title: Gene Function Prediction Based on Developmental Transcriptomes of the Two Sexes in C. elegans.
abstract: We compare whole-animal RNA-seq transcriptomes for C. elegans males and hermaphrodites from the late L3 larval stage to young adulthood. During this interval, male sexual structures develop, including extensive neurogenesis and synaptogenesis that nearly doubles the size of the nervous system. Previous genome-wide expression studies in C. elegans have usually focused on only one sex-the hermaphrodite-and there are a relatively large number of genes that remain without meaningful annotation. In the present study, differential expression analysis of the RNA-seq data revealed 1,751 genes expressed at a higher level in the male. By differential expression and co-expression analyses, we identified transcription factors required for differentiation of male genital structures, semen proteins, and candidates for components of synapse function. Comparison with other prediction tools suggests that our dataset can expand gene predictions. The results validate the dataset as a rich resource for future gene discovery in C. elegans.
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Byunghyuk
authors.initials: B
authors.lastname: Kim
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Bangxia
authors.initials: B
authors.lastname: Suo
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Electronic address: scott.emmons@einstein.yu.edu.
authors.forename: Scott W
authors.initials: SW
authors.lastname: Emmons
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000196:embryology* / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics / Q000378:metabolism; D002923:Cilia / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D005260:Female; D018507:Gene Expression Regulation, Developmental; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017238:Genes, Helminth; D056726:Genetic Association Studies; D008297:Male; D012661:Semen / Q000378:metabolism; D017423:Sequence Analysis, RNA; D019849:Sex Determination Processes; D012741:Sexual Maturation / Q000235:genetics; D013569:Synapses / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D029742:Caenorhabditis elegans Proteins; D014157:Transcription Factors
keywords: C. elegans male; RNA sequencing; co-expression analysis; differential expression; male transcription factors; semen protein; sex-specific gene expression; sexual dimorphism; synapse function