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In addition, a change in miRNA or mRNA expression does not necessarily lead to a change in encoded protein levels, protein modification, or protein function.
However, gene expression regulation is much more complex, involving other direct and indirect factors such as post-translational modification or protein signaling cascades.
Searching the whole genome of C. botulinum ATCC 3502 revealed 81 genes for chaperones or proteins involved in posttranslational modification or protein turnover, representing 2.85% of the total gene number [ 11].
We wanted to know how many of the 1166 differentially expressed genes can be associated with protein processing, trafficking and post-translational modification or protein degradation via any of the above-listed CFTR-relevant pathways in order to provide a second mode of data analysis independent of the hypothesis-free gene-enrichment analysis.
Alternatively, the act of transcription per se through a lncRNA locus could be critical because of the changes this generates in chromatin structure, modification or protein binding: in this case the resultant RNA could be an incidental by-product (Petruk et al., 2006; Latos et al., 2012; Marquardt et al., 2014).
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Third, the discrepancies in affinity may arise from differences between expression systems and native tissue receptors resulting from post-translational modification or protein-protein interactions.
However, it is not known if any of these enzymatic modifications or protein interactions liberates P-TEFb directly from the 7SK snRNP.
Additional mechanisms might act in cells that cooperate with PIP2 or offer alternative regulation, including posttranslational modifications or protein cofactors.
Although lncRNAs may require post-transcriptional modifications or protein interactions to function, because the mature product is the functional end-product, measurement of its expression directly represents the levels of the active molecule.
Modifications can be grouped according to their stability or transience (reversible versus irreversible): irreversible types (such as irreversible redox modifications or protein deamidation) are often associated with aging or tissue injury, whereas transient modifications are associated with signal propagation and regulation.
Therefore, and although most of the attention when analyzing protein expression in plants has been directed towards protein accumulation, protein activity may play a bigger role in the final analysis, especially when compartmentalization results in protein with low or no activity, which in many cases is due to a lack of post-translational modifications or protein truncation [ 29].
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