Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary
- University of California, Davis, United States
- Mount Desert Island Biological Laboratory, United States
Abstract
Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage (≥5 dpf). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells and ovarian stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, we used gene knockout experiments to determine the roles of foxl2l and wnt9b for oocyte development and sex determination and/or differentiation, respectively. Our results reveal novel insights into zebrafish ovarian development and function and the transcriptome profiles will provide a valuable resource for future studies.
Data availability
The raw and processed data reported in this paper are archived at NCBI GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE191137) and in an interactively browsable forms at the Broad Institute Single-Cell Portal (https://singlecell.broadinstitute.org/single_cell/study/SCP928/40dpf-ovary-all-cells). Analysis code and objects are archived at github (https://github.com/yulongliu68/zeb_ov_ssRNAseq). Gene expression tables for the cell clusters identified are archived at Dryad: (https://datadryad.org/stash/share/CEd0Zs4oZKdinTWeJPKbWYjBq6hYq4QhVacQcFjf37E).
-
Single-cell transcriptome reveals insights into the development and function of the zebrafish ovaryNCBI Gene Expression Omnibus, GSE191137.
-
Single-cell transcriptome reveals insights into the development and function of the zebrafish ovaryDryad Digital Repository, doi:10.25338/B8FH12.
Article and author information
Author details
Funding
National Institutes of Health (R01 HD-081551)
- Yulong Liu
- Matthew E McFaul
- Lana N Christensen
- Bruce W Draper
National Science Foundation (IOS-1456737)
- Michelle E Kassack
- Lana N Christensen
- Bruce W Draper
National Institutes of Health (T32 training grant ES-0070599)
- Michelle E Kassack
National Institutes of Health (T32 training grant GM-007377)
- Matthew E McFaul
- Sydney R Wyatt
National Science Foundation (GRFP 2036201)
- Sydney R Wyatt
National Institutes of Health (R35 GM133689)
- Stefan Siebert
- Celina E Juliano
National Institutes of Health (R01 DK126021)
- Iain A Drummond
National Institutes of Health (R01)
- Caramai N Kamei
- Iain A Drummond
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols (#20200 and #20201) of the University of California, Davis.
Copyright
© 2022, Liu et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 7,289
- views
-
- 1,079
- downloads
-
- 74
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary
eLife 11:e76014.
https://doi.org/10.7554/eLife.76014
Further reading
-
- Developmental Biology
- Evolutionary Biology
Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genome assemblies revealed suggestive gene content differences and provided the opportunity for detailed genetic analyses. We created a single-cell RNA sequencing atlas of Gulf pipefish embryos to understand the developmental basis of four traits: derived head shape, toothlessness, dermal armor, and male pregnancy. We completed marker gene analyses, built genetic networks, and examined the spatial expression of select genes. We identified osteochondrogenic mesenchymal cells in the elongating face that express regulatory genes bmp4, sfrp1a, and prdm16. We found no evidence for tooth primordia cells, and we observed re-deployment of osteoblast genetic networks in developing dermal armor. Finally, we found that epidermal cells expressed nutrient processing and environmental sensing genes, potentially relevant for the brooding environment. The examined pipefish evolutionary innovations are composed of recognizable cell types, suggesting that derived features originate from changes within existing gene networks. Future work addressing syngnathid gene networks across multiple stages and species is essential for understanding how the novelties of these fish evolved.
-
- Developmental Biology
- Genetics and Genomics
Smads and their transcription factor partners mediate the transcriptional responses of target cells to secreted ligands of the transforming growth factor-β (TGF-β) family, including those of the conserved bone morphogenetic protein (BMP) family, yet only a small number of direct target genes have been well characterized. In C. elegans, the BMP2/4 ortholog DBL-1 regulates multiple biological functions, including body size, via a canonical receptor-Smad signaling cascade. Here, we identify functional binding sites for SMA-3/Smad and its transcriptional partner SMA-9/Schnurri based on ChIP-seq peaks (identified by modEncode) and expression differences of nearby genes identified from RNA-seq analysis of corresponding mutants. We found that SMA-3 and SMA-9 have both overlapping and unique target genes. At a genome-wide scale, SMA-3/Smad acts as a transcriptional activator, whereas SMA-9/Schnurri direct targets include both activated and repressed genes. Mutations in sma-9 partially suppress the small body size phenotype of sma-3, suggesting some level of antagonism between these factors and challenging the prevailing model for Schnurri function. Functional analysis of target genes revealed a novel role in body size for genes involved in one-carbon metabolism and in the endoplasmic reticulum (ER) secretory pathway, including the disulfide reductase dpy-11. Our findings indicate that Smads and SMA-9/Schnurri have previously unappreciated complex genetic and genomic regulatory interactions that in turn regulate the secretion of extracellular components like collagen into the cuticle to mediate body size regulation.
