0001, <0.0001, 0.6312, 0.9455, respectively. j, Statistics of puncta numbers of Sat I labeled by different dCas12a species and variants and crRNAs in h). P values are <0.0001, <0.0001, <0.0001, >0.9999, 0.0072, respectively. k, Information of target sites and PAM of hyperdLbCas12a (Red) and of dSpCas9 (Gray). l, Repeats number of target sites in k) in human genome. c, h, Nuclei are shown by white dotted lines. b,d,e,g,i,j, Data are dot plotted with mean ± SEM from 20 cells, respectively. #, no obvious signals; i,j, Tukey’s multiple comparisons test.
Extended Data Fig. 2 Characteristics of CRISPR-hyperdLbCas12a in labeling DNA.
a, Schematic of the spacer lengths ranging from 4 nt to 32 nt of crRNAs targeting Sat I. b, Representative images of Sat I labeled by hyperdLbCas12a and different crRNAs shown in a) revealed that hyperdLbCas12a could label Sat I with crRNA spacers as short as 8 nt. c, SNR statistics of Sat I signal labeled by hyperdLbCas12a and crRNAs in a) showed no obvious labeling difference of crRNAs between the effective length from 8 nt to 32 nt. d, Schematic of the positions of single-nucleotide mismatches within the gSatI-4 targeting site. e, Representative images of Sat I labeled by hyperdLbCas12a and crRNAs bearing different single-nucleotide mismatches shown in d). f, SNR statistics of Sat I signal labeled by hyperdLbCas12a and crRNAs in d) showed that single mismatches at PAM-proximal region decreased labeling quality of Sat I. **P value is 0.0018. b,e, Nuclei are shown by white dotted lines. c,f, Data are represented as scatter dot plot with mean ± SEM of SNR from 20 cells, respectively. #, no obvious signals; Tukey’s multiple comparisons test.
Extended Data Fig. 3 DNA labeling with one transcript containing both hyperdLbCas12a-EGFP and CRISPR array.
a, Schematic of streamlining CRISPR array and hyperdLbCas12a-EGFP in one transcript by inserting RNase protection modules between them, with or without weak poly(A) signal at the end of the protein-coding sequence. b, Representative images of Sat I labeled by different single-transcript designs in a), highlighting the improvement in labeling efficiency with the three RNase protection modules. Nuclei are shown by white dotted lines. c, SNR statistics of Sat I signal labeled by hyperdLbCas12a and CRISPR array designed in a) showed obvious DNA labeling differences between transcripts with or without RNase protection modules. Data are represented as scatter dot plots with mean ± SEM of SNR from 20 cells, respectively. P values are 0.0045, 0.0007, <0.0001, 0.339, 0.1290, 0.2572, respectively. #, no obvious signals. Tukey’s multiple comparisons test.
Extended Data Fig. 4 Illustration of crRNA designing for CRISPRdelight imaging.
a, Pipeline of crRNA designing for CRISPRdelight. crRNAs were designed at CHOPCHOP (uib.no) (using CRISPR/Cpf1, for repression). A 10-kb genomic region was input into CHOPCHOP. In the option section, sgRNA length without PAM was set as 20, 5′-PAM of TTTN was selected, and efficiency score was selected as ‘Kim et al.51’, followed by checking self-complementarity. Output crRNAs exhibiting optimal efficiency and minimal mismatches within each 50-base pair target region were identified. Subsequently, these selected crRNAs were ranked based on descending efficiency. Top 48 crRNAs with high efficiency, characterized by fewer off-targets (MM0 < 5, MM1 < 5, MM2 < 10, MM3 < 20, but if the number of qualified crRNAs were not sufficient to construct a 48× crRNA array, crRNAs with MM2 < 25, MM3 < 50 were also considered), were chosen to assemble the CRISPR array with DR sequences.
Extended Data Fig. 5 Non-repetitive DNA imaging by CRISPRdelight.
a, CRISPRdelight shows a high DNA labeling efficiency. The fraction of HeLa cells with different number of labeled CCAT1 loci by CRISPRdelight and DNA FISH was shown. Data are represented as stacked bar graph from 33 and 26 cells, respectively. b, RT-qPCR of tested CRISPR arrays in HeLa cells with or without hyperdLbCas12a protein expression, showing the processing of the CRISPR array. Data are represented as with mean ± SD of three biological replicates. P values are <0.0001, <0.0001, <0.0001, 0.0042, 0.0016, 0.0001, 0.0047, 0.0062, 0.0016, 0.0044, <0.0001, 0.0004, respectively. c, A summary of the tested non-repetitive targets and the length of CRISPR array for imaging. d, Overview of chromosomes and the locations of tested genes in Fig. 3h. Target regions are indicated by red dotted lines. Chr, chromosome.
Extended Data Fig. 6 CRISPRdelight outperforms CARGO-dCas9 in non-repetitive DNA imaging.
a, A summary of the different features between CARGO and CRISPRdelight. Created with BioRender.comb, Comparison of sgRNA/crRNA array plasmids between CARGO-dSpCas9 imaging system and CRISPRdelight system. c, Schematics of CARGO-dSpCas9 imaging system and CRISPRdelight system. d, Representative images of Fgf5 enhancer and promoter labeled by CARGO-dSpCas9 imaging system (left) and CRISPRdelight system (right) in R1 mESCs. Experiment was repeated independently three times. e, CRISPRdelight labeled higher cell fractions than CARGO-dSpCas9. Data are represented as stacked bar graph from 70, 66, 74, 48 and 43 cells, respectively. f, CRISPRdelight showed higher SNR of labeled Fgf5 enhancer and promoter than CARGO-dSpCas9. Data are represented as scatter dot plots with mean ± SEM of SNR from 34, 92, 93, 32 and 52 dots from 70, 66, 74, 48 and 43 cells, respectively. P values are 0.0003, <0.0001, <0.0001, respectively. Dunn’s multiple comparisons test was used.
Extended Data Fig. 7 Dynamics of CCAT1 loci correlate with gene transcription activity.
a, Overview of the construction of SRRM2-BFP-KI HeLa Cell line. The BFP coding sequence was knocked into the 5′ of the SRRM2 stop codon. b, Representative images of the SRRM2-BFP-KI HeLa cell confirmed by SC35-immunofluorescent staining. Nuclei were stained by NucRed 647. Experiments were repeated independently three times. c, The average MSD curves of CCAT1 loci with different distances to SRRM2 in HeLa cells indicated no significant difference in dynamics. The data are displayed as mean ± SE from 8, 18, 27, 8, and 8 loci, respectively. d, The average MSD curves of CCAT1 loci with different distances to LMNB1 in HeLa cells indicated more confined movements of loci connected to LMNB1 compared to other positioned loci. The data are displayed as mean ± SE from 16, 14, 4, 10, 10, and 19 loci, respectively.
Extended Data Fig. 8 HSP genes selectively reposition to nuclear speckles during heat shock.
a, smFISH of HSPH1 intron in SRRM2-BFP-KI HeLa cells without any treatments. HSPH1 loci were labeled by CRISPR-hyperdLbCas12a-StayGold. Experiment was repeated independently twice. b, smFISH of HSPA1 mRNA in SRRM2-TagBFP-KI HeLa cells before and after 10-minute 42 °C treatments indicated the transcription activation of HSPA1A by heat shock. HSPA1A loci were labeled by CRISPR-hyperdLbCas12a-StayGold. Nuclei were stained by NucRed 647. Experiment was repeated independently twice. c, Statistics of nascent transcripts intensity of HSPA1A indicated a positive correlation between the nascent transcription level and nuclear speckle association after 42 °C heat shock. NS, nuclear speckles. Data are represented as scatter dot plots with mean ± SEM. n = 37 and 72 loci, respectively. The nascent transcription intensities were measured using the smFISH signals shown in b). P value is 0.0081 by two-tailed t-test.
Extended Data Fig. 9 RNA aptamer-modified CRISPR array enables multiplexed DNA imaging with a single array.
a, Schematic of hyperdLbCas12a-BFP and RNA aptamer-modified crRNA expression elements. b, Schematic of MCP-3 × RFP and PCP-3 × GFP expression elements (left) and representative images of Sat I DNA labeling by 3′-modified CRISPR-hyperdLbCas12a systems (right), showing that 3′-inserted RNA aptamers impaired DNA labeling notably. Experiments were repeated independently twice. c, Overview of six versions of MS2-modified crRNAs. d, Representative images of Sat III DNA labeling by MS2-modified CRISPR-hyperdLbCas12a system. e, SNR statistics of Sat III signal labeled by hyperdLbCas12a with five versions MS2-modified gSatIII. f, SNR statistics of Sat III signal labeled by MCP-3×GFP with five versions MS2-modified gSatIII. Data are dot plotted with mean ± SEM from 21, 24, 23, 23, and 25 cells, respectively. g, Schematic of the CRISPR array containing MS2-gSatIII-V2 and different versions of PP7-gSatI, along with the structure of MS2 and PP7 aptamers. h, In vitro array processing assay showed arrays containing MS2-gSatIII-V2 and PP7-gSatI-V6 were processed by hyperdLbCas12a most efficiently among the six versions. M, marker. Exact efficiencies were at the down sites of the gel scan. i, In vitro array processing assay showed the less efficient processing of array containing MS2-gSatIII-V2 and PP7-gSatI-V6 compared to wildtype array. Experiments were repeated independently three times. j-k, Statistics of fluorescence intensity of signal labeled by hyperdLbCas12a-BFP j), and PCP-3×SNAPf k) showed that MS2-gSatIII-V2-PP7-gSatI-V6 achieved the best labeling signals for both Sat I and SatIII. Data are represented as violin plots from 70, 148, and 114 loci, respectively in j) and from 286, 552, and 386 loci, respectively in k). l, Statistics of puncta number of each type of Sat DNAs labeled by the multi-color CRISPRdelight. Data are represented as mean ± SEM of puncta number from 18 cells.
Supplementary information
Supplementary Information
Details of sequences used in this study, including gRNA spacer sequences, promoter sequences, ‘stablizer’ sequences, array sequences, smFISH probe sequences, fused protein ORF sequences, DNA FISH probe sequences, primer sequences and gRNA sequences for side-by-side comparison; and scans of unprocessed gels associated with the data presented in main and extended data figures.
Supplementary Video 1
Dynamic tracking of nuclear peripheral CCAT1 locus.
Supplementary Video 2
Dynamic tracking of nuclear interior CCAT1 locus.
Supplementary Video 3
Volume rendering of Satellite DNAs.
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Yang, LZ., Min, YH., Liu, YX. et al. CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02333-3
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DOI: https://doi.org/10.1038/s41592-024-02333-3
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