Spatial transcriptomics of C. elegans males and hermaphrodites identifies sex-specific differences in gene expression patterns


  • A. Ebbing
  • Á. Vértesy
  • M.C. Betist
  • B. Spanjaard
  • J.P. Junker
  • E. Berezikov
  • A. van Oudenaarden
  • H.C. Korswagen


  • Developmental Cell


  • Dev Cell 47 (6): 801-813


  • 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.