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First published online 10 December 2003
doi: 10.1242/dev.00914

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Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans

¹ Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
² Department of Molecular and Cellular Biology, University of Arizona, Tuscon, AZ 85721, USA

View larger version (37K): [in a new window]   Fig. 1. Experimental design. Five sets of differentially expressed genes (I-V, triangles) were defined by indirect comparisons between males and hermaphrodites with and without a germline. For each set of genes, the wide, yellow end of the triangle abuts the sample with higher expression levels, while the blue tip of the triangle points to the sample with lower expression levels. The number of differentially expressed genes is listed within the triangle. For the N2 hermaphrodite and glp-4 hermaphrodite comparison (set I), both L4 and adult stages were included. All samples were compared indirectly through use of a common reference, except fem-1(lf) was compared directly with fem-3(gf).

View larger version (17K): [in a new window]   Fig. 2. Venn diagram analysis of genes with germline-enriched expression. Comparisons between major sets of genes define restricted subsets of germline-enriched expression. Numbers of genes within each subset are listed. (A) Combination of the spermatogenesis and oogenesis sets with the hermaphrodite germline-enriched set defines a subset of germline-intrinsic transcripts. (B) Combination of the male and hermaphrodite germline-enriched sets with the spermatogenesis set defines a subset of male germline-specific transcripts.

View larger version (42K): [in a new window]   Fig. 3. Functional categories of germline- and sex-regulated genes. Pie charts show functional annotation of each of the major gene sets, based on the assigned molecular function using gene ontology (GO) annotation. Most genes with unknown function are not included in this analysis; the few included have a domain of unknown function that has been annotated by GO. (A) Functional categories of the germline-enriched gene sets. The sidebar divides genes encoding nucleic acid binding proteins into three categories: RNA binding, DNA binding or unspecified nucleic acid binding. (B) Functional categories of sex-biased, somatic-expressed gene sets.

View larger version (38K): [in a new window]   Fig. 5. Temporal analysis of wild-type larval and adult gene expression. (A) Diagram of germline development and timepoints taken for analysis. Black, somatic gonad; orange, proliferating germ cells; pink, meiotic germ cells; red, differentiating spermatocytes; blue, differentiating oocytes. (B) Temporal expression profiles for all genes with P<0.01 (ANOVA) in timecourse, organized by similarity in expression using hierarchical clustering. Each row represents a gene, while each column represents an average of each set of comparisons. The log2 ratios have been replaced with color that demonstrates the relative level of expression. Six clusters, a-f, with different temporal patterns are defined by bars down right side of clustergram. (C) The mutant expression profiles of the different genotypes of temporally regulated genes. Genes are present in the same order as B. The mutant data had no weight in the clustering, but were included to demonstrate the mutant profile of each genotype. The `fem' column (column 1) corresponds to the fem-3/fem-1 direct comparison. The + and - notations refer to the presence or absence of the germline (wild type or glp-4 mutants, respectively). For both B and C, yellow indicates higher expression in staged wild-type or mutant sample; blue indicates higher expression in reference sample or fem-1(lf).

View larger version (31K): [in a new window]   Fig. 4. Male germline-specific genes. Shown are relative levels of gene expression of several indirect comparisons between genotypes for eight genes with significantly male germline-enriched expression, but no evidence of hermaphrodite-enriched expression. him, him-5 males; glphim, glp-4;him-5 males; N2, wild-type hermaphrodites; glp, glp-4 hermaphrodites; fem-3, fem-3(gf) hermaphrodites; fem-1, fem-1(lf) hermaphrodites. All comparisons shown were made between adult animals, except for column 4. Yellow represents increased expression in the numerator of each comparison, while blue represents increased expression in the denominator of each comparison.

View larger version (22K): [in a new window]   Fig. 6. Chromosomal distribution of germline- and sex-regulated genes. The ratio of genes in each gene set observed on each chromosome, relative to the expected number for the number of genes per chromosome on the microarray, was plotted. Any statistically significant deviation of observed from expected is marked by an asterisk (P<0.001; hypergeometric probability test). See http://wormgermline.yale.edu for corresponding table with numbers of each gene set on each chromosome.

View larger version (18K): [in a new window]   Fig. 7. RNAi phenotypes of germline- and sex-regulated genes. The fraction of genes in each dataset that display a phenotype when functionally depleted by RNAi are graphed. Above each bar in the graph is the number of genes with an RNAi phenotype. Below the name of each dataset is the total number of genes within that set. Genes with no significant regulation by sex or the presence of a germline are included in the `no regulation' category, while all genes with RNAi assays performed and listed in Wormbase (www.wormbase.org) are counted in the `total' category.