Fig. 6: Methylome dynamics during primary infection.

A Number of reproducible peaks between replicates per time point are compared among the three-time points by simple overlap of at least 50% of the peak length. B Principal component analysis of the H3K4me2 peaks by sample. Principal components are calculated on peak enrichment, i.e., read counts, after removal of the replicate batch effect. C Methylation changes for H3K4me2 and H3K4me3. Count distribution is plotted per time point for the most dynamic regions (DMRs), i.e., those showing the biggest changes in methylation. Read counts per peak are normalized by sequencing depth, peak length, and the replicate batch effect is corrected; they are subsequently centered and scaled by their standard deviation. Peaks are clustered and two global profiles are shown: gain and loss of methylation with respect to UI D H3K4me2 DMRs localization. Percentage and number of UI peaks (loss of methylation) and PI peaks (gain of methylation) according to the localization: Transcription start site (TSS) for peaks overlapping the 2 Kb interval centered around the transcription start site; Intra Genic (IntraG) for peaks located within the gene annotations and outside the TSS interval; Inter Genic (InterG) for all other peaks. E Genome browser snapshots of representative regions (windows of 2 Kbp), gaining H3K4me2 over the time course. Tracks show the normalized coverage, pooled over the two replicates for H3K4me2 ChIP and INPUT samples. Genes predicted to be linked to the peak (see methods) are represented within the window when possible, otherwise their name and distance to the peak are indicated. Clusters are defined with the Multiple Factor Analysis (see Fig. 7). Source Data A–E were deposited into the Gene Expression Omnibus (GEO) repository of the National Center for Biotechnology Information under accession number GSE230142.