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Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis
Oogenesis produces functional eggs and is essential for fertility, embryonic development, and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates, and recent studies have identified multiple regulators in oocyte development through forward genetic screens, as we...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9207522/ https://www.ncbi.nlm.nih.gov/pubmed/35733854 http://dx.doi.org/10.3389/fcell.2022.826892 |
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author | Bogoch, Yoel Jamieson-Lucy, Allison Vejnar, Charles E. Levy, Karine Giraldez, Antonio J. Mullins, Mary C. Elkouby, Yaniv M. |
author_facet | Bogoch, Yoel Jamieson-Lucy, Allison Vejnar, Charles E. Levy, Karine Giraldez, Antonio J. Mullins, Mary C. Elkouby, Yaniv M. |
author_sort | Bogoch, Yoel |
collection | PubMed |
description | Oogenesis produces functional eggs and is essential for fertility, embryonic development, and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates, and recent studies have identified multiple regulators in oocyte development through forward genetic screens, as well as reverse genetics by CRISPR mutagenesis. However, many developmental steps in oogenesis, in zebrafish and other species, remain poorly understood, and their underlying mechanisms are unknown. Here, we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis, from the onset of oocyte differentiation through Stage III, which precedes oocyte maturation. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis, as well as their expression in pair-wise comparisons between stages. We determined their functionally enriched terms, identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish, which we deposit online as a resource for the community. Further, the presence of multiple gene paralogs in zebrafish, and the exclusive curation by many bioinformatic tools of the single paralogs present in humans, challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether, our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development. |
format | Online Article Text |
id | pubmed-9207522 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-92075222022-06-21 Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis Bogoch, Yoel Jamieson-Lucy, Allison Vejnar, Charles E. Levy, Karine Giraldez, Antonio J. Mullins, Mary C. Elkouby, Yaniv M. Front Cell Dev Biol Cell and Developmental Biology Oogenesis produces functional eggs and is essential for fertility, embryonic development, and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates, and recent studies have identified multiple regulators in oocyte development through forward genetic screens, as well as reverse genetics by CRISPR mutagenesis. However, many developmental steps in oogenesis, in zebrafish and other species, remain poorly understood, and their underlying mechanisms are unknown. Here, we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis, from the onset of oocyte differentiation through Stage III, which precedes oocyte maturation. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis, as well as their expression in pair-wise comparisons between stages. We determined their functionally enriched terms, identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish, which we deposit online as a resource for the community. Further, the presence of multiple gene paralogs in zebrafish, and the exclusive curation by many bioinformatic tools of the single paralogs present in humans, challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether, our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development. Frontiers Media S.A. 2022-06-06 /pmc/articles/PMC9207522/ /pubmed/35733854 http://dx.doi.org/10.3389/fcell.2022.826892 Text en Copyright © 2022 Bogoch, Jamieson-Lucy, Vejnar, Levy, Giraldez, Mullins and Elkouby. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Cell and Developmental Biology Bogoch, Yoel Jamieson-Lucy, Allison Vejnar, Charles E. Levy, Karine Giraldez, Antonio J. Mullins, Mary C. Elkouby, Yaniv M. Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis |
title | Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis |
title_full | Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis |
title_fullStr | Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis |
title_full_unstemmed | Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis |
title_short | Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis |
title_sort | stage specific transcriptomic analysis and database for zebrafish oogenesis |
topic | Cell and Developmental Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9207522/ https://www.ncbi.nlm.nih.gov/pubmed/35733854 http://dx.doi.org/10.3389/fcell.2022.826892 |
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