BMB Reports 2022; 55(3): 111-112
Gold and silver plasmonic nanoprobes trace the positions of histone codes
Inhee Choi1,# , Jihwan Song2,# & Hyunsung Park1,*
1Department of Life Science, University of Seoul, Seoul 02504, 2Department of Mechanical Engineering, Hanbat National University, Daejeon 34158, Korea
Correspondence to: E-mail:
#These authors contributed equally to this work.
Received: December 20, 2021; Published online: March 31, 2022.
© Korean Society for Biochemistry and Molecular Biology. All rights reserved.

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We visualized the distribution of heterochromatin in a single nucleus using plasmonic nanoparticle-conjugated H3K9me3 and H3K27me3 antibodies. Due to distance-dependent plasmonic coupling effects between nanoprobes, their scattering spectra shift to longer wavelengths as the distance between heterochromatin histone markers reduced during oncogene-induced senescence (OIS). These observations were supported by simulating scattering profiles based on considerations of particle numbers, interparticle distances, and the spatial arrangements of plasmonic nanoprobes. Using this plasmon-based colourimetric imaging, we estimated changes in distances between H3K9me3 and H3K27me3 during the formation of senescence-associated heterochromatin foci in OIS cells. We anticipate that the devised analytical technique combined with high-spatial imaging and spectral simulation will eventually lead to a new means of diagnosing and monitoring disease progression and cellular senescence.
Keywords: Heterochromatin, Histone modification, Oncogene-induced senescence, Plasmonic coupling effect, Plasmonic nanoparticles, Single-cell imaging

Histones are the most abundant, highly charged polycationic globular proteins located in nuclei. DNA strands wrap histone octamers (two sets of H2A, H2B, H3, and H4) to form a structural unit called a nucleosome (Diagram 1A upper). Tens of modifications in histone isoforms have been found and new modifications continue to be identified. The possible combinations of modifications in individual histone molecules, that is, in histone code, exceed trillions. Considering that each histone octa-mer is wrapped by a 147 bp long nucleotide with a unique DNA sequence, combinations of histone codes and DNA sequences provide enormous information capacity. The histone code determines which gene should be expressed, while DNA sequences of a gene contain information on the functional structures of proteins and RNAs. ChIP-seq analyses using an antibody specific for H3K9me3 (trimethylated 9th lysine of histone), provide an address written in A, C, G, T bases where H3K9me3 locate on genome. However, the DNA-sequence address of a modified histone does not give information about its spatial distribution in a nucleus.

Microscopic imaging of heterochromatin-specific histone modifications such as H3K9me3 and H3K27me3 has shown the presence of distinct spatial distributions in senescent cells. Hutchinson-Gilford Progeria Syndrome is a rare, fetal genetic disease that induces premature senescence, and the syndrome is characterized by a defect in Lamin A protein (a scaffold protein of the nuclear envelope). Furthermore, instability of the nuclear envelope exhibits results in dramatic heterochromatin rearrangement. Oncogene-induced senescence (OIS) dramatically disturbs heterochromatin structure and the nuclear envelope. Oncogenes such as Ras, Raf, and Myc paradoxically induce cellular senescence if no additional mutations of tumor suppressor genes. We found that immunostaining of OIS cells using a nanoparticle conjugated antibody specific for H3K9me3 revealed distinct clustered patterns of senescence-associated heterochromatin foci (SAHF) (Diagram 1A lower). Furthermore, our observations that (i) Lamin A protein interacts with Heterochromatin-Protein 1 (HP1); (ii) HP1 specifically binds H3K9me3, and (iii) Oligomerization of HP1 proteins may explain how H3K9me3 locates along the nuclear envelope in normal growing cells. On the other hand, in senescent cells, H3K9me3 displayed a punctate intranuclear pattern. During OIS, H3K27me3 spatially rearranged to produce SAHF. These spatial arrangements of histone modifications in the nucleus appear to represent unique features of epigenetic status that might be useful for determining cellular status. However conventional histone imaging methods using organic fluorescent dyes are limited by photo-bleaching, poor resolution, and the obligatory use of secondary antibodies.

We first employed gold and silver plasmonic nanoparticles as probes to detect the spatial distributions of histone modifications during OIS. When two or more plasmonic nanoparticles are placed in close proximity, they exhibit plasmonic coupling, which induces spectral shifts in absorbance and scattering (Diagram 1B). These spectral shifts are sensitively dependent on interparticle distance, arrangement, and type of the nanoparticles (Diagram 1C). We utilized plasmonic nanoparticles conjugated with primary antibodies for H3K9me3 and H3K27me3 to achieve high-spatial and colourimetric imaging of histone markers in a single nucleus. The distance-dependent plasmonic coupling effect between the nanoprobes allowed distances between histone modifications to be estimated and interpreted. The proposed method based on spectral analyses of plasmonic probes provides a novel means of visualizing spatial changes of modified histones and other biomarkers at the single cell level and of predicting disease progression or the status of senescence.


This work was supported by a grant from the Research Fund of the University of Seoul (2019) to Hyunsung Park.

Diagram 1. Spatial distribution of histone modifications detected using plasmonic nanoparticles conjugated to histone antibodies. (A) Schematic diagram of nanoprobe-conjugated H3K9me3 antibody and of the specific arrangements of histone octamers in young growing cells (upper) and oncogene-induced senescent (OIS) cells (lower). (B) Representative dark-field scattering images of plasmonic nanoprobes targeting heterochromatin histone markers in a young growing cell (upper) and a senescent (lower) cell. Scale bar, 10 μm. (C) Relationship between the spectral peak (λmax) of simulated scattering and the spatial arrangements of plasmonic nanoprobes. This diagram was reproduced with permission from the cited reference.

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