(A) Cartoon illustrating the maternal-effect sterile (Mes) phenotype in mes-4 mutants. mes-4 M+Z- (M for maternal, Z for zygotic) mutants cannot synthesize MES-4 (Z-) but are fertile because they inherited maternal MES-4 gene product (M+). Removal of maternal MES-4 renders mes-4 M-Z- mutant adults sterile. Germline is green, and soma is white. Transcripts were profiled from single sets of two sister PGCs and from single sets of two early germ cells (EGCs) (red boxes) hand-dissected from mes-4 M-Z- (hereafter called mes-4) mutant and wild-type (wt) L1 and L2 larvae, respectively. (B–D) MA plots showing log2(average expression) versus log2(fold change) of transcript abundance for 20,258 protein-coding genes (circles) between mes-4 and wt PGCs. Numbers of biological replicates (sets of two cells): 19 wt PGCs and 11 mes-4 PGCs. Genes that exceeded one or both plot scales (triangles) were set at the maximum value of the scale. Genes belonging to a specific gene set are colored: (B) 168 germline-specific genes are blue, (C) 861 soma-specific genes are green, and (D) 2808 X-chromosome genes are red. Differentially expressed genes in mes-4 vs. wt PGCs were identified using Wald tests in DESeq2 and by setting a q-value < 0.05 significance threshold. Numbers of all misregulated genes (black) and numbers of those in gene sets (colored) are indicated in the corners; top is upregulated (UP) and bottom is downregulated (DOWN) in mes-4 vs. wt. (E–G) Bar plots showing the expected number (gray) and observed number (black) of misregulated genes that are members of the indicated gene sets. Hypergeometric tests were performed in R to test for gene-set enrichment. p-value designation is ****<1e-5. (E) Enrichment analyses for DOWN genes were restricted to 5858 protein-coding genes that we defined as ‘expressed’ (minimum average read count of 1) in wt PGCs. Gene-set sizes: germline-specific (140), germline-enriched (1867), MES-4-bound (3702), soma-specific (73). (F, G) Enrichment analyses for UP genes included all 20,258 protein-coding genes in the transcriptome. Gene-set sizes: germline-specific (168), germline-enriched (2176), MES-4-bound (4132), soma-specific (861), chrI (2888), chrII (3508), chrIII (2670), chrIV (3300), chrV (5084), and chrX (2808).