Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns

• DOI: 10.1016/j.devcel.2018.10.016
• Publication Date: 2018-11-08T15:40:51Z
• Authors: Annabel Ebbing; Ábel Vértesy; Marco C. Betist; Bastiaan Spanjaard; Jan Philipp Junker; Eugene Berezikov; Alexander van Oud...; Hendrik C. Korswagen
• Keywords: Male; 0301 basic medicine; CEL-seq; Disorders of Sex Development; mRNA sequencing; germline; sperm; male fertility; VESICLES; 03 medical and health sciences; Spatio-Temporal Analysis; NEUROPEPTIDE GENE; 5. Gender equality; Journal Article; Animals; Hermaphroditic Organisms; RNA, Messenger; Caenorhabditis elegans; Caenorhabditis elegans Proteins; Gonads; NEURONS; GERM-LINE; Sex Characteristics; 0303 health sciences; spatial transcriptomics; Gene Expression Profiling; Ovary; Gene Expression Regulation, Developmental; Nuclear Proteins; Cell Differentiation; NEMATODE; Sex Determination Processes; 16. Peace & justice; MALE MATING-BEHAVIOR; Spermatozoa; Sperm; READ ALIGNMENT; FAMILY; Meiosis; Germ Cells; C. elegans; Female; SPERM

To advance our understanding of the genetic programs that drive cell and tissue specialization, it is necessary to obtain a comprehensive overview of gene expression patterns. Here, we have used spatial transcriptomics to generate high-resolution, anteroposterior gene expression maps of C. elegans males and hermaphrodites. To explore these maps, we have developed computational methods for discovering region- and tissue-specific genes. We have found extensive sex-specific gene expression differences in the germline and sperm and discovered genes that are specifically expressed in the male reproductive tract. These include a group of uncharacterized genes that encode small secreted proteins that are required for male fertility. We conclude that spatial gene expression maps provide a powerful resource for identifying tissue-specific gene functions in C. elegans. Importantly, we found that expression maps from different animals can be precisely aligned, enabling transcriptome-wide comparisons of gene expression patterns.