Fig 1.
Dynamic locations of the host chromatin.
(A) Immunofluorescence analysis by confocal microscopy. Fixed BmN cells and BmNPV-infected cells were incubated with anti-histone H3 and anti-lamin Dm0 antibody, followed by treatment with secondary Alexa 488-conjugated antibody (green) and Alexa 546-conjugated antibody (red), respectively. DAPI was used to indicate the location of DNA (blue). The presented cells are representative of a large number of cells. (B) HPF/FS-TEM analysis of uninfected BmN cells and BmNPV-infected cells. Over the course of viral infection, electron density (white arrows) in the nucleoplasm was gradually reduced concomitantly with the expansion of virogenic stroma (VS). Black arrows indicate the marginalized chromatin.
Fig 2.
Landscape of DNA accessibility in BmN cells and BmNPV-infected cells.
(A) The accessible peak numbers of each sample. Student’s t-test was performed between BmN samples and 48 h p.i. samples. (B) PCA of peak accessibility in all samples. Each symbol represents an independent biological replicate. PC1 (38.91%) and PC2 (17.04%). (C) Distribution of genomic features of all accessible regions. Five annotations were examined, transcription terminal site (TTS), promoter-transcription start site (TSS), exon, intron, and intergenic. (D) Circle diagram depicting the chromatin accessibility of the 30 longest scaffolds.
Fig 3.
Differentially accessible peaks analysis.
(A) The number of differentially accessible peaks at 8, 24, and 48 h.p.i. (B) Volcano plot of differentially accessible peaks between BmN cells and the 48 h p.i. group. (C) Correlation of chromatin accessibility at all peak and gene expression between BmN cells and the 48 h p.i. group. (D) Boxplot of the expression levels of cell adhesion associated genes and the proportion of floating cells during viral infection. Two-way ANOVA was performed to analyze the significance of gene expression levels between BmN cells, and the 24 and 48 h p.i. groups. Student’s t-test was performed for floating cell data between BmN cells, and 24 and 48 h p.i. samples. (E) Normalized ATAC-seq and RNA-seq profiles at SCB loci. Shaded regions are representative of a decline by 48 h p.i.
Fig 4.
Genome-wide increase in DNA accessibility is associated with chromatin assembly and disassembly of different GO group clusters.
(A) Heatmap of 61,421 elements. Each row represents one element. Peaks are grouped using K-means clustering. The numbers on the right indicate relative signal intensity. (B) Distribution of genomic features of four clusters. (C) Biological processes (GO terms) enriched in genes which corresponding to the cluster III region. (D) Boxplot of the expression of genes related to chromatin assembly and disassembly. Two-way ANOVA was performed between BmN and the 48 h p.i. groups. (E) Normalized ATAC-seq and RNA-seq profiles at ASF1 and CBX5 loci. Shaded regions representative an increase at 48 h p.i.
Fig 5.
Widespread increase in DNA accessibility is accompanied by nucleosome disassembly.
(A) DNase I TUNEL assay. Immunostaining of VP39 indicates VS regions. (B) Fragment length distribution plots of ATAC-seq samples. (C) ATAC-seq insert size for four clusters visualized by V-plots. The density of insert size is shown by aggregation based on distance from the ATAC-seq peak center. (D) BmN cells and BmNPV-infected cells were analyzed by western blot with the indicated antibodies.
Fig 6.
Histone modifications regulate the maintenance of DNA accessibility.
(a) Heatmap of H3K4me3, H3K27ac and H3K27me3 ChIP-seq data. The numbers on the left indicate relative signal intensity. (b-e) Average of normalized ChIP-seq read counts of four clusters.
Fig 7.
The relationship between H3K27ac and accessibility.
(a) Heatmap of H3K27ac ChIP-seq data. The numbers on the left indicate relative signal intensity. (b-e) Average of normalized ChIP-seq read counts of four clusters.
Fig 8.
Summary of changes in chromatin organization and accessibility during BmNPV infection.
In uninfected BmN cells, the host genome tightly compacted by multi-nucleosome depositions and is accessible in limited locations. During baculovirus infection, host chromatin is marginalized combined with the VS expansion. Up-regulated accessibility and expression at CBX5 locus indicated that CBX5 is a potential regulator for this process via interacting with the lamin B receptor. At the very late stage of infection, genome-wide regions gain accessibility and ASF1 may mediate the disassembly of multi-nucleosome depositions. This schematic modeled on our data, and dotted line and arrows indicated the possible underlying mechanisms based on extrapolation of data.