Gene expression analysis was performed at all three timepoints to identify early gene signatures predictive of the magnitude of the subsequent adaptive T cell response using the significance analysis of microarrays (SAM) statistical package and gene set enrichment analysis.
In contrast with SGLp1, where gene inactivation has affected the majority of CDSs of the prophage region, in SGLp2 only 5 out of 47 CDSs are pseudogenes, retaining a completely functional lysis gene cassette for cell adhesion and invasion together with functional genes for capside formation and DNA packaging, and genes involved in the biosynthesis of the contractile phage tail [ 64].
Core histone proteins are a highly evolutionary conserved basic structural unit of chromatin with roles in DNA packaging and gene expression, however, it has been suggested that different cell types possess unique combinations of these histone proteins [62], [63].
More than two dozens of site-specific histone modifications have been described [13], [14], and the acetylation and methylation of lysine residues in the tails of nucleosomal histones have been shown to exert crucial influences on chromatin packaging and gene expression [15], [16].
Changes in histone modifications directly affect chromatin packaging and gene expression [ 30].
HP1γ is a member of the HPI family of proteins involved in chromatin packaging and gene regulation.
Modifications of the N-terminal tails of histone proteins play a crucial role in chromatin packaging and gene expression.
The genomics resources (e.g., improved assemblies, gene annotations, genome browsers) produced in this study provide a foundation for future investigations into the factors that impact chromatin packaging and gene expression in a heterochromatic domain.
CBX3 has been reported to function in chromatin packaging and gene expression regulation and has also been found to possibly regulate euchromatin repression by associating with nucleosomes in heterochromatin [ 113].
Each type has recognizable head packaging and morphogenesis genes, structural genes, lysis and attachment, lysogeny control and DNA replication, and metabolism genes (supplementary tables S3 and S5, Supplementary Material online).
