Furthermore, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1 A9 but down-regulated in A3 A9, whereas miRNA159 showed the opposite regulation.
Comparing the two sets, we found that miRNA160 and miRNA172 were up-regulated in A1 A9 but down-regulated in A3 A9, whereas miRNA159 showed the opposite regulation.
In addition, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1 A9 but down-regulated in A3 A9, whereas miRNA159 showed the opposite regulation.
Among the DEGs, which are annotated with chromatin-related GO terms, 2 showed an opposite regulation in the two cultivars, LOC_Os02g04050 and LOC_Os02g50370, both being down-regulated in Eurosis and up-regulated in Loto (Additional file 4: Table S4).
Additionally, 1.4 Gy often exerted opposite regulation on gene expression compared to the other absorbed doses.
Here, we discuss two examples of loci, the transcripts of which exhibit simply distinguished striking opposite regulation in Nipponbare.
According to the NSF45K array data, 1.2% (13/1,124) of the transcripts clearly show opposite regulation compared to the primary transcript in light vs. dark.
Scrutiny of genome-wide rice small RNA libraries suggests that there is opposite regulation of GER3 and GER4 genes (Davidson et al. 2009).
The Ltf gene, sole gene in cluster 4 with almost opposite regulation to Mfsd2, was downregulated after 211At administration with the exception of a 22-fold upregulation after 0.5 Gy at 24 h, and upregulated after 131I administration.
Interestingly, some genes associated with these GO terms showed an opposite regulation in the 3 h-treated roots of the two genotypes, all of them exhibiting a down-regulation in Eurosis and an up-regulation in Loto.
Three additional genes, which showed an opposite regulation in the 3 h-treated roots of the two genotypes, belong to the kinesin gene family, namely, LOC_Os06g36080, LOC_Os07g44400 and LOC_Os09g25380.
