Figure 4.

mRNAs more abundant in fbf-1; lip-1 than in puf-8 fbf-1; lip-1 are enriched for oogenic mRNAs. (A) Boxplots of “germline-enriched” (left) and “not germline-enriched” (right) mRNAs found in fbf-1; lip-1 plus puf-8 fbf-1; lip-1 transcriptomes. Each boxplot shows the average counts per million for all mRNAs, normalized by library size. Sorting into the two categories was done following the classification of Reinke et al. (2004). (B) Differentially expressed mRNAs in fbf-1; lip-1 (reprogramming competent, “RC”) vs. puf-8 fbf-1; lip-1 (noncompetent, “non-RC”) transcriptomes. A total of 350 mRNAs differed between RC and non-RC transcriptomes (FDR < 0.01 with twofold change or more), with 335 increased mRNAs (red) and 15 reduced mRNAs (blue). All other mRNAs are shown in black. (C) Tissue expression of mRNAs differentially expressed between reprogramming competent and noncompetent animals. The NEXTDB database contained hybridizations for 117 of the 350 differentially expressed mRNAs; these were scored for expression in germline, intestine, and other somatic tissues (pharynx, hypodermis, body wall muscle, vulva, and neuron) (top pie chart). Germline-expressed mRNAs were separated into RC-increased and RC-reduced lists and scored for expression in oogenesis (pink), spermatogenesis (blue), or both (gender neutral, black). Bottom pie chart shows breakdown for mRNAs at higher levels in the reprogramming competent strain (“RC-increased”); the single germline mRNA that was reduced in the reprogramming competent strain (“RC-reduced”) was gender neutral. (D–G) Representation of mRNAs in distinct data sets to 335 RC-increased mRNAs (red), 15 RC-reduced mRNAs (blue), and the genome (gray). (D) Maternally expressed mRNAs (Baugh et al. 2003). (E) Oogenesis mRNAs (Reinke et al. 2004). (F) Regulatory targets of EFL-1 (Gerstein et al. 2010). (G) Regulatory targets of GLD-1 (Jungkamp et al. 2011). n.s., not significant; ***FDR < 1E-9; ****FDR < 1E-15.