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Pham-Bui HA, Lee M. Germ granule-mediated mRNA storage and translational control. RNA Biol 2025; 22:1-11. [PMID: 39895378 PMCID: PMC11810088 DOI: 10.1080/15476286.2025.2462276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Revised: 12/24/2024] [Accepted: 01/28/2025] [Indexed: 02/04/2025] Open
Abstract
Germ cells depend on specialized post-transcriptional regulation for proper development and function, much of which is mediated by dynamic RNA granules. These membrane-less organelles form through the condensation of RNA and proteins, governed by multivalent biomolecular interactions. RNA granules compartmentalize cellular components, selectively enriching specific factors and modulating biochemical reactions. Over recent decades, various types of RNA granules have been identified in germ cells across species, with extensive studies uncovering their molecular roles and developmental significance. This review explores the mRNA regulatory mechanisms mediated by RNA granules in germ cells. We discuss the distinct spatial organization of specific granule components and the variations in material states of germ granules, which contribute to the regulation of mRNA storage and translation. Additionally, we highlight emerging research on how changes in these material states, during developmental stages, reflect the dynamic nature of germ granules and their critical role in development.
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Affiliation(s)
- Hoang-Anh Pham-Bui
- Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan-si, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si, Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan-si, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si, Korea
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2
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Miskel D, Kurzella J, Rings F, Tholen E, Tesfaye D, Schellander K, Salilew-Wondim D, Held-Hoelker E, Große-Brinkhaus C, Hoelker M. Functional COPA is indispensable for early embryo development beyond major genome activation in bovines. Theriogenology 2025; 241:117415. [PMID: 40215828 DOI: 10.1016/j.theriogenology.2025.117415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 03/28/2025] [Accepted: 03/28/2025] [Indexed: 04/23/2025]
Abstract
Embryonic genome activation is divided into a minor and a major wave of transition to endogenous transcription. In bovines, minor genome activation begins early in the 2-cell stage and is completed by the 8-cell stage when major genome activation becomes dominant. While the activation of genes known to regulate early development have been studied extensively, genes involved in more central cellular functions have not been examined. Taking advantage of the CRISPR Cas9 system, the present study investigated the effect of knocking out the Golgi retrograde protein transporter COPA on early bovine development. After the electroporation of presumptive zygotes with Cas9 ribonucleoproteins targeting COPA exon 6, sequences of 2 (11 %) and 4-cell (16 %) embryos showed knockouts of COPA whereas 8-cell embryos and blastocysts did not, demonstrating that COPA is necessary for development to the 8-cell stage and beyond. Using a repair template containing silent mutations along the target site, COPA loss of wildtype was observed in 5 blastocysts, with successful knock-in of the template on at least one allele. This shows that an edited yet functional copy of COPA can save the developmental capacity of the embryo and demonstrates that Cas9 activity at the target region itself is not responsible for the loss of function. Together, the present study revealed that COPA is necessary for embryonic development, and that the timing of this necessity is before major genome activation onset. More generally, this study further demonstrates the utility of genome editing within reproductive biotechnology for the interrogation of gene function and early embryonic development.
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Affiliation(s)
- Dennis Miskel
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Jessica Kurzella
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Franca Rings
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Ernst Tholen
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Dawit Tesfaye
- Department of Biomedical Sciences, Animal Reproduction and Biotechnology Laboratory, Colorado State University, 3105 Rampart Rd, Fort Collins, CO, 80521, United States.
| | - Karl Schellander
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Dessie Salilew-Wondim
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany; Department of Animal Science, Biotechnology and Reproduction of farm animals, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany.
| | - Eva Held-Hoelker
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany; Department of Animal Science, Biotechnology and Reproduction of farm animals, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany.
| | - Christine Große-Brinkhaus
- Institute of Animal Sciences, Animal Breeding, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
| | - Michael Hoelker
- Department of Animal Science, Biotechnology and Reproduction of farm animals, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany.
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Fan Y, Pavani KC, Bogado Pascottini O, Broeckx BJG, Smits K, Van Soom A, Peelman L. Tracing the dynamic changes in the lncRNA-mediated competing endogenous RNA network during bovine preimplantation embryo development. J Dairy Sci 2025; 108:6367-6380. [PMID: 40139367 DOI: 10.3168/jds.2024-25919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Accepted: 02/13/2025] [Indexed: 03/29/2025]
Abstract
Long noncoding RNAs (lncRNAs) can regulate gene expression by "sponging" microRNAs (miRNAs), reducing their inhibitory effects on mRNAs. However, this mechanism has been minimally investigated in preimplantation embryo development. In this study, we revisited existing RNA sequencing and small RNA sequencing data to investigate the role of lncRNAs in in vitro-produced bovine preimplantation embryos. Our findings revealed that although lncRNAs exhibit expression patterns similar to mRNAs, maternal lncRNAs degrade earlier than mRNAs during embryonic genome activation (EGA). Weighted gene co-expression network analysis identified 27 modules of mRNA and lncRNA, with enrichment analysis showing a significant negative correlation between the polycomb repressive complex pathway and blastocyst formation (R2 = -0.98). Additionally, bioinformatics analysis was used to predict and construct lncRNA-miRNA-mRNA networks, highlighting that lncRNAs bind more to miRNAs compared with mRNAs. Moreover, lncRNA-induced lncRNA-miRNA-mRNA axes participated in mRNA degradation and biogenesis around the EGA stage. These interactions became stronger after EGA, especially after the 16-cell stage. Overall, our study provides new insights into lncRNA-mediated regulatory networks during bovine preimplantation development.
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Affiliation(s)
- Yuan Fan
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke-Melle, Belgium
| | - Krishna Chaitanya Pavani
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke-Melle, Belgium; Department for Reproductive Medicine, Ghent University Hospital, 9000 Ghent, Belgium
| | - Osvaldo Bogado Pascottini
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke-Melle, Belgium; School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Bart J G Broeckx
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke-Melle, Belgium
| | - Katrien Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke-Melle, Belgium
| | - Ann Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke-Melle, Belgium
| | - Luc Peelman
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke-Melle, Belgium.
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Wen D, Wang J. Totipotency or plenipotency: rethinking stem cell bipotentiality. Curr Opin Genet Dev 2025; 92:102342. [PMID: 40107116 DOI: 10.1016/j.gde.2025.102342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 02/13/2025] [Accepted: 02/26/2025] [Indexed: 03/22/2025]
Abstract
The term 'totipotency' has often been misapplied in stem cell research to describe cells with embryonic and extraembryonic bipotentiality, despite a lack of evidence that they can generate an entire organism from a single cell. Additionally, no specific term currently distinguishes bipotential stem cells from pluripotent cells, which contribute poorly to extraembryonic tissues. This review examines the developmental continuum from totipotency to pluripotency in early embryos and revisits the previously proposed concept of plenipotency in preimplantation development. We evaluate emerging stem cell models that exhibit bipotentiality but have lost the ability to autonomously initiate and sustain the sequential fate decisions necessary to develop into a complete organism. Unlike totipotent embryonic cells, which retain the information required to initiate fate decisions at the correct timing and cell numbers, these stem cells have lost that capacity. This loss of critical developmental information distinguishes totipotency from plenipotency, with bipotential stem cells aligning more closely with the latter. By distinguishing plenipotency from totipotency and pluripotency, we aim to refine terminology, enhance our understanding of early embryonic development, and address ethical considerations in human research.
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Affiliation(s)
- Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Yang J, Peng Q, Shen M, Liu G, Xu X, Wang C, Ning J. A C1q domain-containing protein from Scapharca subcrenata may participate in the immune defense against pathogen infection. FISH & SHELLFISH IMMUNOLOGY 2025; 164:110438. [PMID: 40404027 DOI: 10.1016/j.fsi.2025.110438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 05/13/2025] [Accepted: 05/20/2025] [Indexed: 05/24/2025]
Abstract
The C1q domain-containing proteins (C1qDCs) have been shown to play crucial roles in immune responses among invertebrates, but few studies have focused on immune regulatory pathways in bivalves. In this study, we identified a C1qDC gene with a typical C1q domain (designated as SsC1qDC1) from Scapharca subcrenata and characterized its potential immune response against pathogen infection. The full-length cDNA sequence of SsC1qDC1 was 870 bp, encoding a peptide of 259 amino acids with an N-terminal signal peptide. Sequence analysis indicated that SsC1qDC1 was not conserved compared with C1qDCs from other bivalves. SsC1qDC1 was detected in all examined tissues, with higher expression levels in hepatopancreas, mantle, and gill. Concurrently, the expressions of SsC1qDC1 increased significantly from eggs to the gastrula stage and increased remarkably following Vibrio parahaemolyticus challenge. RNA interference-mediated knockdown of SsC1qDC1 significantly repressed the expressions of maternally derived immune-related genes (Vg, Lysozyme, Dscam, TEP, complement C3, and C1qDC3), while remarkably augmenting the expression of phenoloxidase activation factor PAF3. Furthermore, compared to the controls, the phagocytosis rate and total number of hemocytes were markedly reduced in the SsC1qDC1-silenced ark shells post V. parahaemolyticus infection, and thus, a significant increase in mortality rate and hemocyte apoptotic levels. Collectively, these findings implied that SsC1qDC1 may play crucial roles in immune defense against pathogen infection in ark shells.
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Affiliation(s)
- Jing Yang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Peng
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Min Shen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Guilong Liu
- Yantai Spring-Sea AquaSeed Co., Ltd., Yantai, Shandong, 264006, China
| | - Xin Xu
- Yantai Spring-Sea AquaSeed Co., Ltd., Yantai, Shandong, 264006, China
| | - Chunde Wang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Yantai Spring-Sea AquaSeed Co., Ltd., Yantai, Shandong, 264006, China.
| | - Junhao Ning
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China.
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Xu M, Wang W, Lu S, Xiong M, Zhao T, Yu Y, Song C, Yang J, Zhang N, Cao L, Sun G, Chen S, Wang P. The advances in acetylation modification in senescence and aging-related diseases. Front Physiol 2025; 16:1553646. [PMID: 40421455 PMCID: PMC12104306 DOI: 10.3389/fphys.2025.1553646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Accepted: 04/28/2025] [Indexed: 05/28/2025] Open
Abstract
Aging is a process in which organisms or cells undergo a decline in their functions. Epigenetic modification changes have been recognized as a senescence hallmark in both natural aging and stimulation-induced senescence. An acetylation modification is a dynamic process, which plays a crucial role in the senescence process through DNA stability, metabolism, and signaling pathways. We summarized the role and regulatory pathways of acetylation modifications in senescence. Various cell fate-determining proteins regulate multiple cellular processes through acetylation modifications. These processes interact and coordinate with each other, forming an integrated regulatory network framework that collectively drives cellular senescence via multiple systemic mechanisms. Based on these findings, we proposed the "acetylation-network regulation-cellular senescence" model, to elaborate how acetylation contributes to senescence. We believe this insight could provide new directions and intervention strategies for senescence and aging-related diseases.
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Affiliation(s)
- Maiqi Xu
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Wenbin Wang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Saien Lu
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Mengyao Xiong
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Tong Zhao
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Yao Yu
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Chunyu Song
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Jinjing Yang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Naijin Zhang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Liu Cao
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Guozhe Sun
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Sichong Chen
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
- Department of Pharmaceutical Toxicology, School of Pharmacy, China Medical University, Shenyang, China
| | - Pengbo Wang
- Department of Cardiology, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
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7
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Budelli G, Ferreiro MJ, Bolatto C. Taking flight, the use of Drosophila melanogaster for neuroscience research in Uruguay. Neuroscience 2025; 573:104-119. [PMID: 40058485 DOI: 10.1016/j.neuroscience.2025.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 02/27/2025] [Accepted: 03/04/2025] [Indexed: 03/25/2025]
Abstract
The Sociedad de Neurociencias del Uruguay is celebrating its 30th anniversary, sustained by more than a century of neuroscience research in the country. During this time, different approaches and experimental organisms have been incorporated to study diverse aspects of neurobiology. One of these experimental animals, successfully used in a variety of biological fields, is the fruit fly Drosophila melanogaster. Although Drosophila has been a model organism for neuroscience research worldwide for many decades, its use in Uruguay for that purpose is relatively new and just taking flight. In this special issue article, we will describe some of the research lines that are currently using Drosophila for neuroscience studies, questioning a wide range of issues including thermoreception, neurodegenerative diseases such as Parkinson's, screening of bioactive compounds with a neuroprotective effect, and gene/protein function during development of the nervous system. The consolidation of these research lines has been achieved due to unique features of D. melanogaster as an experimental model. We will review the advantages of using Drosophila to study neurobiology and describe some of its useful genetic tools. Advantages such as having powerful genetics, highly conserved disease pathways, a complete connectome, very low comparative costs, easy maintenance, and the support of a collaborative community allowing access to a vast toolkit, all make D. melanogaster an ideal model organism for neuroscientists in countries with low levels of investment in research and development. This review focuses on the strengths and description of useful techniques to study neurobiology using Drosophila, from the perspective of a Latin-American experience.
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Affiliation(s)
- Gonzalo Budelli
- Unidad Académica de Biofísica, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay.
| | - María José Ferreiro
- Departamento de Neurofarmacología Experimental, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Ministerio de Educación y Cultura (MEC), Montevideo, Uruguay
| | - Carmen Bolatto
- Unidad Académica de Histología y Embriología, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay; Departamento de Neurobiología y Neuropatología, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Ministerio de Educación y Cultura (MEC), Montevideo, Uruguay
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Kassim Y, Sheng H, Xu G, Jin H, Iqbal T, Elashry M, Zhang K. Integrated Multi-Omics Analysis Reveals Key Regulators of Bovine Oocyte Maturation. Int J Mol Sci 2025; 26:3973. [PMID: 40362214 PMCID: PMC12071811 DOI: 10.3390/ijms26093973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2025] [Revised: 04/11/2025] [Accepted: 04/15/2025] [Indexed: 05/15/2025] Open
Abstract
A well-regulated metabolism is crucial for optimal oocyte development and embryonic health. However, the metabolic framework governing oocyte maturation remains poorly understood. Using bovine oocytes as a model, we examined metabolomic and transcriptomic alterations during the transition from the germinal vesicle (GV) to the metaphase II (MII) stage. Our findings reveal distinct metabolic shifts, including suppressed β-oxidation combined with the accumulation of long-chain fatty acids (LCFAs). Notably, progesterone emerged as a key regulator of meiotic resumption through its influence on cAMP levels. We also observed enhanced glycolysis, moderate activation of the citric acid cycle (TCA cycle), and suppression of oxidative phosphorylation (OXPHOS), alongside reduced urea cycle flux and shifts in amino acid metabolism favoring glutamate synthesis. Intriguingly, discrepancies between metabolic and transcriptional activities in pathways such as the TCA cycle and nucleotide metabolism suggest asynchronous regulation. These findings provide a comprehensive multi-omics resource, advancing our understanding of the dynamic metabolic and transcriptional landscape during bovine oocyte maturation.
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Affiliation(s)
- Yassin Kassim
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Animal and Poultry Production, Faculty of Agriculture, Minia University, El-Minya 61519, Egypt
| | - Hao Sheng
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Guangjun Xu
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hao Jin
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tariq Iqbal
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mostafa Elashry
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kun Zhang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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Xing J, Yang S, Liang Y, Hu P, Dai B, Li H, Xing Y, Zuo Y. Deciphering Sequence Determinants of Zygotic Genome Activation Genes: Insights From Machine Learning and the ZGAExplorer Platform. Cell Prolif 2025:e70039. [PMID: 40251810 DOI: 10.1111/cpr.70039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Revised: 03/11/2025] [Accepted: 03/28/2025] [Indexed: 04/21/2025] Open
Abstract
The mammalian life cycle initiates with the transition of genetic control from the maternal to the embryonic genome during zygotic genome activation (ZGA), which becomes pivotal for development. Nevertheless, understanding the conservation of genes and transcription factors (TFs) that underlie mammalian ZGA remains limited. Here, we compiled a comprehensive set of ZGA genes from mice, humans, pigs, bovines and goats, including Nr5a2 and TPRX1/2. The identification of 111 homologous genes through comparative analyses was followed by the discovery of a conserved genetic coding region, suggesting potential sequence preferences for ZGA genes. Notably, an interpretable machine learning model based on k-mer core features showed excellent performance in predicting ZGA genes (area under the ROC curve [AUC] > 0.81), revealing abundant and intricate 6-base sequence specific patterns and potential binding TFs, including motifs from NR5A2 and TPRX1/2. Further analysis demonstrated that gene sequence features and epigenetic modification features play equally important roles in regulating ZGA genes. Ultimately, we developed the ZGAExplorer platform to provide an invaluable resource for screening ZGA genes. Our study unravels the sequence determinants of ZGA genes across species through multi-omics data integration and machine learning, yielding insights into ZGA regulatory mechanisms and embryonic developmental arrest.
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Affiliation(s)
- Jixiang Xing
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Siqi Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yuchao Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Pengwei Hu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Bingjie Dai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Hanshuang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yongqiang Xing
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, China
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Leroy E, Gao S, Gonzalez M, Ellies-Oury MP, Tuda M. Wolbachia infection facilitates adaptive increase in male egg size in response to environmental changes. Sci Rep 2025; 15:13213. [PMID: 40240454 PMCID: PMC12003752 DOI: 10.1038/s41598-025-96680-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Accepted: 03/31/2025] [Indexed: 04/18/2025] Open
Abstract
Under challenging conditions such as maladapted biotic and abiotic conditions, females can plastically adjust their egg size (gamete or zygote size) to counteract fitness declines early in life. Recent evidence suggests that endosymbionts may enhance this egg-size plasticity. Possible endosymbionts' modification of impact of multiple stressors is not well explored. Therefore, this study aims to test (1) whether Wolbachia infection influences the plasticity of parental investment in egg size under suboptimal environmental conditions and (2) whether the plasticity depends on the sex of eggs. We used three lines of the azuki bean beetle (Callosobruchus chinensis): a line coinfected with the wBruCon and wBruOri Wolbachia strains, a cured line infected solely with the wBruCon, and an uninfected (cured) line. These lines were subjected to either a control environment or a simulated climate change environment (elevated temperature and carbon dioxide levels, eT&CO2) to examine Wolbachia infection effects on parental investment in their offspring (egg size) and its subsequent impact on offspring fitness, including survival, development, and adult lifespan under starvation. After two days of eT&CO2 exposure, coinfected parents increased male egg size only. Larger eggs developed faster in both sexes and exhibited higher survival. However, offspring adult lifespan was not influenced by egg size but by environment, sex, Wolbachia infection, and development time: eT&CO2 reduced male lifespan but not female lifespan, the singly-infected line females lived longer than coinfected and uninfected line females, and shorter development time linked to longer lifespan. The negative correlation between development time and lifespan was higher under eT&CO2 but not sex-specific. This study is the first to demonstrate sex-specific egg size plasticity associated with Wolbachia infection in species with sex determination systems other than haplodiploid.
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Affiliation(s)
- Eloïse Leroy
- Laboratory of Insect Natural Enemies, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
- Bordeaux Sciences Agro, 33170, Gradignan, France
| | - Siyi Gao
- Laboratory of Insect Natural Enemies, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
| | | | | | - Midori Tuda
- Laboratory of Insect Natural Enemies, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan.
- Institute of Biological Control, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan.
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Pérez-Roldán J, Henn L, Bernués J, Torras-LLort M, Tamirisa S, Belloc E, Rodríguez-Muñoz L, Timinszky G, Jiménez G, Méndez R, Carbonell A, Azorín F. Maternal histone mRNAs are uniquely processed through polyadenylation in a Stem-Loop Binding Protein (SLBP) dependent manner. Nucleic Acids Res 2025; 53:gkaf288. [PMID: 40239992 PMCID: PMC11997800 DOI: 10.1093/nar/gkaf288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 03/22/2025] [Accepted: 04/01/2025] [Indexed: 04/18/2025] Open
Abstract
During early embryogenesis the zygotic genome remains transcriptionally silent and expression relies on maternally deposited products. Maternal deposition of histones is crucial to preserve chromatin integrity during early embryo development, when the number of nuclei exponentially increases in the absence of zygotic expression. In the Drosophila embryo, histones are maternally deposited as both proteins and mRNAs. Histone transcripts are the only nonpolyadenylated cellular mRNAs. They contain a highly conserved 3'UTR stem-loop structure, which is recognized by the Stem-Loop Binding Protein (SLBP) that, in conjunction with U7 snRNP, regulates their unique 3'-end processing. Here we report that, unexpectedly, maternal histone mRNAs are polyadenylated and have a truncated 3' stem-loop. This noncanonical 3'-end processing of maternal histone mRNAs occurs at their synthesis during oogenesis and requires SLBP, but not U7 snRNP. We show that maternal histone transcripts are subjected to cytoplasmic poly(A) tail elongation by Wisp, which results in their stabilization and is a requisite for translation. We also show that maternal histone transcripts remain largely quiescent and that their translation is activated upon loss of the embryonic linker histone dBigH1, which impairs chromatin assembly and induces DNA damage. Here, we discuss possible models to integrate these observations.
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Affiliation(s)
- Juan Pérez-Roldán
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - László Henn
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Mònica Torras-LLort
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Srividya Tamirisa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Eulàlia Belloc
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Laura Rodríguez-Muñoz
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
| | - Gyula Timinszky
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Gerardo Jiménez
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Raúl Méndez
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Albert Carbonell
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
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12
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Pankammoon P, Salinas MBS, Thitaram C, Sathanawongs A. The Complexities of Interspecies Somatic Cell Nuclear Transfer: From Biological and Molecular Insights to Future Perspectives. Int J Mol Sci 2025; 26:3310. [PMID: 40244161 PMCID: PMC11989385 DOI: 10.3390/ijms26073310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2025] [Revised: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/18/2025] Open
Abstract
For nearly three decades, interspecies somatic cell nuclear transfer (iSCNT) has been explored as a potential tool for cloning, regenerative medicine, and wildlife conservation. However, developmental inefficiencies remain a major challenge, largely due to persistent barriers in nucleocytoplasmic transport, mitonuclear communication, and epigenome crosstalk. This review synthesized peer-reviewed English articles from PubMed, Web of Science, and Scopus, spanning nearly three decades, using relevant keywords to explore the molecular mechanisms underlying iSCNT inefficiencies and potential improvement strategies. We highlight recent findings deepening the understanding of interspecies barriers in iSCNT, emphasizing their interconnected complexities, including the following: (1) nucleocytoplasmic incompatibility may disrupt nuclear pore complex (NPC) assembly and maturation, impairing the nuclear transport of essential transcription factors (TFs), embryonic genome activation (EGA), and nuclear reprogramming; (2) mitonuclear incompatibility could lead to nuclear and mitochondrial DNA (nDNA-mtDNA) mismatches, affecting electron transport chain (ETC) assembly, oxidative phosphorylation, and energy metabolism; (3) these interrelated incompatibilities can further influence epigenetic regulation, potentially leading to incomplete epigenetic reprogramming in iSCNT embryos. Addressing these challenges requires a multifaceted, species-specific approach that balances multiple incompatibilities rather than isolating a single factor. Gaining insight into the molecular interactions between the donor nucleus and recipient cytoplast, coupled with optimizing strategies tailored to specific pairings, could significantly enhance iSCNT efficiency, ultimately transforming experimental breakthroughs into real-world applications in reproductive biotechnology, regenerative medicine, and species conservation.
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Affiliation(s)
- Peachanika Pankammoon
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (P.P.); (C.T.)
| | - Marvin Bryan Segundo Salinas
- Department of Basic Veterinary Sciences, College of Veterinary Science and Medicine, Central Luzon State University, Science City of Muñoz 3120, Nueva Ecija, Philippines;
| | - Chatchote Thitaram
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (P.P.); (C.T.)
- Elephant, Wildlife and Companion Animals Research Group, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Anucha Sathanawongs
- Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; (P.P.); (C.T.)
- Elephant, Wildlife and Companion Animals Research Group, Chiang Mai University, Chiang Mai 50100, Thailand
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13
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Lin Z, Liu M, Chen F, Zhao C, Liu Y, Sun H. Lethal toxicity of metformin on zebrafish during early embryonic development by multi-omics analysis. Sci Rep 2025; 15:11309. [PMID: 40175592 PMCID: PMC11965512 DOI: 10.1038/s41598-025-95816-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 03/24/2025] [Indexed: 04/04/2025] Open
Abstract
Metformin is an antidiabetic drug used in type 2 diabetes as well as indicators in polycystic ovary syndrome (PCOS) and cancer. Due to their increase in popularity, high amounts of metformin are being released into aquatic environments. However, the toxic effect of metformin on embryonic development in aquatic organisms remains limited. Therefore, this study aimed to elucidate the lethal embryotoxicity of metformin and determine the underlying molecular pathways influencing embryonic development using a zebrafish model through multi-omics analysis. Metformin was microinjected into zebrafish embryos at the 1-cell stage with varying concentrations (50 mM, 100 mM, 200 mM, 400 mM, and 800 mM). From the results, hatching rates decreased in a dose dependent manner. Fetal malformation and mortality (LC50 = 339.8 mM) increased in a dose dependent manner. In situ hybridization of whole-embryo assays demonstrated that metformin exerts a significant impact on the initial stages of embryonic development, leading to aberrant differentiation of the germ layers, perturbed organogenesis, and delayed development. Furthermore, transcriptomics, metabolomics, and lipidomics were used to study the molecular mechanisms of embryonic toxicity. The results showed that the cell cycle, dorsoventral axis formation, and collecting duct acid secretion pathways were significantly altered in treated embryos. In brief, these results provide useful information on the lethal toxicity mechanism of metformin overdose and provide clues for further studies in humans.
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Affiliation(s)
- Ziyuan Lin
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Zebrafish Research Platform, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, Sichuan, China
- Children's Medicine Key Laboratory of Sichuan Province, Chengdu, China
| | - Mingfeng Liu
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Zebrafish Research Platform, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, Sichuan, China
| | - Feng Chen
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Zebrafish Research Platform, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, Sichuan, China
| | - Chanjuan Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, Sichuan, China
| | - Yanyan Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, Sichuan, China.
| | - Huaqin Sun
- SCU-CUHK Joint Laboratory for Reproductive Medicine, Zebrafish Research Platform, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, Sichuan, China.
- Children's Medicine Key Laboratory of Sichuan Province, Chengdu, China.
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14
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Shukla Y, Ghatpande V, Hu CF, Dickinson DJ, Cenik C. Landscape and regulation of mRNA translation in the early C. elegans embryo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.12.13.628416. [PMID: 39829802 PMCID: PMC11741243 DOI: 10.1101/2024.12.13.628416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Animal embryos rely on regulated translation of maternally deposited mRNAs to drive early development. Using low-input ribosome profiling combined with RNA sequencing on precisely staged embryos, we measured mRNA translation during the first four cell cycles of C. elegans development. We uncovered stage-specific patterns of developmentally coordinated translational regulation. We confirmed that mRNA localization correlates with translational eLiciency, though initial translational repression in germline precursors occurs before P-granule association. Our analysis suggests that the RNA-binding protein OMA-1 represses the translation of its target mRNAs in a stage-specific manner, while indirectly promoting the translational eLiciency of other transcripts. These findings illuminate how post-transcriptional mechanisms shape the embryonic proteome to direct cell diLerentiation, with implications for understanding similar regulation across species where maternal factors guide early development.
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Affiliation(s)
- Yash Shukla
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Vighnesh Ghatpande
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Cindy F. Hu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel J. Dickinson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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15
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Alaniz-Fabián J, Xiang D, Del Toro-De León G, Gao P, Abreu-Goodger C, Datla R, Gillmor CS. A maternal transcriptome bias in early Arabidopsis embryogenesis. Development 2025; 152:dev204449. [PMID: 40067256 DOI: 10.1242/dev.204449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Accepted: 02/25/2025] [Indexed: 04/09/2025]
Abstract
After fertilization in animals, maternal mRNAs and proteins regulate development until the onset of zygotic transcription. In plants, the extent of maternal regulation of early embryo development has been less clear: two hybrid combinations of rice zygotes have a strong maternal transcript bias, zygotes of a third rice hybrid produced by gamete fusion show a small percentage of maternally biased genes, while Arabidopsis Col/Cvi and Col/Ler hybrid embryos display symmetric and asymmetric parental genome activation, respectively. Here, we explore parent-of-origin transcriptome behavior in the Arabidopsis Col/Tsu hybrid, which was previously shown to display maternal effects for embryo defective mutants indistinguishable from those of the reference ecotype, Col. Analysis of Col/Tsu transcriptomes revealed a reciprocal maternal bias in thousands of genes in zygotes and octant stage embryos. Several lines of evidence suggest that this transient maternal bias is due to preferential transcription of maternal alleles in the zygote, rather than inheritance of transcripts from the egg. Our results extend previous observations that parent-of-origin contributions to early embryogenesis differ between hybrids of Arabidopsis, show that the maternal genome plays a predominant role in early embryos of Col/Tsu, and point to a maternal transcriptome bias in early embryos of the Arabidopsis reference ecotype Columbia.
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Affiliation(s)
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | | | - Peng Gao
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - C Stewart Gillmor
- Unidad de Genómica Avanzada, Cinvestav, Irapuato, Guanajuato 36824, Mexico
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16
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Kotb NM, Ulukaya G, Ramamoorthy A, Park LS, Tang J, Hasson D, Rangan P. TORC1-driven translation of Nucleoporin44A promotes chromatin remodeling and germ cell-to-maternal transition in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.14.643309. [PMID: 40161787 PMCID: PMC11952567 DOI: 10.1101/2025.03.14.643309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Oocyte specification is a critical developmental transition that requires the coordinated repression of germ cell-specific genes and activation of the maternal program to support embryogenesis. In Drosophila, the timely repression of germ cell and early oogenesis genes is essential for this transition, yet the mechanisms that coordinate this process remain unclear. Here, we uncover an unexpected translation-chromatin axis, where transient Target of Rapamycin Complex 1 (TORC1)-driven translation triggers chromatin remodeling, ensuring irreversible oocyte fate commitment. Through a screen, we identified ribosome biogenesis regulators, including Zinc finger protein RP-8 (Zfrp8) and TORC1 components, as key mediators of gene silencing. We show that TORC1 activity increases during oocyte specification, and disrupting ribosome biogenesis, translation, or TORC1 function prevents proper heterochromatin formation, leading to epigenetic instability. Polysome-seq analysis of zfrp8-depleted ovaries revealed that Zfrp8 is required for the translation of Nucleoporin 44A (Nup44A), a key nuclear pore complex (NPC) component. Given the role of the NPC in chromatin organization, independent disruption of Nup44A results in defective silencing of the germ cell and early oogenesis genes. Our findings reveal a mechanism in which translation-driven NPC remodeling coordinates heterochromatin establishment, facilitating the germ cell-to-maternal transition and ensuring proper oocyte fate commitment.
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Affiliation(s)
- Noor M. Kotb
- Department of Biomedical Sciences/Wadsworth Center, University at Albany State University of New York (SUNY), Albany, New York 12202, USA
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
- Current address, Hologic Diagenode, 400 Morris Avenue, Suite 101, Denville, New Jersey 07834, USA
| | - Gulay Ulukaya
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Anupriya Ramamoorthy
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
| | - Lina Seojin Park
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
| | - Julia Tang
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
| | - Dan Hasson
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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17
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Rock AQ, Srivastava M. The gain and loss of plasticity during development and evolution. Trends Cell Biol 2025:S0962-8924(25)00030-3. [PMID: 40037967 DOI: 10.1016/j.tcb.2025.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 01/22/2025] [Accepted: 01/24/2025] [Indexed: 03/06/2025]
Abstract
Studies of embryonic plasticity, which were foundational for developmental biology, revealed variation across species and patterns of association with cleavage programs and adult regenerative capacity. Modern molecular and genetic tools now enable a reexamination of these classical experiments in diverse species and have the potential to reveal mechanisms that regulate plasticity over developmental time. This review synthesizes previous work on plasticity in embryos and adults and associated genetic mechanisms, providing a framework to organize data from a wide range of species. Mechanisms that explain how plasticity is lost in mammalian embryos are highlighted and crystallize a proposal for future studies in new research organisms that could identify shared principles for embryonic plasticity and, potentially, its maintenance into adulthood.
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Affiliation(s)
- Amber Q Rock
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
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18
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Trevena RL, Veire BM, Chamberlain TJ, Moravec CE, Pelegri F. Embryonic Lethality, Juvenile Growth Variation, and Adult Sterility Correlate With Phylogenetic Distance of Danionin Hybrids. Evol Dev 2025; 27:e12495. [PMID: 39639649 PMCID: PMC11621593 DOI: 10.1111/ede.12495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 10/01/2024] [Accepted: 11/08/2024] [Indexed: 12/07/2024]
Abstract
Hybrid incompatibility, which plays a pivotal role in speciation, is expected to correlate with greater phylogenetic distance. Here, we investigate the fitness of interspecies hybrids within the Danionin subfamily, which includes the model species, Danio rerio, and its relatives - Danio kyathit, Danio albolineatus, Danio margaritatus, and Devario aequipinnatus. We generated hybrids through in vitro fertilization, using Danio rerio as the maternal species, with normal fertilization rates showing no incompatibilities in sperm-egg interactions within these two genera. Generally, all hybrids exhibit normal patterns and timelines in early developmental transitions, from cleavage stages to the initiation of epiboly, although inter-genera Danio-Devario hybrids subsequently exhibit fully penetrant embryonic lethality. Intra-genus Danio hybrids, on the other hand, can survive through embryogenesis and into adulthood. However, rates of survival during these stages diminish according to phylogenetic distance, with increasing early lethality in hybrids from more distantly related species. Additionally, Danio hybrids exhibit increased growth rate variability during juvenile stages. All Danio hybrids have reduced testes sizes, sperm counts, and sperm viabilities, with sperm displaying defects in flagellum formation and integrity. Adult male intra-genus hybrids are invariably sterile, except in the case of Danio rerio hybrids with the closely related Danio kyathit, which produced a backcrossed F2 generation that did not survive juvenile stages. Our studies highlight a loss of hybrid compatibility at various life stages in the Danio and Devario genera, based on deleterious effects and reduced developmental robustness, emphasizing a correlation between the severity of incompatibility outcomes and the degree of phylogenetic relatedness.
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Affiliation(s)
- Ryan L. Trevena
- Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Benton M. Veire
- Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | | | - Cara E. Moravec
- Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Francisco Pelegri
- Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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19
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Teimuri S, Suter B. Drosophila Topoisomerase 3β binds to mRNAs in vivo, contributes to their localization and stability, and counteracts premature aging. PLoS One 2025; 20:e0318142. [PMID: 39932982 DOI: 10.1371/journal.pone.0318142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 01/12/2025] [Indexed: 02/13/2025] Open
Abstract
Topoisomerase 3β (Top3β) works not only on DNA but also on RNA. We isolated and identified the naturally cross-linked RNA targets of Drosophila Top3β from an early embryonic stage that contains almost exclusively maternal mRNAs. Favorite targets were long RNAs, particularly with long 3'UTRs, and RNAs that become localized in large cells. Top3β lacking only the hydroxyl group that makes the covalent bond to the RNA, did not allow normal expression and localization of Top3β mRNA targets or their protein products, demonstrating the importance of the enzymatic activity of Top3 β for optimized gene expression. Top3β is not essential for development to the adult stage but to maintain the morphology of the adult neuromuscular junction and to prevent premature loss of coordinated movement and aging. Alterations in human Top3β have been associated with several neurological diseases and cancers. The homologs of genes and (pre)mRNAs mis-expressed in these conditions show the same characteristics identified in the Drosophila Top3β targets, suggesting that Drosophila could model human Top3β. An in vivo test of this model showed that the enzymatic activity of Top3β reduces the neurodegeneration caused by the cytotoxic human (G4C2)49 RNA. Top3β supports normal gene expression, particularly of long and complex transcripts that must be transported and translationally controlled. These RNAs encode large cytoskeletal, cortical, and membrane proteins that are particularly important in large and long cells like motoneurons. Their reduced expression in the mutant seems to stress the cells, increasing the chances of developing neurodegenerative diseases.
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Affiliation(s)
- Shohreh Teimuri
- Institute of Cell Biology, University of Bern, Berne, Switzerland
| | - Beat Suter
- Institute of Cell Biology, University of Bern, Berne, Switzerland
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20
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O'Haren T, Aoki T, Rieder LE. Zelda is dispensable for Drosophila melanogaster histone gene regulation. Mol Biol Cell 2025; 36:br3. [PMID: 39661467 PMCID: PMC11809315 DOI: 10.1091/mbc.e24-01-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 11/26/2024] [Accepted: 12/06/2024] [Indexed: 12/13/2024] Open
Abstract
To ensure that the embryo can package exponentially increasing amounts of DNA, replication-dependent histones are some of the earliest transcribed genes from the zygotic genome. However, how the histone genes are identified is not known. The Drosophila melanogaster pioneer factor CLAMP regulates the embryonic histone genes and helps establish the histone locus body, a suite of factors that controls histone mRNA biosynthesis, but CLAMP is not unique to the histone genes. Zelda collaborates with CLAMP across the genome to regulate zygotic genome activation and target early activated genes. We hypothesized that Zelda helps identify histone genes for early embryonic expression. We found that Zelda targets the histone gene locus early during embryogenesis, prior to histone gene expression. However, depletion of zelda in the early embryo does not affect histone mRNA levels or prevent the recruitment of other factors. These results suggest the earliest events responsible for specifying the zygotic histone genes remain undiscovered.
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Affiliation(s)
- Tommy O'Haren
- Department of Biology, Emory University, Atlanta, GA 30322
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
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21
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Nunes OBDS, Buranello TW, Farias FDA, Rosero J, Recchia K, Bressan FF. Can cell-cultured meat from stem cells pave the way for sustainable alternative protein? Curr Res Food Sci 2025; 10:100979. [PMID: 40040753 PMCID: PMC11878651 DOI: 10.1016/j.crfs.2025.100979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 01/09/2025] [Accepted: 01/18/2025] [Indexed: 03/06/2025] Open
Abstract
As the global population grows, the demand for food and animal-derived products rises significantly, posing a notable challenge to the progress of society in general. Alternative protein production may adequately address such a challenge, and cell-based meat production emerges as a promising solution. This review investigates methodologies for in vitro myogenesis and adipogenesis from stem cells (adult, embryonic, or induced pluripotent stem cells - iPSCs) across different animal species, as well as the remaining challenges for scalability, the possibility of genetic modification, along with safety concerns regarding the commercialization of cell-cultured meat. Regarding such complexities, interdisciplinary approaches will be vital for assessing the potential of cell-cultured meat as a sustainable protein source, mimicking the sensory and nutritional attributes of conventional livestock meat whilst meeting the demands of a growing global population while mitigating environmental impacts.
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Affiliation(s)
- Octavio Bignardi da Silva Nunes
- Department of Food Engineering, Faculty of Animal Sciences and Food Engineering, University of São Paulo 13635-000, Pirassununga, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo 13635-000, Pirassununga, SP, Brazil
| | - Tiago Willian Buranello
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo 13635-000, Pirassununga, SP, Brazil
- Postgraduate Program in Anatomy of Domestic and Wils Species, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo 01001-010, SP, Brazil
| | - Fabiana de Andrade Farias
- Department of Food Engineering, Faculty of Animal Sciences and Food Engineering, University of São Paulo 13635-000, Pirassununga, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo 13635-000, Pirassununga, SP, Brazil
| | - Jenyffer Rosero
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo 13635-000, Pirassununga, SP, Brazil
- Postgraduate Program in Anatomy of Domestic and Wils Species, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo 01001-010, SP, Brazil
| | - Kaiana Recchia
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo 13635-000, Pirassununga, SP, Brazil
- Postgraduate Program in Anatomy of Domestic and Wils Species, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo 01001-010, SP, Brazil
| | - Fabiana Fernandes Bressan
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo 13635-000, Pirassununga, SP, Brazil
- Postgraduate Program in Anatomy of Domestic and Wils Species, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo 01001-010, SP, Brazil
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22
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Weissenboeck FP, Pieper M, Schepers H, Hötte S, Klöcker N, Hüwel S, van Impel A, Schulte-Merker S, Rentmeister A. Spatiotemporal control of translation in live zebrafish embryos via photoprotected mRNAs. Commun Chem 2025; 8:16. [PMID: 39828804 PMCID: PMC11743775 DOI: 10.1038/s42004-025-01411-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 01/07/2025] [Indexed: 01/22/2025] Open
Abstract
Translation of mRNA into protein is a fundamental process and tightly controlled during development. Several mechanisms acting on the mRNA level regulate when and where an mRNA is expressed. To explore the effects of conditional and transient gene expression in a developing organism, it is vital to experimentally enable abrogation and restoration of translation. We recently developed the FlashCaps technology allowing preparation of translationally muted mRNAs and their controlled activation by light. Here, we validate its functionality in vivo. We demonstrate that translation of FlashCap-eGFP-mRNA can be triggered in zebrafish embryos with spatiotemporal control. The injected FlashCap-mRNA is stable for hours and remains muted. Light-mediated activation up to 24 h post fertilization produces visible amounts of eGFP and can be restricted to distinct parts of the embryo. This methodology extends the toolbox for vertebrate models by enabling researchers to locally activate mRNA translation at different timepoints during development.
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Affiliation(s)
| | - Melissa Pieper
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Helena Schepers
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Sophie Hötte
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, University of Münster, Münster, Germany
- Multiscale Imaging Center, University of Münster, Münster, Germany
| | - Nils Klöcker
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Andreas van Impel
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, University of Münster, Münster, Germany
- Multiscale Imaging Center, University of Münster, Münster, Germany
| | - Stefan Schulte-Merker
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, University of Münster, Münster, Germany
- Multiscale Imaging Center, University of Münster, Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Münster, Germany.
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany.
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23
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Toda E, Koshimizu S, Kinoshita A, Higashiyama T, Izawa T, Yano K, Okamoto T. Transcriptional dynamics during karyogamy in rice zygotes. Development 2025; 152:DEV204497. [PMID: 39777484 PMCID: PMC11829756 DOI: 10.1242/dev.204497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 12/18/2024] [Indexed: 01/11/2025]
Abstract
Upon fertilization, male and female nuclei fuse to form the zygotic nucleus in angiosperms. Karyogamy is considered to be essential for proper embryogenesis; however, the transcriptional dynamics during karyogamy in plant zygotes remain unclear. In this study, we performed a single-cell transcriptome analysis of rice zygotes at six early developmental stages (15 min, 30 min, 1 h, 2 h, 4 h, and 6 h after gamete fusion) to reveal gene expression profiles during karyogamy in plant zygotes. The time-series RNA-sequencing analysis detected possible de novo and altered gene expression in zygotes from 15 min post-fertilization. Fertilization-induced transcription during karyogamy was characterized by protein interaction database and gene ontology (GO) analyses. Furthermore, paternal allele transcription was initiated approximately 30 min to 1 h after gamete fusion, when nuclear fusion begins in the zygote. Some transcripts preferentially expressed in egg cells were downregulated after gamete fusion. Moreover, a dynamic shift from maternal-biased transcripts to bi-parental expression occurred during early zygotic development. These results suggest that transcriptional dynamics during karyogamy plays an initial role in proper and sequential zygotic development and embryogenesis.
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Affiliation(s)
- Erika Toda
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
- Department of Biological Sciences, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
- Department of Agricultural and Environmental Biology, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Shizuka Koshimizu
- Department of Life Sciences, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Atsuko Kinoshita
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Tetsuya Higashiyama
- Department of Biological Sciences, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Takeshi Izawa
- Department of Agricultural and Environmental Biology, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Kentaro Yano
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
- WellGreen-i Co. Ltd., Kawasaki, Kanagawa 215-0007, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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24
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O'Leary TS, Mikucki EE, Tangwancharoen S, Boyd JR, Frietze S, Helms Cahan S, Lockwood BL. Single-nuclei multiome ATAC and RNA sequencing reveals the molecular basis of thermal plasticity in Drosophila melanogaster embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.08.631745. [PMID: 39829925 PMCID: PMC11741353 DOI: 10.1101/2025.01.08.631745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Embryogenesis is remarkably robust to temperature variability, yet there is limited understanding of the homeostatic mechanisms that offset thermal effects during early development. Here, we measured the thermal acclimation response of upper thermal limits and profiled chromatin state and the transcriptome of D. melanogaster embryos (Bownes Stage 11) using single-nuclei multiome ATAC and RNA sequencing. We report that thermal acclimation, while preserving a common set of primordial cell types, rapidly shifted the upper thermal limit. Cool-acclimated embryos showed a homeostatic response characterized by increased chromatin accessibility at transcription factor binding motifs for the transcriptional activator Zelda, along with enhanced activity of gene regulatory networks in the primordial cell types including the foregut and hindgut, mesoderm, and peripheral nervous system. In addition, cool-acclimated embryos had higher expression of genes encoding ribosomal proteins and enzymes involved in oxidative phosphorylation. Despite the hypothesis that differential heat tolerance might be explained by differential expression of molecular chaperones, we did not observe widespread differences in the chromatin accessibility or expression of heat shock genes. Overall, our results suggest that environmental robustness to temperature during embryogenesis necessitates homeostatic gene expression responses that regulate the speed of development, potentially imposing metabolic costs that constrain upper thermal limits.
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Affiliation(s)
- Thomas S O'Leary
- Department of Biology, University of Vermont, Burlington, VT 05405
| | - Emily E Mikucki
- Department of Biology, University of Vermont, Burlington, VT 05405
| | | | - Joseph R Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05401
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05401
| | - Sara Helms Cahan
- Department of Biology, University of Vermont, Burlington, VT 05405
| | - Brent L Lockwood
- Department of Biology, University of Vermont, Burlington, VT 05405
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25
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Biel N, Rashid F, Natua S, Wang TY, Chou TF, Nguyen TVP, Golding I, Kalsotra A, Sokac AM. Reducing Cofilin dosage makes embryos resilient to heat stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.02.631102. [PMID: 39803506 PMCID: PMC11722379 DOI: 10.1101/2025.01.02.631102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2025]
Abstract
In addition to regulating the actin cytoskeleton, Cofilin also senses and responds to environmental stress. Cofilin can promote cell survival or death depending on context. Yet, many aspects of Cofilin's role in survival need clarification. Here, we show that exposing early Drosophila embryos to mild heat stress (32°C) induces a Cofilin-mediated Actin Stress Response and upregulation of heat- and ER- stress response genes. However, these responses do not alleviate the negative impacts of heat exposure. Instead, heat stressed embryos show downregulation of hundreds of developmental genes, including determinants of the embryonic body plan, and are less likely to hatch as larvae and adults. Remarkably, reducing Cofilin dosage blunts induction of all stress response pathways, mitigates downregulation of developmental genes, and completely rescues survival. Thus, Cofilin intersects with multiple stress response pathways, and modulates the transcriptomic response to heat stress. Strikingly, Cofilin knockdown emerges as a potent pro-survival manipulation for embryos.
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Affiliation(s)
- Natalie Biel
- Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Faizan Rashid
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- These authors contributed equally
| | - Subhashis Natua
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- These authors contributed equally
| | - Ting-Yu Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Thu Vu Phuc Nguyen
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ido Golding
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Anna Marie Sokac
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Lead contact
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26
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Liu M, Li E, Mu H, Zhao Z, Chen X, Gao J, Gao D, Liu Z, Han J, Zhong L, Cao S. LncRNA XLOC-040580 targeted by TPRA1 coordinate zygotic genome activation during porcine embryonic development. Cell Transplant 2025; 34:9636897251332527. [PMID: 40245181 PMCID: PMC12035016 DOI: 10.1177/09636897251332527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Revised: 02/26/2025] [Accepted: 03/11/2025] [Indexed: 04/19/2025] Open
Abstract
Long noncoding RNAs (lncRNAs) are crucial in porcine preimplantation embryonic development, yet their regulatory role during zygote genome activation (ZGA) is poorly understood. We analyzed transcriptome data from porcine fetal fibroblasts (PEF), induced pluripotent stem cells (iPS), and preimplantation embryos, identifying ZGA-specific lncRNAs like XLOC-040580, and further predicted its potentially interacting genes TPRA1 and BCL2L1 via co-expression network. XLOC-040580 was knocked down by siRNA microinjection and the expression of ZGA-related genes was detected by qRT-PCR. After microinjecting siRNA targeting TPRA1 and BCL2L1 at the one-cell stage, we counted the blastocyst development rate. The blastocyst development rate was consistent with the results from si-XLOC-040580 after si-TPRA1. Through dual-luciferase reporter assays, we found that XLOC-040580 was a downstream target of TPRA1. To further elucidate the mechanism of XLOC-040580, Single-cell mRNA sequencing after XLOC-040580 knockdown revealed its regulatory network involved in embryonic developmental defects. Transcriptome analysis revealed that XLOC-040580 was specifically expressed during zygote activation. Knockdown of XLOC-040580 decreased the blastocyst development rate and reduced both the total blastocyst cell number and TE cell number. TPRA1 and BCL2L1 were specifically co-expressed with XLOC-040580 during ZGA stage, and TPRA1 could interact with the promoter region of XLOC-040580 and regulate its expression. Knockdown of TPRA1 or XLOC-040580 blocked porcine embryonic development by affecting the expression of ZGA-related genes. We found and validated that lncRNA XLOC-040580 played a key role in the ZGA process, which was regulated by TPRA1. These results implied that the functional axis of TPRA1-XLOC-040580-downstream genes involved in ZGA-related functions also coordinated early embryonic development in porcine.
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Affiliation(s)
- Mengxin Liu
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Enhong Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haiyuan Mu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zimo Zhao
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xinze Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jie Gao
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Dengfeng Gao
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhiyu Liu
- National-Local Associated Engineering Laboratory for Personalized Cell Therapy, Shenzhen, China
| | - Jianyong Han
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Liang Zhong
- Hebei Provincial Key Laboratory of Basic Medicine for Diabetes, The Shijiazhuang Second Hospital, Shijiazhuang, China
| | - Suying Cao
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
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27
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Karami N, Taei A, Eftekhari-Yazdi P, Hassani F. Signaling pathway regulators in preimplantation embryos. J Mol Histol 2024; 56:57. [PMID: 39729177 DOI: 10.1007/s10735-024-10338-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Accepted: 12/12/2024] [Indexed: 12/28/2024]
Abstract
Embryonic development during the preimplantation stages is highly sensitive and critically dependent on the reception of signaling cues. The precise coordination of diverse pathways and signaling factors is essential for successful embryonic progression. Even minor disruptions in these factors can result in physiological dysfunction, fetal malformations, or embryonic arrest. This issue is particularly evident in assisted reproductive technologies, such as in vitro fertilization, where embryonic arrest is frequently observed. A detailed understanding of these pathways enhances insight into the fundamental mechanisms underlying cellular processes and their contributions to embryonic development. The significance of elucidating signaling pathways and their regulatory factors in preimplantation development cannot be overstated. The application of this knowledge in laboratory settings has the potential to support strategies for modeling developmental stages and diseases, drug screening, therapeutic discovery, and reducing embryonic arrest. Furthermore, using various factors, small molecules, and pharmacological agents can enable the development or optimization of culture media for enhanced embryonic viability. While numerous pathways influence preimplantation development, this study examines several critical signaling pathways in this contex.
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Affiliation(s)
- Narges Karami
- MSc., Faculty of Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Adeleh Taei
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Poopak Eftekhari-Yazdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, P.O.Box 16635-148, Tehran, Iran
| | - Fatemeh Hassani
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, P.O.Box 16635-148, Tehran, Iran.
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28
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Yamazaki H, Furuichi M, Katagiri M, Kajitani R, Itoh T, Chiba K. Recycling of Uridylated mRNAs in Starfish Embryos. Biomolecules 2024; 14:1610. [PMID: 39766317 PMCID: PMC11674185 DOI: 10.3390/biom14121610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 12/11/2024] [Accepted: 12/11/2024] [Indexed: 01/11/2025] Open
Abstract
In eukaryotes, mRNAs with long poly(A) tails are translationally active, but deadenylation and uridylation of these tails generally cause mRNA degradation. However, the fate of uridylated mRNAs that are not degraded quickly remains obscure. Here, using tail-seq and microinjection of the 3' region of mRNA, we report that some mRNAs in starfish are re-polyadenylated to be translationally active after deadenylation and uridylation. In oocytes, uridylated maternal cyclin B mRNAs are stable without decay, and they are polyadenylated to be translated after hormonal stimulation to resume meiosis, whereas they are deadenylated and re-uridylated at the blastula stage, followed by decay. Similarly, deadenylated and uridylated maternal ribosomal protein mRNAs, Rps29 and Rpl27a, were stable and inactive after hormonal stimulation, but they had been polyadenylated and active before hormonal stimulation. At the morula stage, uridylated maternal ribosomal protein mRNAs were re-polyadenylated, rendering them translationally active. These results indicate that uridylated mRNAs in starfish exist in a poised state, allowing them to be recycled or decayed.
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Affiliation(s)
- Haruka Yamazaki
- Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.K.)
| | - Megumi Furuichi
- Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.K.)
| | - Mikoto Katagiri
- Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.K.)
| | - Rei Kajitani
- School of Life Science and Technology, Institute of Science Tokyo, Meguro-ku, Tokyo 152-8550, Japan; (R.K.); (T.I.)
| | - Takehiko Itoh
- School of Life Science and Technology, Institute of Science Tokyo, Meguro-ku, Tokyo 152-8550, Japan; (R.K.); (T.I.)
| | - Kazuyoshi Chiba
- Department of Biological Sciences, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan (M.K.)
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29
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Bhatt AD, Brown MG, Wackford AB, Shindo Y, Amodeo AA. Local nuclear to cytoplasmic ratio regulates H3.3 incorporation via cell cycle state during zygotic genome activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603602. [PMID: 39071352 PMCID: PMC11275841 DOI: 10.1101/2024.07.15.603602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Early embryos often have unique chromatin states prior to zygotic genome activation (ZGA). In Drosophila, ZGA occurs after 13 reductive nuclear divisions during which the nuclear to cytoplasmic (N/C) ratio grows exponentially. Previous work found that histone H3 chromatin incorporation decreases while its variant H3.3 increases leading up to ZGA. In other cell types, H3.3 is associated with sites of active transcription and heterochromatin, suggesting a link between H3.3 and ZGA. Here, we test what factors regulate H3.3 incorporation at ZGA. We find that H3 nuclear availability falls more rapidly than H3.3 leading up to ZGA. We generate H3/H3.3 chimeric proteins at the endogenous H3.3A locus and observe that chaperone binding, but not gene structure, regulates H3.3 behavior. We identify the N/C ratio as a major determinant of H3.3 incorporation. To isolate how the N/C ratio regulates H3.3 incorporation we test the roles of genomic content, zygotic transcription, and cell cycle state. We determine that cell cycle regulation, but not H3 availability or transcription, controls H3.3 incorporation. Overall, we propose that local N/C ratios control histone variant usage via cell cycle state during ZGA.
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Affiliation(s)
- Anusha D. Bhatt
- Department of Biological sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Madeleine G. Brown
- Department of Biological sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Aurora B. Wackford
- Department of Biological sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Yuki Shindo
- Department of Biological sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Amanda A. Amodeo
- Department of Biological sciences, Dartmouth College, Hanover, NH 03755, USA
- Lead contact
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30
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Degen EA, Croslyn C, Mangan NM, Blythe SA. Bicoid-nucleosome competition sets a concentration threshold for transcription constrained by genome replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.10.627802. [PMID: 39713295 PMCID: PMC11661180 DOI: 10.1101/2024.12.10.627802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Transcription factors (TFs) regulate gene expression despite constraints from chromatin structure and the cell cycle. Here we examine the concentration-dependent regulation of hunchback by the Bicoid morphogen through a combination of quantitative imaging, mathematical modeling and epigenomics in Drosophila embryos. By live imaging of MS2 reporters, we find that, following mitosis, the timing of transcriptional activation driven by the hunchback P2 (hb P2) enhancer directly reflects Bicoid concentration. We build a stochastic model that can explain in vivo onset time distributions by accounting for both the competition between Bicoid and nucleosomes at hb P2 and a negative influence of DNA replication on transcriptional elongation. Experimental modulation of nucleosome stability alters onset time distributions and the posterior boundary of hunchback expression. We conclude that TF-nucleosome competition is the molecular mechanism whereby the Bicoid morphogen gradient specifies the posterior boundary of hunchback expression.
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Affiliation(s)
- Eleanor A Degen
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston Illinois 60208, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Corinne Croslyn
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston Illinois 60208, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Niall M Mangan
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL, USA
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL, USA
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31
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Serradimigni R, Rojas A, Pal U, Pathirajage KS, Bryan M, Sharma S, Dasgupta S. Flame retardant tetrabromobisphenol A (TBBPA) disrupts histone acetylation during zebrafish maternal-to-zygotic transition. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135845. [PMID: 39305598 PMCID: PMC11822891 DOI: 10.1016/j.jhazmat.2024.135845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/28/2024] [Accepted: 09/14/2024] [Indexed: 09/25/2024]
Abstract
3,3',5.5'-Tetrabromobisphenol A (TBBPA) is a widely used brominated flame-retardant. The objective of this study is to use zebrafish as a model and determine the effects of TBBPA exposure on early embryogenesis. We initiated TBBPA exposures at 0.75 h post fertilization (hpf) and showed that TBBPA induced developmental delays during maternal-to-zygotic transition (MZT) and zygotic genome activation (ZGA). To examine the genetic basis of TBBPA-induced delays, we conducted mRNA-sequencing on embryos exposed to 0 or 40 μM TBBPA from 0.75 hpf to 2, 3.5 or 4.5 hpf. Read count data showed that while TBBPA exposures had no overall impacts on maternal or maternal-zygotic genes, collective read counts for zygotically activated genes were lower in TBBPA treatment at 4.5 hpf compared to time-matched controls, suggesting that TBBPA delays ZGA. Gene ontology assessments for both time- and stage-matched differentially expressed genes revealed TBBPA-induced inhibition of chromatin assembly- a process regulated by histone modifications. Immunostaining and in vitro experiments showed inhibition of histone H3 lysine 27 acetylation (H3K27Ac) as well as its catalyzing enzyme, p300. Finally, co-exposure with a p300 activator showed partial mitigation of effects, demonstrating that inhibition of histone acetylation drives TBBPA-induced developmental delays.
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Affiliation(s)
| | - Alfredo Rojas
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Uttam Pal
- Technical Research Centre, S.N. Bose National Centre for Basic Sciences, Kolkata, WB, India
| | | | - Madeline Bryan
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Sunil Sharma
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Subham Dasgupta
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.
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32
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Cui X, Li H, Huang X, Xue T, Wang S, Zhu X, Jing X. N 6-Methyladenosine Modification on the Function of Female Reproductive Development and Related Diseases. Immun Inflamm Dis 2024; 12:e70089. [PMID: 39660878 PMCID: PMC11632877 DOI: 10.1002/iid3.70089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Revised: 10/17/2024] [Accepted: 11/20/2024] [Indexed: 12/12/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) modification is a widespread and reversible epigenetic alteration in eukaryotic mRNA, playing a pivotal role in various biological functions. Its significance in female reproductive development and associated diseases has recently become a focal point of research. OBJECTIVE This review aims to consolidate current knowledge of the role of m6A modification in female reproductive tissues, emphasizing its regulatory dynamics, functional significance, and implications in reproductive health and disease. METHODS A comprehensive analysis of recent studies focusing on m6A modification in ovarian development, oocyte maturation, embryo development, and the pathogenesis of reproductive diseases. RESULTS m6A modification exhibits dynamic regulation in female reproductive tissues, influencing key developmental stages and processes. It plays critical roles in ovarian development, oocyte maturation, and embryo development, underpinning essential aspects of reproductive health. m6A modification is intricately involved in the pathogenesis of several reproductive diseases, including polycystic ovary syndrome (PCOS), premature ovarian failure (POF), and endometriosis, offering insights into potential molecular mechanisms and therapeutic targets. CONCLUSION The review highlights the crucial role of m6A modification in female reproductive development and related diseases. It underscores the need for further research to explore innovative diagnostic and therapeutic strategies for reproductive disorders, leveraging the insights gained from understanding m6A modification's impact on reproductive health.
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Affiliation(s)
- Xiangrong Cui
- Reproductive Medicine CenterThe affiliated Children's Hospital of Shanxi Medical University, Children's Hospital of Shanxi, Shanxi Maternal and Child Health HospitalTaiyuanChina
| | - Huihui Li
- Reproductive Medicine CenterThe affiliated Children's Hospital of Shanxi Medical University, Children's Hospital of Shanxi, Shanxi Maternal and Child Health HospitalTaiyuanChina
| | - Xia Huang
- Department of Clinical LaboratoryShanxi Provincial People's Hospital, Shanxi Medical UniversityTaiyuanChina
| | - Tingting Xue
- Department of Clinical LaboratoryShanxi Provincial People's Hospital, Shanxi Medical UniversityTaiyuanChina
| | - Shu Wang
- Department of Clinical LaboratoryShanxi Provincial People's Hospital, Shanxi Medical UniversityTaiyuanChina
| | - Xinyu Zhu
- Department of Clinical LaboratoryShanxi Provincial People's Hospital, Shanxi Medical UniversityTaiyuanChina
| | - Xuan Jing
- Department of Clinical LaboratoryShanxi Provincial People's Hospital, Shanxi Medical UniversityTaiyuanChina
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Li XH, Lee SH, Lu QY, Zhan CL, Lee GH, Kim JD, Sim JM, Song HJ, Cui XS. MAT2A is essential for zygotic genome activation by maintaining of histone methylation in porcine embryos. Theriogenology 2024; 230:81-90. [PMID: 39276507 DOI: 10.1016/j.theriogenology.2024.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/18/2024] [Accepted: 09/08/2024] [Indexed: 09/17/2024]
Abstract
Methionine adenosyltransferase 2A (MAT2A) is an essential enzyme in the methionine cycle that generates S-adenosylmethionine (SAM) by reacting with methionine and ATP. SAM acts as a methyl donors for histone and DNA methylation, which plays key roles in zygotic genome activation (ZGA). However, the effects of MAT2A on porcine ZGA remain unclear. To investigate the function of MAT2A and its underlying mechanism in porcine ZGA, MAT2A was knocked down by double-stranded RNA injection at the 1-cell stage. MAT2A is highly expressed at every stage of porcine embryo development. The percentages of four-cell-stage embryos and blastocysts were lower in the MAT2A-knockdown (KD) group than in the control group. Notably, depletion of MAT2A decreased the levels of H3K4me2, H3K9me2/3, and H3K27me3 at the four-cell stage, whereas MAT2A KD reduced the transcriptional activity of ZGA genes. MAT2A KD decreased embryonic ectoderm development (EED) and enhancer of zeste homolog 2 (EZH2) expression. Exogenous SAM supplementation rescued histone methylation levels and developmental arrest induced by MAT2A KD. Additionally, MAT2A KD significantly increased DNA damage and apoptosis. In conclusion, MAT2A is involved in regulating transcriptional activity and is essential for regulating histone methylation during porcine ZGA.
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Affiliation(s)
- Xiao-Han Li
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Song-Hee Lee
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Qin-Yue Lu
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Cheng-Lin Zhan
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Gyu-Hyun Lee
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Ji-Dam Kim
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Jae-Min Sim
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Hyeon-Ji Song
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Xiang-Shun Cui
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
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Pascual A, Taibo C, Rivera-Pomar R. Central role of squid gene during oocyte development in the Hemiptera Rhodnius prolixus. JOURNAL OF INSECT PHYSIOLOGY 2024; 159:104719. [PMID: 39489393 DOI: 10.1016/j.jinsphys.2024.104719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 10/30/2024] [Accepted: 10/31/2024] [Indexed: 11/05/2024]
Abstract
Oocyte polarity establishment is a conserved and crucial phenomenon for embryonic development. It relies on the precise spatial localization of maternal factors deposited during oocyte development, which is essential for establishing and maintaining cell polarity and subsequently specifying embryonic axes. The heterogeneous nuclear ribonucleoprotein (hnRNP) encoded by the squid (sqd) gene has been implicated in mRNA localization and embryonic axis establishment in Drosophila melanogaster. Comparative genomics allowed for the identification of a homologue in Rhodnius prolixus. In this study, we investigated the function of Rp-sqd during oogenesis and early embryonic development. We observed persistent expression of Rp-sqd during oocyte development, with localization in the cytoplasm of ovary germarium and growing oocytes in previtellogenic and vitellogenic stages. A Parental RNA interference (RNAi) experiment targeting Rp-sqd resulted in female sterility. The ovaries showed disrupted oocyte development, disarray of follicular epithelium, and affected nurse cells integrity. Immunostaining and microscopic techniques revealed microtubule disarray and a reduction in the presence of organelles in the trophic cords that connect the germarium with the oocytes. The Rp-sqd depletion impacted the transcript expression of maternal mRNAs involved in apoptosis, axis formation, oogenesis, and cytoskeleton maintenance, indicating a pleiotropic function of Rp-sqd during oogenesis. This study provides new insights into the genetic basis of R. prolixus oogenesis, highlighting the crucial role of Rp-sqd in oocyte development, fertility, and germarium integrity. These findings contribute to our understanding of insect developmental processes, provide a foundation for future investigations into reproduction, and reveal the regulatory mechanisms governing the process.
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Affiliation(s)
- Agustina Pascual
- Centro de BioInvestigaciones (CeBio‑CICBA), Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA), Pergamino, Argentina; Centro de Investigaciones y Transferencias del Noroeste de la Provincia de Buenos Aires (CITNOBA‑CONICET), Pergamino, Argentina
| | - Catalina Taibo
- Laboratorio de Microscopia Integral (LIM), (CICVyA, INTA), Hurlingham, Argentina
| | - Rolando Rivera-Pomar
- Centro de BioInvestigaciones (CeBio‑CICBA), Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA), Pergamino, Argentina; Centro de Investigaciones y Transferencias del Noroeste de la Provincia de Buenos Aires (CITNOBA‑CONICET), Pergamino, Argentina; Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, La Plata, Argentina; Max Planck Institute for Multidisciplinary Sciences, Dept. Tissue Dynamics and Regeneration, Göttingen, Germany.
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Xu LK, Ma CY, Zhang FY, Wang W, Zhao M, Jin X, Yin JJ, Ma LB, Chen W, Xu JY, Ma KY, Liu ZQ. Embryonic Genome Activation (EGA) Occurred at 1-Cell Stage of Embryonic Development in the Mud Crab, Scylla paramamosain, Revealed by RNA-Seq. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:1246-1259. [PMID: 39249630 DOI: 10.1007/s10126-024-10369-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024]
Abstract
As a prerequisite for the success of embryo development, embryonic genome activation (EGA) is an important biological event in which zygotic gene products in the embryo are activated to replace maternal-derived transcripts. Although EGA has been extensively studied in a large number of vertebrates and invertebrates, there is a lack of information regarding this event in crustacean crab. In this study, the timing of EGA was confirmed by examining a transcriptomic dataset of early embryonic development, including mature oocytes and embryos through six early developmental stages, and signaling pathways associated with EGA were identified in the mud crab, S. paramamosain. The comprehensive transcriptomic data identified a total of 53,915 transcripts from these sequencing samples. Notable transcriptomic change was evident at the 1-cell stage, indicated by a 36% transcript number shift and a reduction in transcript fragment length, compared to those present in the mature oocytes. Concurrently, a substantial increase in the expression of newly transcribed transcripts was observed, with gene counts reaching 3485 at the 1-cell stage, indicative of the onset of EGA. GO functional enrichment revealed key biological processes initiated at the 1-cell stage, such as protein complex formation, protein metabolism, and various biosynthetic processes. KEGG analysis identified several critical signaling pathways activated during EGA, including the "cell cycle," "spliceosome," "RNA degradation", and "RNA polymerase", pathways. Furthermore, transcription factor families, including zinc finger, T-box, Nrf1, and Tub were predominantly enriched at the 1-cell stage, suggesting their pivotal roles in regulating embryonic development through the targeting of specific DNA sequences during the EGA process. This groundbreaking study not only addresses a significant knowledge gap regarding the developmental biology of S. paramamosain, especially for the understanding of the mechanism underlying EGA, but also provides scientific data crucial for the research on the individual synchronization of seed breeding within S. paramamosain aquaculture. Additionally, it serves as a reference basis for the study of early embryonic development in other crustacean species.
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Affiliation(s)
- Li-Kun Xu
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China
- College of Fisheries and Life Science, Shanghai Ocean University, Pudong New Area, Shanghai, People's Republic of China
| | - Chun-Yan Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China
| | - Feng-Ying Zhang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China
| | - Wei Wang
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China
| | - Ming Zhao
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China
| | - Xin Jin
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China
- College of Fisheries and Life Science, Shanghai Ocean University, Pudong New Area, Shanghai, People's Republic of China
| | - Jin-Ju Yin
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China
- College of Fisheries and Life Science, Shanghai Ocean University, Pudong New Area, Shanghai, People's Republic of China
| | - Ling-Bo Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China
| | - Wei Chen
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China
| | - Jia-Yuan Xu
- Ninghai Fishery Innovation Research Center, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ningbo, Zhejiang, People's Republic of China
| | - Ke-Yi Ma
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China.
| | - Zhi-Qiang Liu
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, No.300 Jungong Road, Yangpu Area, Shanghai, 200090, People's Republic of China.
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36
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Ishibashi K, Shichino Y, Han P, Wakabayashi K, Mito M, Inada T, Kimura S, Iwasaki S, Mishima Y. Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish. PLoS Biol 2024; 22:e3002887. [PMID: 39636823 PMCID: PMC11620358 DOI: 10.1371/journal.pbio.3002887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 10/07/2024] [Indexed: 12/07/2024] Open
Abstract
Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision, which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes, triggering ribosome-associated quality control (RQC) to rescue stalled ribosomes and no-go decay (NGD) to degrade stall-prone mRNAs. However, the impact of RQC and NGD on maintaining the translational homeostasis of endogenous mRNAs has remained unclear. In this study, we investigated the endogenous substrate mRNAs of NGD during the maternal-to-zygotic transition (MZT) of zebrafish development. RNA-Seq analysis of zebrafish znf598 mutant embryos revealed that Znf598 down-regulates mRNAs encoding the C2H2-type zinc finger domain (C2H2-ZF) during the MZT. Reporter assays and disome profiling indicated that ribosomes stall and collide while translating tandem C2H2-ZFs, leading to mRNA degradation by Znf598. Our results suggest that NGD maintains the quality of the translatome by mitigating the risk of ribosome collision at the abundantly present C2H2-ZF sequences in the vertebrate genome.
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Affiliation(s)
- Kota Ishibashi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Peixun Han
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Kimi Wakabayashi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Toshifumi Inada
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seisuke Kimura
- Department of Industrial Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yuichiro Mishima
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
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37
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Wang W, Xiong H, Sun MX. Gamete activation for fertilization and seed development in flowering plants. Curr Top Dev Biol 2024; 162:1-31. [PMID: 40180506 DOI: 10.1016/bs.ctdb.2024.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2025]
Abstract
Double fertilization is a defining feature of flowering plants, in which two male gametes (sperm cells) fuse with two female gametes (egg and central cell) to trigger embryogenesis and endosperm development. Gamete activation before fertilization is essential for the success of fertilization, while gamete activation after fertilization is the prerequisite for embryo and endosperm development. The two phases of activation are an associated and continuous process. In this review, we focus on current understanding of gamete activation both before and after fertilization in flowering plants, summarize and discuss the detailed cellular and molecular mechanisms underlying gamete activation for fertilization or initiation of embryogenesis and endosperm development.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, P.R. China
| | - Hanxian Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, P.R. China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, P.R. China.
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38
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Xie D, Ma Y, Ye P, Liu Y, Ding Q, Huang G, Félix MA, Cai Z, Zhao Z. A newborn F-box gene blocks gene flow by selectively degrading phosphoglucomutase in species hybrids. Proc Natl Acad Sci U S A 2024; 121:e2418037121. [PMID: 39514314 PMCID: PMC11573670 DOI: 10.1073/pnas.2418037121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Accepted: 10/04/2024] [Indexed: 11/16/2024] Open
Abstract
The establishment of reproductive barriers such as postzygotic hybrid incompatibility (HI) remains the key to speciation. Gene duplication followed by differential functionalization has long been proposed as a major model underlying HI, but little supporting evidence exists. Here, we demonstrate that a newborn F-box gene, Cni-neib-1, of the nematode Caenorhabditis nigoni specifically inactivates an essential phosphoglucomutase encoded by Cbr-shls-1 in its sister species Caenorhabditis briggsae and their hybrids. Zygotic expression of Cni-neib-1 specifically depletes Cbr-SHLS-1, but not Cni-SHLS-1, in approximately 40 min starting from gastrulation, causing embryonic death. Cni-neib-1 is one of thirty-three paralogues emerging from a recent surge in F-box gene duplication events within C. nigoni, all of which are evolving under positive selection. Cni-neib-1 undergoes turnover even among C. nigoni populations. Differential expansion of F-box genes between the two species could reflect their distinctive innate immune responses. Collectively, we demonstrate how recent duplication of genes involved in protein degradation can cause incidental destruction of targets in hybrids that leads to HI, providing an invaluable insight into mechanisms of speciation.
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Affiliation(s)
- Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Yiqing Liu
- Department of Biology, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Gefei Huang
- Department of Biology, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
- Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris75005, France
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
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39
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Ignatz EH, Xue X, Hall JR, Islam SS, Rise ML, Fleming IA. Defence-relevant gene expression differences in hatchlings among wild Newfoundland and farmed European and North American Atlantic salmon and their hybrids. Mol Ecol 2024; 33:e17535. [PMID: 39314041 DOI: 10.1111/mec.17535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/16/2024] [Accepted: 09/12/2024] [Indexed: 09/25/2024]
Abstract
Escape of genetically distinct farmed Atlantic salmon (Salmo salar) raises concerns about their potential interactions with wild populations and the disruption of local adaptation through genetic admixture. It is often unknown whether genetic origin or common domestication effects will have a greater influence on consequences posed by escaped farmed fish. Previous work showed that domestication could have prevalent effects on the behaviour and growth of farmed salmon, independent of their genetic origin. Yet, less is known whether this extends more broadly to gene expression, particularly at critical early life stages. Thus, we compared the expression of 24 transcripts related to the immune response, structural maintenance, stress response and iron metabolism among distinct farmed (North American [NA] and European [EO]), wild (Newfoundland) and F1 hybrid salmon at hatching under controlled conditions using qPCR analyses. A slightly higher number of transcripts were differentially expressed between the wild population relative to EO (i.e. atf3a, atf3b, bnip3, trim37a, ftm, hp and gapdh) than NA-farmed salmon (i.e. epdl2, hba1a, hba1b, hbb4 and ftm). The most differences existed between the two farmed strains themselves (11 of 24 transcripts), with the fewest differentially expressed transcripts found between the F1 hybrids and the domesticated/wild maternal strains (4 of 24 transcripts). Interestingly, despite similarities in the overall extent of gene expression differences among cross types, the expression patterns differed relative to a past study that compared fry from the same cross types at the end of yolk sac absorption. Overall, our findings suggest that interbreeding of escaped farmed salmon with wild Newfoundland populations would alter transcript expression levels and that developmental stage influences these changes.
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Affiliation(s)
- Eric H Ignatz
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Marine Affairs Program, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Jennifer R Hall
- Aquatic Research Cluster, CREAIT Network, Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Shahinur S Islam
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Ian A Fleming
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
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40
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DeVore ML, Bazzini AA. Codon optimality influences homeostatic gene expression in zebrafish. G3 (BETHESDA, MD.) 2024; 14:jkae247. [PMID: 39446991 PMCID: PMC11631405 DOI: 10.1093/g3journal/jkae247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 10/11/2024] [Accepted: 10/22/2024] [Indexed: 10/26/2024]
Abstract
The ribosome plays a crucial role in translating mRNA into protein; however, the genetic code extends beyond merely specifying amino acids. Upon translation, codons, the three-nucleotide sequences interpreted by ribosomes, have regulatory properties affecting mRNA stability, a phenomenon known as codon optimality. Codon optimality has been previously observed in vertebrates during embryogenesis, where specific codons can influence the stability and degradation rates of mRNA transcripts. In our previous work, we demonstrated that codon optimality impacts mRNA stability in human cell lines. However, the extent to which codon content influences vertebrate gene expression in vivo remained unclear. In this study, we expand on our previous findings by demonstrating that codon optimality has a robust effect on homeostatic mRNA and protein levels in whole zebrafish during normal physiological conditions. Using reporters with nearly identical nucleotide sequences but different codon compositions, all expressed from the same genomic locus, we show that codon composition can significantly influence gene expression. This study provides new insights into the regulatory roles of codon usage in vertebrate gene expression and underscores the importance of considering codon optimality in genetic and translational research. These findings have broad implications for understanding the complexities of gene regulation and could inform the design of synthetic genes and therapeutic strategies targeting mRNA stability.
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Affiliation(s)
- Michelle L DeVore
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
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Wang Y, Yang C, Sun H, Jiang H, Zhang P, Huang Y, Liu Z, Yu Y, Xu Z, Xiang H, Yi C. The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae050. [PMID: 38937660 PMCID: PMC11514847 DOI: 10.1093/gpbjnl/qzae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 06/02/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
The most common epigenetic modification of messenger RNAs (mRNAs) is N6-methyladenosine (m6A), which is mainly located near the 3' untranslated region of mRNAs, near the stop codons, and within internal exons. The biological effect of m6A is dynamically modulated by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers). By controlling post-transcriptional gene expression, m6A has a significant impact on numerous biological functions, including RNA transcription, translation, splicing, transport, and degradation. Hence, m6A influences various physiological and pathological processes, such as spermatogenesis, oogenesis, embryogenesis, placental function, and human reproductive system diseases. During gametogenesis and embryogenesis, genetic material undergoes significant changes, including epigenomic modifications such as m6A. From spermatogenesis and oogenesis to the formation of an oosperm and early embryogenesis, m6A changes occur at every step. m6A abnormalities can lead to gamete abnormalities, developmental delays, impaired fertilization, and maternal-to-zygotic transition blockage. Both mice and humans with abnormal m6A modifications exhibit impaired fertility. In this review, we discuss the dynamic biological effects of m6A and its regulators on gamete and embryonic development and review the possible mechanisms of infertility caused by m6A changes. We also discuss the drugs currently used to manipulate m6A and provide prospects for the prevention and treatment of infertility at the epigenetic level.
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Affiliation(s)
- Yujie Wang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, China
- MOE Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Hefei 230032, China
| | - Chen Yang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, China
- MOE Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Hefei 230032, China
| | - Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Jiang
- Department of Interventional Therapy, the Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Pin Zhang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, China
- MOE Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Hefei 230032, China
| | - Yue Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, China
- MOE Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Hefei 230032, China
| | - Zhenran Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, China
- MOE Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Hefei 230032, China
| | - Yaru Yu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, China
- MOE Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Hefei 230032, China
| | - Zuying Xu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, China
- MOE Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Hefei 230032, China
| | - Huifen Xiang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, China
- MOE Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Hefei 230032, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Jackson EW, Romero E, Kling S, Lee Y, Tjeerdema E, Hamdoun A. Stable germline transgenesis using the Minos Tc1/mariner element in the sea urchin Lytechinus pictus. Development 2024; 151:dev202991. [PMID: 39023164 PMCID: PMC11361634 DOI: 10.1242/dev.202991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
Abstract
Stable transgenesis is a transformative tool in model organism biology. Although the sea urchin is one of the oldest animal models in cell and developmental biology, studies in this animal have largely relied on transient manipulation of wild animals, without a strategy for stable transgenesis. Here, we build on recent progress to develop a more genetically tractable sea urchin species, Lytechinus pictus, and establish a robust transgene integration method. Three commonly used transposons (Minos, Tol2 and piggyBac) were tested for non-autonomous transposition, using plasmids containing a polyubiquitin promoter upstream of a H2B-mCerulean nuclear marker. Minos was the only transposable element that resulted in significant expression beyond metamorphosis. F0 animals were raised to sexual maturity, and spawned to determine germline integration and transgene inheritance frequency, and to characterize expression patterns of the transgene in F1 progeny. The results demonstrate transgene transmission through the germline, the first example of a germline transgenic sea urchin and, indeed, of any echinoderm. This milestone paves the way for the generation of diverse transgenic resources that will dramatically enhance the utility, reproducibility and efficiency of sea urchin research.
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Affiliation(s)
- Elliot W. Jackson
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Emilio Romero
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Svenja Kling
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Yoon Lee
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Evan Tjeerdema
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Amro Hamdoun
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
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Hu S, Tian G, Bai Y, Qu A, He Q, Chen L, Xu P. Alternative splicing dynamically regulates common carp embryogenesis under thermal stress. BMC Genomics 2024; 25:918. [PMID: 39358679 PMCID: PMC11448050 DOI: 10.1186/s12864-024-10838-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 09/26/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Thermal stress is a major environmental factor affecting fish development and survival. Common carp (Cyprinus carpio) are susceptible to heat stress in their embryonic and larval phases, but the thermal stress response of alternative splicing during common carp embryogenesis remains poorly understood. RESULTS Using RNA-seq data from eight developmental stages and four temperatures, we constructed a comprehensive profile of alternative splicing (AS) during the embryogenesis of common carp, and found that AS genes and events are widely distributed among all stages. A total of 5,835 developmental stage-specific AS (SAS) genes, 21,368 temperature-specific differentially expressed genes (TDEGs), and 2,652 temperature-specific differentially AS (TDAS) genes were identified. Hub TDAS genes in each developmental stage, such as taf2, hnrnpa1, and drg2, were identified through protein-protein interaction (PPI) network analysis. The early developmental stages may be more sensitive to temperature, with thermal stress leading to a massive increase in the number of expressed transcripts, TDEGs, and TDAS genes in the morula stage, followed by the gastrula stage. GO and KEGG analyses showed that from the morula stage to the neurula stage, TDAS genes were more involved in intracellular transport, protein modification, and localization processes, while from the optic vesicle stage to one day post-hatching, they participated more in biosynthetic processes. Further subgenomic analysis revealed that the number of AS genes and events in subgenome B was generally higher than that in subgenome A, and the homologous AS genes were significantly enriched in basic life activity pathways, such as mTOR signaling pathway, p53 signaling pathway, and MAPK signaling pathway. Additionally, lncRNAs can play a regulatory role in the response to thermal stress by targeting AS genes such as lmnl3, affecting biological processes such as apoptosis and axon guidance. CONCLUSIONS In short, thermal stress can affect alternative splicing regulation during common carp embryogenesis at multiple levels. Our work complemented some gaps in the study of alternative splicing at both levels of embryogenesis and thermal stress in C. carpio and contributed to the comprehension of environmental adaptation formation in polyploid fishes during embryogenesis.
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Affiliation(s)
- Shuimu Hu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Guopeng Tian
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ang Qu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Qian He
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lin Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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Rosero J, Monzani PS, Pessoa GP, Coelho GCZ, Carvalho GB, López LS, Senhorini JA, Dos Santos SCA, Yasui GS. Traceability of primordial germ cells in three neotropical fish species aiming genetic conservation actions. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:2025-2042. [PMID: 38060079 DOI: 10.1007/s10695-023-01279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Primordial germ cells (PGCs) are embryonic pluripotent cells that can differentiate into spermatogonia and oogonia, and therefore, PGCs are a genetic source for germplasm conservation through cryobanking and the generation of germline chimeras. The knowledge of PGC migration routes is essential for transplantation studies. In this work, the mRNA synthesized from the ddx4 3'UTR sequence of Pseudopimelodus mangurus, in fusion with gfp or dsred, was microinjected into zygotes of three neotropical species (P. mangurus, Astyanax altiparanae, and Prochilodus lineatus) for PGC labeling. Visualization of labeled PGCs was achieved by fluorescence microscopy during embryonic development. In addition, ddx4 and dnd1 expressions were evaluated during embryonic development, larvae, and adult tissues of P. mangurus, to validate their use as a PGC marker. As a result, the effective identification of presumptive PGCs was obtained. DsRed-positive PGC of P. mangurus was observed in the hatching stage, GFP-positive PGC of A. altiparanae in the gastrula stage, and GFP-positive PGCs from P. lineatus were identified at the segmentation stage, with representative labeling percentages of 29% and 16% in A. altiparanae and P. lineatus, respectively. The expression of ddx4 and dnd1 of P. mangurus confirmed the specificity of these genes in germ cells. These results point to the functionality of the P. mangurus ddx4 3'UTR sequence as a PGC marker, demonstrating that PGC labeling was more efficient in A. altiparanae and P. lineatus. The procedures used to identify PGCs in P. mangurus consolidate the first step for generating germinal chimeras as a conservation action of P. mangurus.
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Affiliation(s)
- Jenyffer Rosero
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil.
- Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil.
| | - Paulo Sérgio Monzani
- Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil
- Institute of Bioscience, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Giselle Pessanha Pessoa
- Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil
- Institute of Bioscience, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Geovanna Carla Zacheo Coelho
- Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil
- Institute of Bioscience, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Gabriella Braga Carvalho
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
- Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil
| | - Lucia Suárez López
- Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil
- Institute of Bioscience, São Paulo State University, Botucatu, São Paulo, Brazil
| | - José Augusto Senhorini
- Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil
- Institute of Bioscience, São Paulo State University, Botucatu, São Paulo, Brazil
| | | | - George Shigueki Yasui
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
- Laboratory of Fish Biotechnology, National Center for Research and Conservation of Continental Aquatic Biodiversity, Chico Mendes Institute of Biodiversity Conservation, Pirassununga, São Paulo, Brazil
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Zou Z, Wang Q, Wu X, Schultz RM, Xie W. Kick-starting the zygotic genome: licensors, specifiers, and beyond. EMBO Rep 2024; 25:4113-4130. [PMID: 39160344 PMCID: PMC11467316 DOI: 10.1038/s44319-024-00223-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 06/14/2024] [Accepted: 07/24/2024] [Indexed: 08/21/2024] Open
Abstract
Zygotic genome activation (ZGA), the first transcription event following fertilization, kickstarts the embryonic program that takes over the control of early development from the maternal products. How ZGA occurs, especially in mammals, is poorly understood due to the limited amount of research materials. With the rapid development of single-cell and low-input technologies, remarkable progress made in the past decade has unveiled dramatic transitions of the epigenomes, transcriptomes, proteomes, and metabolomes associated with ZGA. Moreover, functional investigations are yielding insights into the key regulators of ZGA, among which two major classes of players are emerging: licensors and specifiers. Licensors would control the permission of transcription and its timing during ZGA. Accumulating evidence suggests that such licensors of ZGA include regulators of the transcription apparatus and nuclear gatekeepers. Specifiers would instruct the activation of specific genes during ZGA. These specifiers include key transcription factors present at this stage, often facilitated by epigenetic regulators. Based on data primarily from mammals but also results from other species, we discuss in this review how recent research sheds light on the molecular regulation of ZGA and its executors, including the licensors and specifiers.
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Affiliation(s)
- Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Qiuyan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xi Wu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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Marhabaie M, Wharton TH, Kim SY, Wharton RP. Widespread regulation of the maternal transcriptome by Nanos in Drosophila. PLoS Biol 2024; 22:e3002840. [PMID: 39401257 PMCID: PMC11501031 DOI: 10.1371/journal.pbio.3002840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 10/24/2024] [Accepted: 09/14/2024] [Indexed: 10/23/2024] Open
Abstract
The translational repressor Nanos (Nos) regulates a single target, maternal hunchback (hb) mRNA, to govern abdominal segmentation in the early Drosophila embryo. Nos is recruited to sites in the 3' UTR of hb mRNA in collaboration with the sequence-specific RNA-binding protein Pumilio (Pum); on its own, Nos has no binding specificity. Nos is expressed at other stages of development, but very few mRNA targets that might mediate its action at these stages have been described. Nor has it been clear whether Nos is targeted to other mRNAs in concert with Pum or via other mechanisms. In this report, we identify mRNAs targeted by Nos via 2 approaches. First, we identify mRNAs depleted upon expression of a chimera bearing Nos fused to the nonsense mediated decay (NMD) factor Upf1. We find that, in addition to hb, Upf1-Nos depletes approximately 2,600 mRNAs from the maternal transcriptome in early embryos. Virtually all of these appear to be targeted in a canonical, hb-like manner in concert with Pum. In a second, more conventional approach, we identify mRNAs that are stabilized during the maternal zygotic transition (MZT) in embryos from nos- females. Most (86%) of the 1,185 mRNAs regulated by Nos are also targeted by Upf1-Nos, validating use of the chimera. Previous work has shown that 60% of the maternal transcriptome is degraded in early embryos. We find that maternal mRNAs targeted by Upf1-Nos are hypoadenylated and inefficiently translated at the ovary-embryo transition; they are subsequently degraded in the early embryo, accounting for 59% of all destabilized maternal mRNAs. We suggest that the late ovarian burst of Nos represses a large fraction of the maternal transcriptome, priming it for later degradation by other factors in the embryo.
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Affiliation(s)
- Mohammad Marhabaie
- Department of Molecular Genetics, Department of Cancer Biology and Genetics, Center for RNA Biology, Ohio State University, Columbus, Ohio, United States of America
| | - Tammy H. Wharton
- Department of Molecular Genetics, Department of Cancer Biology and Genetics, Center for RNA Biology, Ohio State University, Columbus, Ohio, United States of America
| | - Sung Yun Kim
- Department of Molecular Genetics, Department of Cancer Biology and Genetics, Center for RNA Biology, Ohio State University, Columbus, Ohio, United States of America
| | - Robin P. Wharton
- Department of Molecular Genetics, Department of Cancer Biology and Genetics, Center for RNA Biology, Ohio State University, Columbus, Ohio, United States of America
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Guan T, Guo J, Lin R, Liu J, Luo R, Zhang Z, Pei D, Liu J. Single-cell analysis of preimplantation embryonic development in guinea pigs. BMC Genomics 2024; 25:911. [PMID: 39350018 PMCID: PMC11440810 DOI: 10.1186/s12864-024-10815-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 09/19/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Guinea pigs exhibit numerous physiological similarities to humans, yet the details of their preimplantation embryonic development remain largely unexplored. RESULTS To address this, we conducted single-cell sequencing on the transcriptomes of cells isolated from the zygote stage through preimplantation stages in guinea pigs. This study identified seven distinct cell types within guinea pig preimplantation embryos and pinpointed the timing of zygotic gene activation (ZGA). Trajectory analysis revealed a bifurcation into two lineage-specific branches, accompanied by alterations in specific pathways, including oxidative phosphorylation and vascular endothelial growth factor (VEGF). Additionally, co-expressed gene network analysis highlighted the most enriched functional modules for the epiblast (EPI), primitive endoderm (PrE), and inner cell mass (ICM). Finally, we compared the similarities and differences between human and guinea pig epiblasts (EPIs). CONCLUSION This study systematically constructs a cell atlas of guinea pig preimplantation embryonic development, offering fresh insights into mammalian embryonic development and providing alternative experimental models for studying human embryonic development.
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Affiliation(s)
- Tongxing Guan
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jing Guo
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Runxia Lin
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jinpeng Liu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Science, Beijing, 100049, People's Republic of China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Rongping Luo
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Zhen Zhang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Duanqing Pei
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.
| | - Jing Liu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Joint School of Life Sciences,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Center for Development and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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Sharma A, Dsilva GJ, Deshpande G, Galande S. Exploring the versatility of zygotic genome regulators: A comparative and functional analysis. Cell Rep 2024; 43:114680. [PMID: 39182225 DOI: 10.1016/j.celrep.2024.114680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/30/2024] [Accepted: 08/08/2024] [Indexed: 08/27/2024] Open
Abstract
The activation of the zygotic genome constitutes an essential process during early embryogenesis that determines the overall progression of embryonic development. Zygotic genome activation (ZGA) is tightly regulated, involving a delicate interplay of activators and repressors, to precisely control the timing and spatial pattern of gene expression. While regulators of ZGA vary across species, they accomplish comparable outcomes. Recent studies have shed light on the unanticipated roles of ZGA components both during and after ZGA. Moreover, different ZGA regulators seem to have acquired unique functional modalities to manifest their regulatory potential. In this review, we explore these observations to assess whether these are simply anecdotal or contribute to a broader regulatory framework that employs a versatile means to arrive at the conserved outcome.
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Affiliation(s)
- Ankita Sharma
- Department of Biology, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune 411008, India; Center of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR 201314, India
| | - Greg Jude Dsilva
- Department of Biology, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune 411008, India; Center of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR 201314, India
| | - Girish Deshpande
- Department of Biology, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune 411008, India; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA.
| | - Sanjeev Galande
- Department of Biology, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune 411008, India; Center of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR 201314, India.
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Cannarella R, Rando OJ, Condorelli RA, Chamayou S, Romano S, Guglielmino A, Yin Q, Hans TG, Mancuso F, Arato I, Bellucci C, Luca G, Lundy SD, La Vignera S, Calogero AE. Sperm-carried IGF2: towards the discovery of a spark contributing to embryo growth and development. Mol Hum Reprod 2024; 30:gaae034. [PMID: 39312692 PMCID: PMC11975288 DOI: 10.1093/molehr/gaae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
Spermatozoa have been shown to carry key RNAs which, according to animal evidence, seem to play a role in early embryo development. In this context, a potential key growth regulator is insulin-like growth factor 2 (IGF2), a highly conserved paternally expressed imprinted gene involved in cell growth and proliferation which, recent observations indicate, is expressed in human spermatozoa. We herein hypothesized that sperm IGF2 gene expression and transmission at fertilization is required to support early embryo development. To test this hypothesis, we analyzed sperm IGF2 mRNA levels in the same semen aliquot used for homologous assisted reproductive technique (ART) in infertile couples and correlated these levels with embryo morphokinetics. To find a mechanistic explanation for the observed results, the transcriptomes of blastocysts obtained after injection of Igf2 mRNA in mouse parthenotes were analyzed. Sperm IGF2 mRNA negatively correlated with time of 2-cell stage (t2), t3, t4, t5, and time of expanded blastocyst (tEB), independently of maternal age, body mass index, anti-Müllerian hormone levels, and oocyte quality. An IGF2 mRNA index >4.9 predicted the ability of the embryos to reach the blastocyst stage on Day 5, with a sensitivity of 100% and a specificity of 71.6% (AUC 0.845; P < 0.001). In the animal study, transcriptome analysis demonstrated that 65 and 36 genes were, respectively, up- and down-regulated in the experimental group compared to the control group. These genes belong to pathways that regulate early embryo development, thus supporting the findings found in humans. This study has the potential to challenge the longstanding tenet that spermatozoa are simply vehicles carrying paternal DNA. Instead, it suggests that IGF2 mRNA in healthy spermatozoa provides critical support for early embryo development. Pre-ART sperm-carried IGF2 mRNA levels may be used as a marker to predict the chances of obtaining blastocysts to be transferred for infertile couples undergoing ART.
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Affiliation(s)
- Rossella Cannarella
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rosita A Condorelli
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | | | - Simona Romano
- Centro HERA—Unità di Medicina della Riproduzione, Catania, Italy
| | | | - Qiangzong Yin
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Tobias Gustafsson Hans
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Francesca Mancuso
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Iva Arato
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Catia Bellucci
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Giovanni Luca
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Scott D Lundy
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sandro La Vignera
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Aldo E Calogero
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
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Arana ÁJ, Sánchez L. Knockout, Knockdown, and the Schrödinger Paradox: Genetic Immunity to Phenotypic Recapitulation in Zebrafish. Genes (Basel) 2024; 15:1164. [PMID: 39336755 PMCID: PMC11431394 DOI: 10.3390/genes15091164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Previous research has highlighted significant phenotypic discrepancies between knockout and knockdown approaches in zebrafish, raising concerns about the reliability of these methods. However, our study suggests that these differences are not as pronounced as was once believed. By carefully examining the roles of maternal and zygotic gene contributions, we demonstrate that these factors significantly influence phenotypic outcomes, often accounting for the observed discrepancies. Our findings emphasize that morpholinos, despite their potential off-target effects, can be effective tools when used with rigorous controls. We introduce the concept of graded maternal contribution, which explains how the uneven distribution of maternal mRNA and proteins during gametogenesis impacts phenotypic variability. Our research categorizes genes into three types-susceptible, immune, and "Schrödinger" (conditional)-based on their phenotypic expression and interaction with genetic compensation mechanisms. This distinction provides new insights into the paradoxical outcomes observed in genetic studies. Ultimately, our work underscores the importance of considering both maternal and zygotic contributions, alongside rigorous experimental controls, to accurately interpret gene function and the mechanisms underlying disease. This study advocates for the continued use of morpholinos in conjunction with advanced genetic tools like CRISPR/Cas9, stressing the need for a meticulous experimental design to optimize the utility of zebrafish in genetic research and therapeutic development.
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