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We first analyzed the adult body expression levels in Tribolium and compared them to their Drosophila orthologs [ 27].
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In keeping with the development of the silkworm body, the expression levels of all miRNAs in adults of both sexes decreased significantly within 2 days (Additional file 11).
Overall, we observed a global enrichment of positive correlations between DNA methylation at CpGs inside gene bodies and expression levels in erythroblasts.
There was also a negative correlation between the hypomethylation level of the gene body and expression level and again we found this to be nonlinear.
To explore whether the expression of FFAR2 paralogs can be dependent of body adiposity, FFAR2 expression levels were measured using qPCR, in abdominal (visceral) adipose tissue from two experimental chicken lines divergently selected for abdominal fatness (Leclercq et al. 1980).
In dissected larvae, a similar trend was observed in all fractions (head, digestive tract and body), with TauT expression levels significantly increasing from 12 until 30 DAH (Fig. 3).
Gene-body methylation and expression levels apparently have a complex relationship.
Positive correlations between DNA methylation inside gene bodies and gene expression levels have been reported previously [ 38].
In these transgenic lines, both the transgenes of EGF and NRG1 were expressed in the whole body, although their relative expression levels were higher in the central nervous system compared with those in the peripheral tissues.
Furthermore, we found a negative correlation of −0.111 (p value of t test = 0.0018) between the hypomethylation level of the gene body and the expression level, where "gene body" includes both exons and introns (Figure 8D).
However, the relationship between gene-body DNA methylation and expression levels shows a non-monotonic correlation.
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