3.5 Validation of select candidate genes by qPCR
We validated a subset of genes from this analysis with qPCR, focusing on
those that overlapped in the RNA-seq/ATAC-seq datasets (Figure S1A-E).
Trend across transcript counts (i.e., counts per million, cpm) and qPCR
expression were generally equivalent, but we note that qPCR picked up
significant differences in gene expression that did not meet the
threshold for RNA-seq significance. For example, actr6, which
plays important roles in heterochromatin formation in yeast,Drosophila and vertebrates (Ohfuchi et al., 2006), was DE
expressed between benthic and pelagic TRC according to qPCR, but not by
cpm (Figure S1A). In addition, gnmt , a methyltransferase involved
in the methionine pathway, which is linked to bone density (Wang et al.,
2011; Wang et al., 2011; Ables et al., 2012; Vijayan et al., 2014),
exhibits an expression pattern that is similar to cpm, but it is also
plasticity expressed among Maylandia reared in different environments
(Figure S1D). We also validated the expression of cdc20 , a gene
that is involved in cell-cycle regulation (Visintin et al., 1997; Yu
2002), and was significantly DE between benthic and pelagic MZ.
Expression of this gene via qPCR did not quite reach significance at the
0.05 alpha level, but exhibited a lot of variation across samples, and
showed a similar pattern that was trending toward significance (p=0.17,
Figure S1E).