Tn5-FISH, a novel cytogenetic method to image chromatin interactions with sub-kilobase resolution

Niu Jing; Zhang Xu; Li Guipeng; Yan Pixi; Yan Qing; Dai Qionghai; Jin Dayong; Shen Xiaohua; Wang Jichang; Zhang Michael Q.; Gao Juntao

doi:10.1016/j.jgg.2020.04.008

Volume 47 Issue 12

Dec. 2020

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2020 > 47(12): 727-734

PDF( 1131 KB)

Tn5-FISH, a novel cytogenetic method to image chromatin interactions with sub-kilobase resolution

doi: 10.1016/j.jgg.2020.04.008

Niu Jing¹,
Zhang Xu^{2, 3},
Li Guipeng^{4, 5},
Yan Pixi¹,
Yan Qing^{2, 6},
Dai Qionghai²,
Jin Dayong^{7, 8},
Shen Xiaohua¹,
Wang Jichang^{9, 10},
Zhang Michael Q.^{11, 1, 2, 6},
Gao Juntao^{2, 6}

1
School of Medicine, Tsinghua University, Beijing 100084, China
2
Department of Automation, Tsinghua University, Beijing 100084, China
3
Beijing Institute of Collaborative Innovation, Beijing 100094, China
4
Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
5
Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
6
MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist; Center for Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
7
Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, NSW 2007, Australia.
8
UTS-SUStech Joint Research Centre for Biomedical Materials and Devices, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
9
Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
10
Department of histology and embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
11
Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas, TX 75080-3021, USA

More Information

Corresponding author: E-mail address: jtgao@tsinghua.edu.cn (Gao Juntao)
Publish Date: 2020-12-25

Abstract

Abstract

There is an increasing interest in understanding how three-dimensional (3D) organization of the genome is regulated. Different strategies have been employed to identify genome-wide chromatin interactions. However, due to current limitations in resolving genomic contacts, visualization and validation of these genomic loci with sub-kilobase resolution remain unsolved to date. Here, we describe Tn5 transposase-based Fluorescencein situhybridization (Tn5-FISH), a PCR-based, cost-effective imaging method, which can co-localize the genomic loci with sub-kilobase resolution, dissect genome architecture, and verify chromatin interactions detected by chromatin configuration capture (3C)-derived methods. To validate this method, short-range interactions in keratin-encoding gene (KRT) locus in topologically associated domain (TAD) were imaged by triple-color Tn5-FISH, indicating that Tn5-FISH is very useful to verify short-range chromatin interactions inside the contact domain and TAD. Therefore, Tn5-FISH can be a powerful molecular tool for the clinical detection of cytogenetic changes in numerous genetic diseases such as cancers.
- Chromatin interaction,
- Cellular imaging,
- Super resolution

FullText(HTML)

References(50)

References

[1]	Aird, D., Ross, M. G., Chen, W. S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D. B., Nusbaum, C., Gnirke, A., 2011. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12, R18.
[2]	Allahyar, A., Vermeulen, C., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M., Geeven, G., van Kranenburg, M., Pieterse, M., Straver, R., Haarhuis, J. H. I., Jalink, K., Teunissen, H., Renkens, I. J., Kloosterman, W. P., Rowland, B. D., de Wit, E., de Ridder, J., de Laat, W., 2018. Enhancer hubs and loop collisions identified from single-allele topologies. Nat. Genet. 50, 1151–1160.
[3]	Bantignies, F., Cavalli, G.,2014. Topological organization of Drosophila Hox genes using DNA fluorescent in situ hybridization. Methods Mol. Biol. 1196, 103–20.
[4]	Bayani, J., Squire, J. A., 2004. Fluorescencein situhybridization (FISH). Curr. Protoc. Cell Biol. Chapter 22, Unit 22 24.
[5]	Beagrie, R. A., Scialdone, A., Schueler, M., Kraemer, D. C., Chotalia, M., Xie, S. Q., Barbieri, M., de Santiago, I., Lavitas, L. M., Branco, M. R., Fraser, J., Dostie, J., Game, L., Dillon, N., Edwards, P. A., Nicodemi, M., Pombo, A., 2017. Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543, 519–524.
[6]	Beliveau, B. J., Apostolopoulos, N., Wu, C. T., 2014. Visualizing genomes with Oligopaint FISH probes. Curr. Protoc. Mol. Biol. 105, Unit 14 23.
[7]	Beliveau, B. J., Boettiger, A. N., Avendano, M. S., Jungmann, R., McCole, R. B., Joyce, E. F., Kim-Kiselak, C., Bantignies, F., Fonseka, C. Y., Erceg, J., Hannan, M. A., Hoang, H. G., Colognori, D., Lee, J. T., Shih, W. M., Yin, P., Zhuang, X., Wu, C. T., 2015. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat. Commun. 6, 7147.
[8]	Beliveau, B. J., Joyce, E. F., Apostolopoulos, N., Yilmaz, F., Fonseka, C. Y., McCole, R. B., Chang, Y., Li, J. B., Senaratne, T. N., Williams, B. R., Rouillard, J. M., Wu, C. T., 2012. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc. Natl. Acad. Sci. U. S. A. 109, 21301–21306.
[9]	Beliveau, B. J., Kishi, J. Y., Nir, G., Sasaki, H. M., Saka, S. K., Nguyen, S. C., Wu, C. T., Yin, P., 2018. OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. Proc. Natl. Acad. Sci. U. S. A. 115, E2183–E2192.
[10]	Bienko, M., Crosetto, N., Teytelman, L., Klemm, S., Itzkovitz, S., van Oudenaarden, A., 2013. A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. Nat. Methods10, 122–124.
[11]	Bintu, B., Mateo, L. J., Su, J. H., Sinnott-Armstrong, N. A., Parker, M., Kinrot, S., Yamaya, K., Boettiger, A. N., Zhuang, X., 2018. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783.
[12]	Bobroff, N., 1986. Position measurement with a resolution and noise‐limited instrument. Rev. Sci. Instrum. 57, 1152–1157.
[13]	Boettiger, A. N., Bintu, B., Moffitt, J. R., Wang, S., Beliveau, B. J., Fudenberg, G., Imakaev, M., Mirny, L. A., Wu, C. T., Zhuang, X., 2016. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529, 418–422.
[14]	Cardozo Gizzi, A. M., Cattoni, D. I., Fiche, J. B., Espinola, S. M., Gurgo, J., Messina, O., Houbron, C., Ogiyama, Y., Papadopoulos, G. L., Cavalli, G., Lagha, M., Nollmann, M., 2019. Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms. Mol. Cell 74, 212–222. e5.
[15]	Chen, B., Guan, J., Huang, B., 2016. Imaging specific genomic DNA in living cells. Annu. Rev. Biophys. 45, 1–23.
[16]	Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., Zhuang, X., 2015. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090.
[17]	de Wit, E., de Laat, W., 2012. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11–24.
[18]	Dekker, J., Mirny, L., 2016. The 3D genome as moderator of chromosomal communication. Cell 164, 1110–1121.
[19]	Deng, W., Shi, X., Tjian, R., Lionnet, T., Singer, R. H., 2015. CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proc. Natl. Acad. Sci. U. S. A. 112, 11870–11875.
[20]	Gall, J. G., 2016. The origin of in situ hybridization - A personal history. Methods 98, 4–9.
[21]	Giorgetti, L., Heard, E., 2016. Closing the loop: 3C versus DNA FISH. Genome Biol. 17, 215.
[22]	Gorbacheva, T., Quispe-Tintaya, W., Popov, V. N., Vijg, J., Maslov, A. Y., 2015. Improved transposon-based library preparation for the Ion Torrent platform. Biotechniques 58, 200–202.
[23]	Gordon,M. P., Ha, T., Selvin, P. R., 2004. Single-molecule high-resolution imaging with photobleaching. Proc. Natl. Acad. Sci. U. S. A. 101, 6462–6465.
[24]	Guo, Y., Nie, Q., MacLean, A. L., Li, Y., Lei, J., Li, S., 2017. Multiscale modeling of inflammation-induced tumorigenesis reveals competing oncogenic and oncoprotective roles for inflammation. Cancer Res. 77, 6429–6441.
[25]	Hanahan, D., Weinberg, R. A., 2000. The hallmarks of cancer. Cell 100, 57–70.
[26]	Homberg, M., Magin, T. M., 2014. Beyond expectations: novel insights into epidermal keratin function and regulation. Int. Rev. Cell Mol. Biol. 311, 265–306.
[27]	Kundu, S., Ji, F., Sunwoo, H., Jain, G., Lee, J. T., Sadreyev, R. I., Dekker, J., Kingston, R. E., 2017. Polycomb repressive complex 1 generates discrete compacted domains that change during differentiation. Mol. Cell 65, 432–446.
[28]	Liu, X., Zhang, Y., Chen, Y., Li, M., Zhou, F., Li, K., Cao, H., Ni, M., Liu, Y., Gu, Z., Dickerson, K. E., Xie, S., Hon, G. C., Xuan, Z., Zhang, M. Q., Shao, Z., Xu, J., 2017.In situcapture of chromatin interactions by biotinylated dCas9. Cell 170, 1028–1043.e19.
[29]	Ma, H., Tu, L. C., Naseri, A., Huisman, M., Zhang, S., Grunwald, D., Pederson, T., 2016. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat. Biotechnol. 34, 528–530.
[30]	Ma, T., Chen, L., Shi, M., Niu, J., Zhang, X., Yang, X., Zhanghao, K., Wang, M., Xi, P., Jin, D., Zhang, M., Gao, J., 2018. Developing novel methods to image and visualize 3D genomes. Cell Biol. Toxicol. 34, 367–380.
[31]	Moffitt, J. R., Hao, J., Wang, G., Chen, K. H., Babcock, H. P., Zhuang, X., 2016. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situhybridization. Proc. Natl. Acad. Sci. U. S. A. 113, 11046–11051.
[32]	Ni, Y. X., Cao, B., Ma, T., Niu, G., Huo, Y. D., Huang, J. D., Chen, D. N., Liu, Y., Yu, B., Zhang, M. Q., Niu, H. B., 2017. Super-resolution imaging of a 2.5 kb non-repetitive DNAin situin the nuclear genome using molecular beacon probes. eLife 6, e21660
[33]	Nir, G., Farabella, I., Perez Estrada, C., Ebeling, C. G., Beliveau, B. J., Sasaki, H. M., Lee, S. D., Nguyen, S. C., McCole, R. B., Chattoraj, S., Erceg, J., AlHaj Abed, J., Martins, N. M. C., Nguyen, H. Q., Hannan, M. A., Russell, S., Durand, N. C., Rao, S. S. P., Kishi, J. Y., Soler-Vila, P., Di Pierro, M., Onuchic, J. N., Callahan, S. P., Schreiner, J. M., Stuckey, J. A., Yin, P., Aiden, E. L., Marti-Renom, M. A., Wu, C. T., 2018. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet. 14, e1007872.
[34]	Ou, H. D., Phan, S., Deerinck, T. J., Thor, A., Ellisman, M. H., O'Shea, C. C., 2017. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science 357, eaag0025.
[35]	Quinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M. M., Shishkin, A. A., Bhat, P., Takei, Y., Trinh, V., Aznauryan, E., Russell, P., Cheng, C., Jovanovic, M., Chow, A., Cai, L., McDonel, P., Garber, M., Guttman, M., 2018. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell 174, 744–757 e724.
[36]	Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., Aiden, E. L., 2014. A 3D Map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680.
[37]	Reznikoff, W. S., 1993. The Tn5 transposon. Annu. Rev. Microbiol. 47, 945–964.
[38]	Rich, J. J., Willis, D. K., 1990. A single oligonucleotide can be used to rapidly isolate DNA-sequences flanking a transposon Tn5 insertion by the polymerase chain-reaction. Nuc. Acids Res. 18, 6673–6676.
[39]	Rowley, M. J., Nichols, M. H., Lyu, X., Ando-Kuri M., Rivera I. S. M., Hermetz K., Wang P., Ruan Y., Corces V. G., 2017. Evolutionarily conserved principles predict 3D chromatin organization. Mol. Cell 67, 837–852.e7.
[40]	Schmidt, T. L., Beliveau, B. J., Uca, Y. O., Theilmann, M., Da Cruz, F., Wu, C. T., Shih, W. M., 2015. Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries. Nat. Commun. 6, 8634.
[41]	Shah, S., Lubeck, E., Zhou, W., Cai, L., 2016.In situtranscription profiling of single cells reveals spatial organization of cells in the mouse hippocampus. Neuron 92, 342–357.
[42]	Shizuya, H., Kouros-Mehr, H., 2001. The development and applications of the bacterial artificial chromosome cloning system. Keio J. Med. 50, 26–30.
[43]	Sigal, Y. M., Zhou, R., Zhuang, X., 2018. Visualizing and discovering cellular structures with super-resolution microscopy. Science 361, 880–887.
[44]	Strausbaugh, L. D., Bourke, M. T., Sommer, M. T., Coon, M. E., Berg, C. M., 1990. Probe mapping to facilitate transposon-based DNA sequencing. Proc. Natl. Acad. Sci. U. S. A. 87, 6213–6217.
[45]	Szabo, Q., Jost, D., Chang, J. M., Cattoni, D. I., Papadopoulos, G. L., Bonev, B., Sexton, T., Gurgo, J., Jacquier, C., Nollmann, M., Bantignies, F., Cavalli, G., 2018. TADs are 3D structural units of higher-order chromosome organization inDrosophila. Sci. Adv. 4, eaar8082.
[46]	Thompson, R. E., Larson, D. R., Webb, W. W., 2002. Precise nanometer localization analysis for individual fluorescent probes. Biophys. J. 82, 2775–2783.
[47]	Williamson, I., Berlivet, S., Eskeland, R., Boyle, S., Illingworth, R. S., Paquette, D., Dostie, J., Bickmore, W. A., 2014. Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes Dev. 28, 2778–2791.
[48]	Yu, M., Ren, B., 2017. The three-dimensional organization of mammalian genomes. Annu. Rev. Cell Dev. Biol. 33, 265–289.
[49]	Zhang, P., Yang, M., Zhang, Y., Xiao, S., Lai, X., Tan, A., Du, S., Li, S., 2019. Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer. Cell Rep. 27, 1934–1947.e5.
[50]	Zheng, M., Tian, S. Z., Maurya, R., Lee, B., Kim, M., Capurso, D., Piecuch, E., Gong, L., Zhu, J. J., Wong, C. H., Ngan, C. Y., Wang, P., Ruan, X., Wei, C. L., Ruan, Y., 2019. Multiplex chromatin interaction analysis with single-molecule precision. Nature 566, 558–562.