POL Scientific / JBM / Volume 11 / Issue 3 / DOI: 10.14440/jbm.2024.0017
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REVIEW

The development and application of cleavage under targets and tagmentation (CUT&Tag) technology

Chaoyang Xiong1,2,3,4 ,  Jiyin Wang1,2,3,4 ,  Xinglin Li1,2,3,4 ,  Guohong Li5* ,  Xi Wang1,2,3,4*
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1 Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
2 Beijing Institute of Infectious Diseases, Beijing, 100015, China
3 National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
4 National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, 100015, China
5 Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
JBM 2024 , 11(3), e99010019; https://doi.org/10.14440/jbm.2024.0017
Submitted: 19 June 2024 | Accepted: 30 July 2024 | Published: 3 September 2024
© 2024 by the Journal of Biological Methods published by POL Scientific. Licensee POL Scientific, USA. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
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Abstract

The regulation of chromatin structure and gene transcription in eukaryotic cells is an involved process mediated by histone modifications, chromatin-binding proteins, and transcription factors. Studying the distribution of histone modifications and transcription factors at the whole-genome level is crucial for understanding the mechanisms of gene transcription. Cleavage under targets and tagmentation (CUT&Tag) is a novel chromatin analysis method that has rapidly gained popularity in the field of epigenetics since its introduction. It has been widely used for the detection of chromatin modifications and transcription factors in different species. Furthermore, CUT&Tag has also been adapted to simultaneously detect multiple epigenetic modifications. Its integration with single-cell transcriptome, and spatial transcriptome analysis allows for a comprehensive examination of cell fate and functions. In this review, we aimed to provide an overview of the recent developments and applications of CUT&Tag and its derivatives, highlighting their significance in advancing our understanding of epigenetic regulation.

Keywords
Epigenetic
Cleavage under targets and tagmentation
Histone modification
Funding
This study was supported by grants from the Ministry of Science and Technology of the People’s Republic of China (grant no.: 2023YFC2306003 to Xi Wang), the National Natural Science Foundation of China (grant no.: 32270635 to Xi Wang), and National Natural Science Foundation of Beijing Municipality (grant no.: 7232082 to Xi Wang).
References
  1. Quina AS, Buschbeck M, Di Croce L. Chromatin structure and epigenetics. Biochem Pharmacol. 2006;72(11):1563-1569. doi: 10.1038/nrm.2017.94

 

  1. Margueron R, Reinberg D. Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet. 2010;11(4):285-296. doi: 10.1038/nrg2752

 

  1. Rando OJ, Chang HY. Genome-wide views of chromatin structure. Annu Rev Biochem. 2009;78:245-271. doi: 10.1146/annurev.biochem.78.071107.134639

 

  1. Venkatesh S, Workman JL. Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol. 2015;16(3):178-189. doi: 10.1038/nrm3941

 

  1. Nurk S, Koren S, Rhie A, et al. The complete sequence of a human genome. Science. 2022;376(6588):44-53. doi: 10.1126/science.abj6987

 

  1. Van Steensel B, Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol. 2000;18(4):424-428. doi: 10.1038/74487

 

  1. Schmid M, Durussel T, Laemmli UK. ChIC and ChEC: Genomic mapping of chromatin proteins. Mol Cell. 2004;16(1):147-157. doi: 10.1016/j.molcel.2004.09.007

 

  1. Skene PJ, Henikoff S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. elife. 2017;6:e21856. doi: 10.7554/eLife.21856

 

  1. Hainer SJ, Fazzio TG. High‐resolution chromatin profiling using CUT&RUN. Curr Protoc Mol Biol. 2019;126(1):e85. doi: 10.1002/cpmb.85

 

  1. Kaya-Okur HS, Wu SJ, Codomo CA, et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun. 2019;10(1):1930. doi: 10.1038/s41467-019-09982-5

 

  1. Kaya-Okur HS, Janssens DH, Henikoff JG, Ahmad K, HenikoffS. Efficient low-cost chromatin profiling with CUT&Tag. Nat Protoc. 2020;15(10):3264-3283. doi: 10.1038/s41596-020-0373-x

 

  1. Ge Y, Chen X, Nan N, et al. Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation. Nucleic Acids Res. 2023;51(5):2151-2176. doi: 10.1093/nar/gkad026

 

  1. Zhang L, Huo Q, Ge C, et al. ZNF143-mediated H3K9 trimethylation upregulates CDC6 by activating MDIG in hepatocellular carcinoma. Cancer Res. 2020;80(12): 2599-2611. doi: 10.1158/0008-5472.CAN-19-3226

 

  1. Ye B, Shen W, Zhang C, et al. The role of ZNF143 overexpression in rat liver cell proliferation. BMC Genom. 2022;23(1):483. doi: 10.1186/s12864-022-08714-2

 

  1. Gassler J, Kobayashi W, Gáspár I, et al. Zygotic genome activation by the totipotency pioneer factor Nr5a2. Science. 2022;378(6626):1305-1315. doi: 10.1126/science.abn7478

 

  1. Tan K, Song HW, Wilkinson MF. RHOX10 drives mouse spermatogonial stem cell establishment through a transcription factor signaling cascade. Cell Rep. 2021;36(3):109423. doi: 10.1016/j.celrep.2021.109423

 

  1. Rhodes CT, Thompson JJ, Mitra A, et al. An epigenome atlas of neural progenitors within the embryonic mouse forebrain. Nat Commun. 2022;13(1):4196. doi: 10.1038/s41467-022-31793-4

 

  1. Chen Y, Zander RA, Wu X, et al. BATF regulates progenitor to cytolytic effector CD8+ T cell transition during chronic viral infection. Nat Immunol. 2021;22(8):996-1007. doi: 10.1038/s41590-021-00965-7

 

  1. Crump NT, Smith AL, Godfrey L, et al. MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia. Nat Commun. 2023;14(1):5208. doi: 10.1038/s41467-023-40981-9

 

  1. Lu DY, Ellegast JM, Ross KN, et al. The ETS transcription factor ETV6 constrains the transcriptional activity of EWS-FLI to promote Ewing sarcoma. Nat Cell Biol. 2023;25(2): 285-297. doi: 10.1038/s41556-022-01059-8

 

  1. Long Y, Chong T, Lyu X, et al. FOXD1-dependent RalA-ANXA2-Src complex promotes CTC formation in breast cancer. J Exp Clin Cancer Res. 2022;41(1):301. doi: 10.1186/s13046-022-02504-0

 

  1. Huang Y, Wang X, Hu R, Pan G, Lin X. SOX2 regulates paclitaxel resistance of A549 nonsmall cell lung cancer cells via promoting transcription of ClC3. Oncol Rep. 2022;48(4):181. doi: 10.3892/or.2022.8396

 

  1. Gopalan S, Wang Y, Harper NW, Garber M, Fazzio TG. Simultaneous profiling of multiple chromatin proteins in the same cells. Mol Cell. 2021;81(22):4736-4746.e5. doi: 10.1016/j.molcel.2021.09.019

 

  1. Gopalan S, Fazzio TG. Multi-CUT&Tag to simultaneously profile multiple chromatin factors. STAR Protoc. 2022;3(1):101100. doi: 10.1016/j.xpro.2021.101100

 

  1. Skene PJ, Henikoff JG, Henikoff S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc. 2018;13(5):1006-1019. doi: 10.1038/nprot.2018.015

 

  1. Grosselin K, Durand A, Marsolier J, et al. High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer. Nat Genet. 2019;51(6):1060-1066. doi: 10.1038/s41588-019-0424-9

 

  1. Patty BJ, Hainer SJ. Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts. Nat Protoc. 2021;16(5):2633-2666. doi: 10.1038/s41596-021-00516-2

 

  1. Ku WL, Nakamura K, Gao W, et al. Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. Nat Methods. 2019;16(4):323-325. doi: 10.1038/s41592-019-0361-7

 

  1. Bartosovic M, Kabbe M, Castelo-Branco G. Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues. Nat Biotechnol. 2021;39(7):825-835. doi: 10.1038/s41587-021-00869-9

 

  1. Bartosovic M, Castelo-Branco G. Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag. Nat Biotechnol. 2023;41(6):794-805. doi: 10.1038/s41587-022-01535-4

 

  1. Bárcenas-Walls JR, Ansaloni F, Hervé B, et al. Nano- CUT&Tag for multimodal chromatin profiling at single-cell resolution. Nat Protoc. 2024;19(3):791-830. doi: 10.1038/s41596-023-00932-6

 

  1. Deng Y, Bartosovic M, Kukanja P, et al. Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science. 2022;375(6581):681-686. doi: 10.1126/science.abg7216

 

  1. Zhang D, Deng Y, Kukanja P, et al. Spatial epigenome-transcriptome co-profiling of mammalian tissues. Nature. 2023;616(7955):113-122. doi: 10.1038/s41586-023-05795-1

 

  1. Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc. 2022;17(6):1518-1552. doi: 10.1038/s41596-022-00692-9

 

  1. Segal E, Fondufe-Mittendorf Y, Chen L, et al. A genomic code for nucleosome positioning. Nature. 2006;442(7104):772-778. doi: 10.1038/nature04979
Conflict of interest
The authors have no competing interest to declare.
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Journal of Biological Methods, Electronic ISSN: 2326-9901 Print ISSN: TBA, Published by POL Scientific
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