PMID- 30416013 OWN - NLM STAT- MEDLINE VI - 47 IP - 6 TI - Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns. PG - 801-813.e6 CI - Copyright © 2018 Elsevier Inc. All rights reserved. LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Dev Cell JT - Developmental cell JID - 101120028 IS - 1878-1551 (Electronic) LID - S1534-5807(18)30837-2 [pii] LID - 10.1016/j.devcel.2018.10.016 [doi] FAU - Ebbing, Annabel AU - Ebbing A AD - Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. FAU - Vértesy, Ábel AU - Vértesy Á AD - Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. FAU - Betist, Marco C AU - Betist MC AD - Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. FAU - Spanjaard, Bastiaan AU - Spanjaard B AD - Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin-Buch, Germany. FAU - Junker, Jan Philipp AU - Junker JP AD - Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin-Buch, Germany. FAU - Berezikov, Eugene AU - Berezikov E AD - European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands. FAU - van Oudenaarden, Alexander AU - van Oudenaarden A AD - Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. FAU - Korswagen, Hendrik C AU - Korswagen HC AD - Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address: r.korswagen@hubrecht.eu. IS - 1534-5807 (Linking) RN - 0 (Caenorhabditis elegans Proteins) RN - 0 (Nuclear Proteins) RN - 0 (RNA, Messenger) RN - 0 (Transcription Factors) SB - IM MH - Animals MH - Caenorhabditis elegans/genetics/metabolism MH - Caenorhabditis elegans Proteins/genetics/metabolism MH - Cell Differentiation MH - Disorders of Sex Development/genetics MH - Female MH - Gene Expression Profiling/*methods MH - Gene Expression Regulation, Developmental/genetics MH - Germ Cells/metabolism MH - Gonads/metabolism MH - Hermaphroditic Organisms/metabolism MH - Male MH - Meiosis MH - Nuclear Proteins/metabolism MH - Ovary/metabolism MH - RNA, Messenger/genetics MH - *Sex Characteristics MH - Sex Determination Processes/*genetics MH - Spatio-Temporal Analysis MH - Spermatozoa/metabolism MH - Transcription Factors/metabolism MH - Transcriptome/*genetics OTO - NOTNLM OT - *C. elegans OT - *CEL-seq OT - *germline OT - *mRNA sequencing OT - *male fertility OT - *spatial transcriptomics OT - *sperm DCOM- 20190520 LR - 20190520 DP - 20181217 DEP - 20181108 AB - 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.