Behavioral adaptations to permanent exposure to pathogenic bacteria include diapause entry in the second generation of C. elegans populations (Palominos et al., 2017). Our aim is to dissect the genes and their regulators involved in this defensive strategy. We analyzed the transcriptomes and performed differential expression analysis of RNAs expressed in worms fed with pathogens Salmonella Typhimurium (MST1) and Pseudomona aeruginosa (PAO1) for two generations. These analyses revealed that
mir-243-3p and
mir-51-5p are upregulated in response to both pathogens in the F1 and F2 and are indispensable for dauer formation under pathogenesis (unpublished). Promoter expression quantified as gfp fluorescence shows that these miRNAs are transcriptionally activated in response to pathogen exposure. To study the transcription factors (TFs) that induce
mir-243 and
mir-51 expression under pathogenesis, we generated a reference gene regulatory network (GRN) formed by miRNA-gen and TF-gen regulations. Experimentally supported interactions to build the network between miRNAs and their targets were obtained from DIANA database, miRTarbase and MiRecords. TF binding sites obtained from MODENCODE and occurrences of TF binding motives located within 2kb of the transcription start were employed to assign TFs to the regulation of specific genes. We selected TFs with a) intestinal expression b) that interact with both miRNAs and c) are expressed in the F2 of animals feeding on PAO1. Putative regulators of
mir-51 and
mir-243 include NHR-28, AMA-1, ELT-3, SNPC-4, UNC-130 ALY-2, DAF-16, FOS-1, JUN-1, LSY-2, MDL-1, NHR-25, PHA-4, UNC-62, ZTF-7, PQM-1, CRH-2, ALR-1, and MEF-2. We tested the ability of mutant animals for most of these TFs to form dauers under pathogenesis. While
mef-2,
jun-1,
nhr-25 and
lsy-1 animals form wild type amounts of dauers,
aly-2,
nhr-28,
pqm-1,
alr-1 and
crh-2 failed to enter diapause in the second generation on pathogens, but not on starvation. This suggests a specific role on diapause formation in response to pathogens for ALY-2, NHR-28, PQM-1, ALR-1 and CRH-2. These results support the use of knowledge based GRNs for the discovery of context specific regulatory functions for transcription factors, such as their role on diapause formation under pathogenesis.