Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING

Zhao, L.-Y., Song, J., Liu, Y., Song, C.-X. & Yi, C. Mapping the epigenetic modifications of DNA and RNA. Protein Cell 11, 792–808 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Raiber, E.-A., Hardisty, R., van Delft, P. & Balasubramanian, S. Mapping and elucidating the function of modified bases in DNA. Nat. Rev. Chem. 1, 0069 (2017).Article 
CAS 

Google Scholar 
Conibear, A. C. Deciphering protein post-translational modifications using chemical biology tools. Nat. Rev. Chem. 4, 674–695 (2020).Article 
CAS 
PubMed 

Google Scholar 
Weinberg, D. N. et al. The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape. Nature 573, 281–286 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Xia, B. et al. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nat. Methods 12, 1047–1050 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).Article 
CAS 
PubMed 

Google Scholar 
Voigt, P. et al. Asymmetrically modified nucleosomes. Cell 151, 181–193 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Blanco, E., González-Ramírez, M., Alcaine-Colet, A., Aranda, S. & Di Croce, L. The bivalent genome: characterization, structure, and regulation. Trends Genet. 36, 118–131 (2020).Article 
CAS 
PubMed 

Google Scholar 
Gu, T. et al. The disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development. Nat. Genet. 54, 625–636 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Li, X., Xiong, X. & Yi, C. Epitranscriptome sequencing technologies: decoding RNA modifications. Nat. Methods 14, 23–31 (2017).Article 
CAS 

Google Scholar 
Simpson, J. T. et al. Detecting DNA cytosine methylation using nanopore sequencing. Nat. Methods 14, 407–410 (2017).Article 
CAS 
PubMed 

Google Scholar 
Bartee, D., Thalalla Gamage, S., Link, C. N. & Meier, J. L. Arrow pushing in RNA modification sequencing. Chem. Soc. Rev. 50, 9482–9502 (2021).Article 
CAS 
PubMed 

Google Scholar 
Wang, Y., Zhang, X., Liu, H. & Zhou, X. Chemical methods and advanced sequencing technologies for deciphering mRNA modifications. Chem. Soc. Rev. 50, 13481–13497 (2021).Article 
CAS 
PubMed 

Google Scholar 
Ku, W. L. et al. Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. Nat. Methods 16, 323–325 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Weiner, A. et al. Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution. Nat. Biotechnol. 34, 953–961 (2016).Article 
CAS 
PubMed 

Google Scholar 
Zhong, S., Li, Z., Jiang, T., Li, X. & Wang, H. Immunofluorescence imaging strategy for evaluation of the accessibility of DNA 5-hydroxymethylcytosine in chromatins. Anal. Chem. 89, 5702–5706 (2017).Article 
CAS 
PubMed 

Google Scholar 
Pfaffeneder, T. et al. The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew. Chem. Int. Ed. 50, 7008–7012 (2011).Article 
CAS 

Google Scholar 
Pfaffeneder, T. et al. Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nat. Chem. Biol. 10, 574–581 (2014).Article 
CAS 
PubMed 

Google Scholar 
Larsson, C. et al. In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nat. Methods 1, 227–232 (2004).Article 
CAS 
PubMed 

Google Scholar 
Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat. Biotechnol. 28, 1208–1212 (2010).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Trcek, T. et al. Single-mRNA counting using fluorescent in situ hybridization in budding yeast. Nat. Protoc. 7, 408–419 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cao, X. et al. Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging. Nucleic Acids Res. 51, e13–e13 (2023).Article 
CAS 
PubMed 

Google Scholar 
Cao, X. et al. RNA-primed amplification for noise-suppressed visualization of single-cell splice variants. Anal. Chem. 92, 9356–9361 (2020).Article 
CAS 
PubMed 

Google Scholar 
Zhang, K., Deng, R., Gao, H., Teng, X. & Li, J. Lighting up single-nucleotide variation in situ in single cells and tissues. Chem. Soc. Rev. 49, 1932–1954 (2020).Article 
CAS 
PubMed 

Google Scholar 
Chen, F., Xue, J., Bai, M., Fan, C. & Zhao, Y. Lighting up nucleic acid modifications in single cells with DNA-encoded amplification. Acc. Chem. Res. 55, 2248–2259 (2022).Article 
CAS 
PubMed 

Google Scholar 
Bai, M. et al. Bioorthogonal chemical signature enabling amplified visualization of cellular oxidative thymines. Anal. Chem. 93, 10495–10501 (2021).Article 
CAS 
PubMed 

Google Scholar 
Xue, J. et al. Pairwise proximity-differentiated visualization of single-cell DNA epigenetic marks. Angew. Chem. Int. Ed. 60, 3428–3432 (2021).Article 
CAS 

Google Scholar 
Xue, J. et al. Branched immunochip-integrated pairwise barcoding amplification exploring the spatial proximity of two post-translational modifications in distinct cell subpopulations. Chem. Commun. 58, 10020–10023 (2022).Article 
CAS 

Google Scholar 
Chen, F. et al. Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications. Nat. Commun. 12, 1965 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chen, F. et al. Click-encoded rolling FISH for visualizing single-cell RNA polyadenylation and structures. Nucleic Acids Res. 47, e145–e145 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Wang, Y. et al. Detection and application of 5-formylcytosine and 5-formyluracil in DNA. Acc. Chem. Res 52, 1016–1024 (2019).Article 
CAS 
PubMed 

Google Scholar 
Chen, F. et al. Programming enzyme-initiated autonomous DNAzyme nanodevices in living cells. ACS Nano 11, 11908–11914 (2017).Article 
CAS 
PubMed 

Google Scholar 
Chen, F. et al. Fabricating MnO2 nanozymes as intracellular catalytic DNA circuit generators for versatile imaging of base-excision repair in living cells. Adv. Funct. Mater. 27, 1702748 (2017).Article 

Google Scholar 
Chen, F., Xue, J., Bai, M., Qin, J. & Zhao, Y. Programming in situ accelerated DNA walkers in diffusion-limited microenvironments. Chem. Sci. 10, 3103–3109 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
von Diezmann, L., Shechtman, Y. & Moerner, W. E. Three-dimensional localization of single molecules for super-resolution imaging and single-particle tracking. Chem. Rev. 117, 7244–7275 (2017).Article 

Google Scholar 
Weibrecht, I. et al. In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay. Nat. Protoc. 8, 355–372 (2013).Article 
CAS 
PubMed 

Google Scholar 
Schjoldager, K. T., Narimatsu, Y., Joshi, H. J. & Clausen, H. Global view of human protein glycosylation pathways and functions. Nat. Rev. Mol. Cell Bio. 21, 729–749 (2020).Article 
CAS 

Google Scholar 
Flynn, R. A. et al. Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell 184, 3109–3124.e3122 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ren, J. et al. Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape. Nat. Methods 20, 695–705 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zeng, H. et al. Spatially resolved single-cell translatomics at molecular resolution. Science 380, eadd3067 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chen, X. et al. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nat. Methods 13, 1013–1020 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chen, F. et al. Differentiated visualization of single-cell 5-hydroxymethylpyrimidines with microfluidic hydrogel encoding. J. Am. Chem. Soc. 142, 2889–2896 (2020).Article 
CAS 
PubMed 

Google Scholar 
Wassie, A. T., Zhao, Y. & Boyden, E. S. Expansion microscopy: principles and uses in biological research. Nat. Methods 16, 33–41 (2019).Article 
CAS 
PubMed 

Google Scholar