Nanoscale shape-dependent histone modifications

Abstract

Recent observations suggest a role for complex nanoscale particulate shape in the regulation of specific immune-related cellular and in vivo processes. We suspect that cellular recognition of nanostructure architecture could involve nonmolecular inputs, including cellular transduction of nanoscale spatially resolved stresses induced by complex shape. Here, we report nanoscale shape-dependent control of the cellular epigenome. Interpretation of ChIP-Seq sequencing suggests that differential marking of H3K27me3 may be linked to sensory and synapse-recognition of nanoscale forces induced by complex shape. The observations raise significant questions on the role of particle-shape-induced immune regulation and memory, with potential consequences in both causes and treatment of immune-related disease.

Keywords: bionanosynapse; epigenetics; gold nanoparticle; histone modification; nanoscale shape.

Fig. 1.

Biophysical characterization of gold nanoparticles with two distinct nanoscale shapes. (a) TEM micrographs of GNPs, scale bar 100 nm. Enlarged TEM images and shape contour 3D models are shown. (b) 2D scatter plot of GNPs from the shape contour analysis. GNP2 overlaps with the shape region of interest identified previously. (c) UV–Vis absorption spectra analysis. (d) Differential centrifugal sedimentation (DCS) analysis of GNPs and corona-GNPs. (e) TEM images of GNP1 or GNP2 internalized by dTHP-1 and A549 cells.

Fig. 2.

Nanoscale shape-dependent effects on histone modifications. (a) Volcano plots of transcriptomics to show differentially expressed genes (DEGs, in blue dots) between GNP1 and GNP2 treated cells. (b) GO term enrichment analysis (biological processes) and cluster analysis (Metascape) of the DEGs, highlighting histone modification. (c) Heatmap showing hierarchical clustering analysis of GNP1- and GNP2-induced methylation and acetylation on histone H3. (d) MS/MS spectrum of −27KSAPATGGVKKPHR40- peptide with tri-methylation on Lys27 (H3K27me3) and (e) the extracted ion signals of H3K27me3 peptides. *P <  0.05 (t-test). (f) Concentration of H3K27me3 quantified by ELISA. Data of untreated or ctrl were set as 1. GSK treated cell lysate was used as a positive control. *P <  0.05; **P <  0.01 (t-test). Western blot of H3K27me3 from dTHP-1 (g) and A549 (h) cells after the treatment with GNP1 or GNP2 for 24 h.

Fig. 3.

Genome-wide differential distribution of H3K27me3 maps to pathways associated with sensory and synapse function. (a) Venn diagram showing the number of consensus peaks of H3K27me3 in ChIP-seq data sets. (b) Volcano plot of the differential H3K27me3 sites. (c) GO enrichment analysis of the differential H3K27me3 sites after annotation with genes. (d) Examples of gene feature tracks showing the differential H3K27me3 peaks, and the associated genes. (e) Venn diagram showing the number of genes identified from the H3K27me3 consensus peaks for each treatment group. The GO term enrichment analysis of the uniquely marked genes for GNP1 and GNP2.