Results from the ChIP-Seq analysis
For the precipitation with H3K27ac, a total number of 14,100 activity
peaks were identified across all groups (two treatment groups * two
replicates). Of these, 3,368 were located in proximal regions
(< 2.0 kb away from either the transcriptional start [TSS]
or end sites [TES]) of annotated coding genes in the painted lady
butterfly genome assembly (Lohse et al., 2021; Shipilina et al., 2022).
Hence, a majority of the H3K27ac activity peaks were detected in
intergenic regions. For the precipitation with H3K4me3, 9,846 activity
peaks were identified in total, of which 4,744 were found within
proximal regions from either the TSS or the TES of genes. Of the total
number of H3K4me3-peaks, 5,383 overlapped with H3K27ac-peaks. The
distribution pattern was consistent with the established association
between H3K4me3 and proximal regulatory elements, with over half of the
peaks annotated in promoters, introns or exons and a decline in the
density of H3K4me3 from first introns (and exons) to genic regions
further downstream (Figure 1). As expected, given the higher density of
regulatory elements in the vicinity of gene regions, there was a
pronounced enrichment of activity peaks close to the TSS and a
considerable drop in activity signal just downstream of the TES for both
the acetylation (H3K27ac) and the methylation (H3K4me3) mark (Figure 1).
The reduced activity directly upstream the TSS is expected since
histones are dislodged from the TSS during active transcription.