These morphogenetic processes include regulated changes of adhesion between cells.
Specifically, we found that genes down-regulated by changes of H3K9Ac and H3K9Me2 at promoter regions upon MSC osteogenic differentiation principally belonged to cell cycle pathway, regulation of actin cytoskeleton pathway, and TGF-beta signaling pathway, etc. (Table S5).
In contrast, genes up-regulated by changes of H3K9Ac and H3K9Me2 were primary distributed to cytokine-cytokine receptor interaction, complement and coagulation cascades and Jak-STAT signaling pathways (Table S5).
The up-regulated stress-specific changes unmasked the major branches of the ER-stress response, which include enhancing protein folding and degradation in the ER, as well as specific osmotically regulated changes linked to cellular responses induced by dehydration.
The regions between bp 336042 and 336685 and bp 1084944 and 1085520 in the St. Maries genome (Table 3) were up-regulated by fold changes of 23.6 and 6.9, respectively (p < 1E-10).
qRT-PCR also confirmed that the expression of mexF and oprN was highly down-regulated by log (fold changes) of 7.6 ± 0.2 and 6.6 ± 1.8 in the parR mutant and by 8.6 ± 1.4 and 7.6 ± 1.6 in the parS mutant compared with wild type, consistent with the RNA-seq data (Additional file 6: Figure S3).
The down-regulated subcluster k1.1 and the up-regulated subcluster k2.1 are characterized by pronounced changes of gene expression in the beginning of germination followed by a plateau, while the subclusters k1.2 and k2.2 had more steady time-dependent kinetic patterns.
In addition to the Fur-regulated iron acquisition systems, numerous other genes are affected by changes of iron concentration.
The up-regulated or down-regulated changes in gene expression following GANT61 treatment and determined by cDNA microarray profiling, were confirmed by qRT-PCR (Figure 5).
There were more up-regulated isoforms than down-regulated ones, and the expression changes of up-regulated isoforms were greater than down-regulated one.
