Figure 3
Prediction and validation of regulatory mechanisms underlying diverging co-expression networks. (A) Potential regulators of the pfcrt co-expression networks by interrogation of the topological relationships between pfcrt partners using the transitivity, t, score. Top scoring candidate regulators- the AP2 transcription factor PF3D7_1007700 (AP2-3) has the highest score in CQS while in CQR the AP2 regulator PF3D7_0420300 (AP2-2) has 3rd highest score considering all genes correlated to pfcrt (FDR ≤ 0.20). The case of t =0 denotes functional (direct) pfcrt partners which also includes another AP2 transcription factor, PF3D7_0802100 (AP2-1). (B) Top scoring regulators are all part of a previously published high confidence protein-protein interaction sub-network [44] and interact with the histone acetyltransferase (Gcn5). Other transcriptional regulators physically interacting with Gcn5 include CAF1- a component of the CCR4-NOT mRNA deadenylase complex- and adenosine deaminase ADA2, leading to the hypothesis that the Gcn5 protein interaction network could be involved in integration of transcriptional regulation and mRNA stability [44]. (C) Validation of dysregulated histone acetylation as a potential regulatory mechanism using drug response assays. QTL mapping of quantitative dose responses to the HDACi apicidin in progeny of the Dd2 × HB3 genetic cross found significant association to genetic loci on chromosome 5, 57.3 cM (LOD = 5.4) and 8, 77.5 cM (LOD 2.3). The chromosome 5 locus includes a gene encoding CCR4 while the chromosome 8 locus contains CAF1, which physically interacts with Gcn5. (D) Validation of dysregulated histone acetylation using data from previous studies [53]. Promoters of the top 100 genes that are not correlated to pfcrt in CQS but show positive correlation in CQR (gain of positive correlation) carry vastly higher levels of H3K9ac compared to the average levels in all genes (Wilcoxon test P < 2.2 x 10−16). In contrast, H3K9ac levels of the top 100 genes that gain negative correlation are significantly lower compared to the genome-wide promoter baseline (Wilcoxon test P = 3.4 x 10−16).