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Maintenance of chromatin silencing, specific histone post-translational modifications, and regulation of DNA methylation and transposition, appeared as co-regulated functions during early embryogenesis in our time-course analysis of functional categories across pine embryogenesis.
In this study we have focused on accurate quantifications of mRNA expression, but it should be noted that changes in mRNA and protein expression are not always similar, and one should keep in mind that post-translational modifications and regulation of protein turnover rates may also affect the co-regulator protein levels (Greenbaum et al, 2003).
Gene profiling studies provide important information for key molecules relevant to a disease but are less informative of protein-protein interactions, post-translational modifications and regulation by targeted subcellular localization.
As a result, 23 proteins classified into 6 functional groups were linked in the network based on diverse linkage relationships like protein-protein interactions, modifications and regulation of expression (Figure 6).
Although gene profiling studies provide important information for key molecules relevant to a disease, they are less informative of protein-protein interactions, post-translational modifications and regulation by targeted subcellular localization.
All three types of epigenetic modulators DNA methylation, histone modifications and regulation by ncRNAs are perturbed by ethanol exposure.
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Correlation between mRNA levels will not necessarily be conserved in the corresponding protein levels because of differences in post-transcriptional modifications and regulations.
In addition to control of gene expression and binding to inhibitory Rb proteins, the activity of E2F proteins is tightly regulated by post-translational modification and regulation of protein turnover [ 29].
It will be interesting to explore the possible relationship between rRNA modification and regulation of IRES dependent translation.
Consistent with this finding, gene ontology (GO) analysis revealed that biological processes, such as chromatin modification and regulation of transcription, were significantly enriched (Figure 2F).
Common epigenetic mechanisms include DNA methylation, histone modification and regulation by microRNAs (miRNAs).
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