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While on one hand, PHA-4 transcriptionally upregulates the expression of a many transcripts, the same set of transcripts are potentially targeted by miRNAs that it transcribes.
Therefore, for many transcripts, the late up or down-regulations seem to be distinct from the early response – The early events seem to stabilize for most transcripts by 1 week post-injury, i.e. no more dramatic global changes in the average gene expression are observed and the level of expressions remains relatively constant.
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This suggests that the evolution of germ plasm in Holometabolous insects involved a large-scale change in the localisation of many transcripts in the oocyte.
Surprisingly, by observing within trans-eQTL distribution, we noticed the linkage of many transcripts to the same chromosomal region, which gave rise to vertical alignments of eQTL.
Nevertheless, we obtain nearly as many transcripts from the neo-Y as from the neo-X.
For a graphical representation of these data see Table 8 and Figure 5. From these data we can deduce that the up-regulation of many transcripts containing the cuticle_1 domain begins at ecdysis; expression then differentiates into two groups, those transcripts up-regulated in post-moult compared to intermoult and those down-regulated in post-moult compared to intermoult.
However, we also detected many transcripts of the Group 1 Tc1 elements in publicly available ESTs of the sea lamprey, the Japanese lamprey, and teleosts (table 1).
These plots revealed a rhythmic component with a period of ∼24 h in many transcripts of the novel set, which was consistent with the estimate using ARSER.
In the dog and mouse comparisons, practically all non-coding transcripts had reading frame changes, and proportionally 3 times as many transcripts in the Potential NC set changed frame compared with the Detected set.
Further, by their nature of being relatively short strands, and in cells, they hybridize to many transcripts, increasing the potential for non-specific signals in a hybridization-based platform, such as microarray, is high.
MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing.
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