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Fig. 2 | BMC Genomics

Fig. 2

From: Genome-wide surveys reveal polarity and cytoskeletal regulators mediate LKB1-associated germline stem cell quiescence

Fig. 2

Identification of genes that interact with AMPK/aak(0) and LKB1/par-4 to regulate germline quiescence during the dauer stage. Candidate genes identified in the genome-wide RNAi screens were categorized based on their functional description on WormBase. a Gene ontology (GO) terms of genes that phenocopied par-4 and aak(0) mutations and caused germline hyperplasia when subjected to RNAi. b and c Genes that suppressed par-4 and aak(0) dependent dauer germline hyperplasia respectively were categorized by GO terms and shown in a pie chart. The most common GO terms include genes with known functions in the regulation of gene expression, DNA and RNA metabolism; in cytoskeletal regulation and cell polarity; in the regulation of cell-ECM adhesion and ECM integrity; cell signal transduction; cell cycle progression; cell growth signalling and metabolism; intracellular trafficking and protein processing. A significant portion of candidate genes remain uncharacterized and fall into the Unknown functional group. d A Venn diagram that illustrates the total number of RNAi candidate genes that suppress the hyperplasia in the par-4 and aak(0) backgrounds. The overlap (green) represents the number of candidates that suppressed the hyperplasia in both genotypes, implying that they act downstream of PAR-4 in an AMPK-dependent manner. e To validate the candidates identified that phenocopy the hyperplasia observed in par-4 and AMPK mutants, daf-2(e1370) dauer larvae were subjected to RNAi against genes representing different functional classes. The germ cell nuclei counts were performed following DAPI staining. RNAi against the LKB1 pseudokinase component strd-1 was used as a positive control. f, g To validate the identified gene candidates and confirm the suppression of par-4 and aak(0) dependent dauer germline hyperplasia, genes from different functional categories were depleted using RNAi and germ cell nuclei counts were performed on extruded DAPI-stained gonads. RNAi of these genes resulted in a significant decrease in the germline hyperplasia typical of par-4 and aak(0) mutant dauer larvae. ***P < 0.0001, **P < 0.001, *P < 0.05 when compared to L4440 using two-tailed t-test, n = 50

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