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Zhu L, Zhou T, Iyyappan R, Ming H, Dvoran M, Wang Y, Chen Q, Roberts RM, Susor A, Jiang Z. High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development. Development 2022; 149:280468. [PMID: 36227586 PMCID: PMC9687001 DOI: 10.1242/dev.200819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
High-resolution ribosome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscapes of early embryo development at an unprecedented level. We analyzed the transcriptome and the polysome- and non-polysome-bound RNA profiles of bovine oocytes (germinal vesicle and metaphase II stages) and early embryos at the two-cell, eight-cell, morula and blastocyst stages, and revealed four modes of translational selectivity: (1) selective translation of non-abundant mRNAs; (2) active, but modest translation of a selection of highly expressed mRNAs; (3) translationally suppressed abundant to moderately abundant mRNAs; and (4) mRNAs associated specifically with monosomes. A strong translational selection of low-abundance transcripts involved in metabolic pathways and lysosomes was found throughout bovine embryonic development. Notably, genes involved in mitochondrial function were prioritized for translation. We found that translation largely reflected transcription in oocytes and two-cell embryos, but observed a marked shift in the translational control in eight-cell embryos that was associated with the main phase of embryonic genome activation. Subsequently, transcription and translation become more synchronized in morulae and blastocysts. Taken together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.
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Affiliation(s)
- Linkai Zhu
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557-0352, USA
| | - Rajan Iyyappan
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Hao Ming
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michal Dvoran
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Yinjuan Wang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - R Michael Roberts
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211-7310, USA
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
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2
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Llano E, Masek T, Gahurova L, Pospisek M, Koncicka M, Jindrova A, Jansova D, Iyyappan R, Roucova K, Bruce AW, Kubelka M, Susor A. Age-related differences in the translational landscape of mammalian oocytes. Aging Cell 2020; 19:e13231. [PMID: 32951297 PMCID: PMC7576272 DOI: 10.1111/acel.13231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/15/2020] [Accepted: 08/01/2020] [Indexed: 12/13/2022] Open
Abstract
Increasing maternal age in mammals is associated with poorer oocyte quality, involving higher aneuploidy rates and decreased developmental competence. Prior to resumption of meiosis, fully developed mammalian oocytes become transcriptionally silent until the onset of zygotic genome activation. Therefore, meiotic progression and early embryogenesis are driven largely by translational utilization of previously synthesized mRNAs. We report that genome‐wide translatome profiling reveals considerable numbers of transcripts that are differentially translated in oocytes obtained from aged compared to young females. Additionally, we show that a number of aberrantly translated mRNAs in oocytes from aged females are associated with cell cycle. Indeed, we demonstrate that four specific maternal age‐related transcripts (Sgk1, Castor1, Aire and Eg5) with differential translation rates encode factors that are associated with the newly forming meiotic spindle. Moreover, we report substantial defects in chromosome alignment and cytokinesis in the oocytes of young females, in which candidate CASTOR1 and SGK1 protein levels or activity are experimentally altered. Our findings indicate that improper translation of specific proteins at the onset of meiosis contributes to increased chromosome segregation problems associated with female ageing.
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Affiliation(s)
- Edgar Llano
- Laboratory of Biochemistry and Molecular Biology of Germ Cells Institute of Animal Physiology and Genetics CAS Libechov Czech Republic
- Laboratory of RNA Biochemistry Department of Genetics and Microbiology Faculty of Science Charles University in Prague Prague Czech Republic
| | - Tomas Masek
- Laboratory of RNA Biochemistry Department of Genetics and Microbiology Faculty of Science Charles University in Prague Prague Czech Republic
| | - Lenka Gahurova
- Laboratory of Biochemistry and Molecular Biology of Germ Cells Institute of Animal Physiology and Genetics CAS Libechov Czech Republic
- Laboratory of Early Mammalian Developmental Biology (LEMDB) Department of Molecular Biology and Genetics Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic
| | - Martin Pospisek
- Laboratory of RNA Biochemistry Department of Genetics and Microbiology Faculty of Science Charles University in Prague Prague Czech Republic
| | - Marketa Koncicka
- Laboratory of Biochemistry and Molecular Biology of Germ Cells Institute of Animal Physiology and Genetics CAS Libechov Czech Republic
| | - Anna Jindrova
- Laboratory of Biochemistry and Molecular Biology of Germ Cells Institute of Animal Physiology and Genetics CAS Libechov Czech Republic
| | - Denisa Jansova
- Laboratory of Biochemistry and Molecular Biology of Germ Cells Institute of Animal Physiology and Genetics CAS Libechov Czech Republic
| | - Rajan Iyyappan
- Laboratory of Biochemistry and Molecular Biology of Germ Cells Institute of Animal Physiology and Genetics CAS Libechov Czech Republic
| | - Kristina Roucova
- Laboratory of RNA Biochemistry Department of Genetics and Microbiology Faculty of Science Charles University in Prague Prague Czech Republic
| | - Alexander W. Bruce
- Laboratory of Early Mammalian Developmental Biology (LEMDB) Department of Molecular Biology and Genetics Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic
| | - Michal Kubelka
- Laboratory of Biochemistry and Molecular Biology of Germ Cells Institute of Animal Physiology and Genetics CAS Libechov Czech Republic
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells Institute of Animal Physiology and Genetics CAS Libechov Czech Republic
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Identifying the Translatome of Mouse NEBD-Stage Oocytes via SSP-Profiling; A Novel Polysome Fractionation Method. Int J Mol Sci 2020; 21:ijms21041254. [PMID: 32070012 PMCID: PMC7072993 DOI: 10.3390/ijms21041254] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022] Open
Abstract
Meiotic maturation of oocyte relies on pre-synthesised maternal mRNA, the translation of which is highly coordinated in space and time. Here, we provide a detailed polysome profiling protocol that demonstrates a combination of the sucrose gradient ultracentrifugation in small SW55Ti tubes with the qRT-PCR-based quantification of 18S and 28S rRNAs in fractionated polysome profile. This newly optimised method, named Scarce Sample Polysome Profiling (SSP-profiling), is suitable for both scarce and conventional sample sizes and is compatible with downstream RNA-seq to identify polysome associated transcripts. Utilising SSP-profiling we have assayed the translatome of mouse oocytes at the onset of nuclear envelope breakdown (NEBD)—a developmental point, the study of which is important for furthering our understanding of the molecular mechanisms leading to oocyte aneuploidy. Our analyses identified 1847 transcripts with moderate to strong polysome occupancy, including abundantly represented mRNAs encoding mitochondrial and ribosomal proteins, proteasomal components, glycolytic and amino acids synthetic enzymes, proteins involved in cytoskeleton organization plus RNA-binding and translation initiation factors. In addition to transcripts encoding known players of meiotic progression, we also identified several mRNAs encoding proteins of unknown function. Polysome profiles generated using SSP-profiling were more than comparable to those developed using existing conventional approaches, being demonstrably superior in their resolution, reproducibility, versatility, speed of derivation and downstream protocol applicability.
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Accumulation of Chromatin Remodelling Enzyme and Histone Transcripts in Bovine Oocytes. Results Probl Cell Differ 2017; 63:223-255. [PMID: 28779321 DOI: 10.1007/978-3-319-60855-6_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During growth, the oocyte accumulates mRNAs that will be required in the later stages of oogenesis and early embryogenesis until the activation of the embryonic genome. Each of these developmental stages is controlled by multiple regulatory mechanisms that ensure proper protein production. Thus mRNAs are stabilized, stored, recruited, polyadenylated, translated and/or degraded over a period of several days. As a consequence, understanding the biological significance of changes in the abundance of transcripts during oocyte growth and differentiation is rather complex. Nevertheless the availability of transcriptomic platforms applicable to scarce samples such as oocytes has generated large amounts of data that depict the transcriptome of oocytes under different conditions. Despite several technical constrains related to protein determination in oocytes that still limit the possibility to verify certain hypothesis, it is now possible to use mRNA levels to start building plausible scenarios. To start deciphering the changes in the level of specific mRNAs involved in chromatin remodelling, we have performed a meta-analysis of existing microarray datasets from germinal vesicle (GV) stage bovine oocytes during the final stages of oocyte differentiation. We then analysed the expression profiles of histone and histone-remodelling enzyme mRNAs and correlated these with the major histone modifications known to occur at the same period, based on data available in the literature. We believe that this approach could reveal the function of specific enzymes in the oocyte. In turn, this information will be useful in future studies, which final ambitious goal is to decipher the 'oocyte-specific histone code'.
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Reyes JM, Ross PJ. Cytoplasmic polyadenylation in mammalian oocyte maturation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:71-89. [PMID: 26596258 DOI: 10.1002/wrna.1316] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 12/21/2022]
Abstract
Oocyte developmental competence is the ability of the mature oocyte to be fertilized and subsequently drive early embryo development. Developmental competence is acquired by completion of oocyte maturation, a process that includes nuclear (meiotic) and cytoplasmic (molecular) changes. Given that maturing oocytes are transcriptionally quiescent (as are early embryos), they depend on post-transcriptional regulation of stored transcripts for protein synthesis, which is largely mediated by translational repression and deadenylation of transcripts within the cytoplasm, followed by recruitment of specific transcripts in a spatiotemporal manner for translation during oocyte maturation and early development. Motifs within the 3' untranslated region (UTR) of messenger RNA (mRNA) are thought to mediate repression and downstream activation by their association with binding partners that form dynamic protein complexes that elicit differing effects on translation depending on cell stage and interacting proteins. The cytoplasmic polyadenylation (CP) element, Pumilio binding element, and hexanucleotide polyadenylation signal are among the best understood motifs involved in CP, and translational regulation of stored transcripts as their binding partners have been relatively well-characterized. Knowledge of CP in mammalian oocytes is discussed as well as novel approaches that can be used to enhance our understanding of the functional and contributing features to transcript CP and translational regulation during mammalian oocyte maturation. WIREs RNA 2016, 7:71-89. doi: 10.1002/wrna.1316 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Juan M Reyes
- Department of Animal Science, University of California, Davis, CA, USA
| | - Pablo J Ross
- Department of Animal Science, University of California, Davis, CA, USA
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6
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Macaulay AD, Gilbert I, Scantland S, Fournier E, Ashkar F, Bastien A, Saadi HAS, Gagné D, Sirard MA, Khandjian ÉW, Richard FJ, Hyttel P, Robert C. Cumulus Cell Transcripts Transit to the Bovine Oocyte in Preparation for Maturation. Biol Reprod 2015; 94:16. [PMID: 26586844 PMCID: PMC4809558 DOI: 10.1095/biolreprod.114.127571] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 11/13/2015] [Indexed: 11/30/2022] Open
Abstract
So far, the characteristics of a good quality egg have been elusive, similar to the nature of the physiological, cellular, and molecular cues leading to its production both in vivo and in vitro. Current understanding highlights a strong and complex interdependence between the follicular cells and the gamete. Secreted factors induce cellular responses in the follicular cells, and direct exchange of small molecules from the cumulus cells to the oocyte through gap junctions controls meiotic arrest. Studying the interconnection between the cumulus cells and the oocyte, we previously demonstrated that the somatic cells also contribute transcripts to the gamete. Here, we show that these transcripts can be visualized moving down the transzonal projections (TZPs) to the oocyte, and that a time course analysis revealed progressive RNA accumulation in the TZPs, indicating that RNA transfer occurs before the initiation of meiosis resumption under a timetable fitting with the acquisition of developmental competence. A comparison of the identity of the nascent transcripts trafficking in the TZPs, with those in the oocyte increasing in abundance during maturation, and that are present on the oocyte's polyribosomes, revealed transcripts common to all three fractions, suggesting the use of transferred transcripts for translation. Furthermore, the removal of potential RNA trafficking by stripping the cumulus cells caused a significant reduction in maturation rates, indicating the need for the cumulus cell RNA transfer to the oocyte. These results offer a new perspective to the determinants of oocyte quality and female fertility, as well as provide insight that may eventually be used to improve in vitro maturation conditions.
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Affiliation(s)
- Angus D Macaulay
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Sara Scantland
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Eric Fournier
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Fazl Ashkar
- Department of Biomedical Sciences, Reproductive Biology Lab, University of Guelph, Guelph, Ontario, Canada
| | - Alexandre Bastien
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Habib A Shojaei Saadi
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Dominic Gagné
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Marc-André Sirard
- Département de Psychiatrie et Neurosciences, Institut universitaire en santé mentale de Québec, Université Laval, Québec City, Québec, Canada
| | - Édouard W Khandjian
- Département de Psychiatrie et Neurosciences, Institut universitaire en santé mentale de Québec, Université Laval, Québec City, Québec, Canada
| | - François J Richard
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Poul Hyttel
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claude Robert
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
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7
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Translation in the mammalian oocyte in space and time. Cell Tissue Res 2015; 363:69-84. [PMID: 26340983 DOI: 10.1007/s00441-015-2269-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/03/2015] [Indexed: 02/07/2023]
Abstract
A hallmark of oocyte development in mammals is the dependence on the translation and utilization of stored RNA and proteins rather than the de novo transcription of genes in order to sustain meiotic progression and early embryo development. In the absence of transcription, the completion of meiosis and early embryo development in mammals relies significantly on maternally synthesized RNAs. Post-transcriptional control of gene expression at the translational level has emerged as an important cellular function in normal development. Therefore, the regulation of gene expression in oocytes is controlled almost exclusively at the level of mRNA and protein stabilization and protein synthesis. This current review is focused on the recently emerged findings on RNA distribution related to the temporal and spatial translational control of the meiotic progression of the mammalian oocyte.
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Caballero J, Gilbert I, Fournier E, Gagné D, Scantland S, Macaulay A, Robert C. Exploring the function of long non-coding RNA in the development of bovine early embryos. Reprod Fertil Dev 2015; 27:40-52. [PMID: 25472043 DOI: 10.1071/rd14338] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Now recognised as part of the cellular transcriptome, the function of long non-coding (lnc) RNA remains unclear. Previously, we found that some lncRNA molecules in bovine embryos are highly responsive to culture conditions. In view of a recent demonstration that lncRNA may play a role in regulating important functions, such as maintenance of pluripotency, modification of epigenetic marks and activation of transcription, we sought evidence of its involvement in embryogenesis. Among the numerous catalogued lncRNA molecules found in oocytes and early embryos of cattle, three candidates chosen for further characterisation were found unexpectedly in the cytoplasmic compartment rather than in the nucleus. Transcriptomic survey of subcellular fractions found these candidates also associated with polyribosomes and one of them spanning transzonal projections between cumulus cells and the oocyte. Knocking down this transcript in matured oocytes increased developmental rates, leading to larger blastocysts. Transcriptome and methylome analyses of these blastocysts showed concordant data for a subset of four genes, including at least one known to be important for blastocyst survival. Functional characterisation of the roles played by lncRNA in supporting early development remains elusive. Our results suggest that some lncRNAs play a role in translation control of target mRNA. This would be important for managing the maternal reserves within which is embedded the embryonic program, especially before embryonic genome activation.
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Affiliation(s)
- Julieta Caballero
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, 2440 boulevard Hochelaga QC, G1V 0A6, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, 2440 boulevard Hochelaga QC, G1V 0A6, Canada
| | - Eric Fournier
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, 2440 boulevard Hochelaga QC, G1V 0A6, Canada
| | - Dominic Gagné
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, 2440 boulevard Hochelaga QC, G1V 0A6, Canada
| | - Sara Scantland
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, 2440 boulevard Hochelaga QC, G1V 0A6, Canada
| | - Angus Macaulay
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, 2440 boulevard Hochelaga QC, G1V 0A6, Canada
| | - Claude Robert
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, 2440 boulevard Hochelaga QC, G1V 0A6, Canada
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9
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Scantland S, Tessaro I, Macabelli CH, Macaulay AD, Cagnone G, Fournier É, Luciano AM, Robert C. The adenosine salvage pathway as an alternative to mitochondrial production of ATP in maturing mammalian oocytes. Biol Reprod 2014; 91:75. [PMID: 25078684 DOI: 10.1095/biolreprod.114.120931] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Although the oocyte is the largest cell in the body and an unavoidable phase in life, its physiology is still poorly understood, and other cell types provide little insight into its unique nature. Even basic cellular functions in the oocyte such as energy metabolism are not yet fully understood. It is known that the mitochondria of the female gamete exhibit an immature form characterized by limited energy production from glucose and oxidative phosphorylation. We show that the bovine oocyte uses alternative means to maintain ATP production during maturation, namely, the adenosine salvage pathway. Meiosis resumption is triggered by destruction of cyclic AMP by phosphodiesterases producing adenosine monophosphate that is converted into ATP by adenylate kinases and creatine kinases. Inhibition of these enzymes decreased ATP production, and addition of their substrates restored ATP production in denuded oocytes. Addition of phosphocreatine to the oocyte maturation medium influenced the phenotype of the resulting blastocysts. We propose a model in which adenylate kinases and creatine kinases act as drivers of ATP production from added AMP during oocyte maturation.
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Affiliation(s)
- Sara Scantland
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Irene Tessaro
- Reproductive and Developmental Biology Laboratory, Department of Health, Animal Science and Food Safety, University of Milan, Milano, Italy
| | - Carolina H Macabelli
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Angus D Macaulay
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Gaël Cagnone
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Éric Fournier
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Alberto M Luciano
- Reproductive and Developmental Biology Laboratory, Department of Health, Animal Science and Food Safety, University of Milan, Milano, Italy
| | - Claude Robert
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
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10
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Expression of UGT2B7 is driven by two mutually exclusive promoters and alternative splicing in human tissues. Pharmacogenet Genomics 2013; 23:684-96. [DOI: 10.1097/fpc.0000000000000008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Gohin M, Fournier E, Dufort I, Sirard MA. Discovery, identification and sequence analysis of RNAs selected for very short or long poly A tail in immature bovine oocytes. Mol Hum Reprod 2013; 20:127-38. [PMID: 24233545 DOI: 10.1093/molehr/gat080] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A major challenge in applying genomics to oocyte physiology is that many RNAs are present but will not be translated into proteins, making it difficult to draw conclusions from RNAseq and array data. Oocyte maturation and early embryo development rely on maternal storage of specific RNAs with a short poly(A) tail, which must be elongated for translation. To resolve the role of key genes during that period, we aimed to characterize both extremes of mRNA: deadenylated RNA and long polyA tails mRNA population in immature bovine oocytes. Using magnetic beads coupled to oligodT, we isolated deadenylated (A-, 20-50 adenosines) from polyadenylated (A+, up to 200 adenosines) RNAs. After transcriptomic analysis, we observed that A+ candidates are associated with short-term processes required for immediate cell survival (translation or protein transport) or meiotic resumption, while several A- candidates are involved in processes (chromatin modification, gene transcription and post-transcriptional modifications) that will be extremely important in the development of the early embryo. In addition to a list of candidates probably translated early or late, sequence analysis revealed that cytoplasmic polyadenylation element (CPE) and U(3)GU(3) were enriched in A- sequences. Moreover, a motif associated with polyadenylation signals (MAPS, U(5)CU(2)) appeared to be enriched in 3'untranslated regions (UTR) with CPE or U(3)GU(3) sequences in bovine but also in zebrafish and Xenopus tropicalis. To further validate our methodology, we measured specific tail length of known candidates (AURKA, PTTG1, H2A1) but also determined the poly(A) tail length of other candidate RNAs (H3F3A, H1FOO, DAZAP2, ATF1, ATF2, KAT5, DAZL, ELAVL2). In conclusion, we have reported a methodology to isolate deadenylated from polyadenylated RNAs in samples with small total RNA quantities such as mammals. Moreover, we identified deadenylated RNAs in bovine oocytes that may be stored for the long-term process of early embryo development and described a conserved motif enriched in the 3'UTR of deadenylated RNAs.
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Affiliation(s)
- Maella Gohin
- Centre de Recherche en Biologie de la Reproduction, Faculté des Sciences de L'Agriculture et de L'Alimentation, Département des Sciences Animales, 2440 Bl. Hochelaga, Pavillon INAF, Université Laval, Québec, QC, Canada G1V 0A6
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12
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Labrecque R, Sirard MA. The study of mammalian oocyte competence by transcriptome analysis: progress and challenges. Mol Hum Reprod 2013; 20:103-16. [DOI: 10.1093/molehr/gat082] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Ménard V, Collin P, Margaillan G, Guillemette C. Modulation of the UGT2B7 Enzyme Activity by C-Terminally Truncated Proteins Derived from Alternative Splicing. Drug Metab Dispos 2013; 41:2197-205. [DOI: 10.1124/dmd.113.053876] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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14
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Tomek W, Wollenhaupt K. The "closed loop model" in controlling mRNA translation during development. Anim Reprod Sci 2012; 134:2-8. [PMID: 22917874 DOI: 10.1016/j.anireprosci.2012.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Translational control is particularly important in situations where the correlation of a distinct mRNA and the abundance of the corresponding protein might be low. This is the case for instance during oocyte maturation, shortly before the GVBD when the chromatin is condensed, until the embryonic genome is activated. In these situations, gene expression relies on the activation of maternal mRNAs which were stored stably in a dormant form. The most sophisticated model for translational initiation at present is the so-called "closed loop" model, where a circularization of the mRNA is mediated by associated 5'-cap- and 3'-poly(A) binding proteins. Depending on differential interactions, this event can result in translational stimulation or repression. Several studies describe correlated regulation mechanisms in model organisms like mouse or Xenopus, but data addressing translational regulation in farm animals are rare. Cytoplasmic mRNA activating or repressing factors, however, might contribute to achieve developmental competence in bovine or porcine oocytes. Recently we showed that, in the pig, embryonic signals can modify essential components of the mRNA-5'-translation initiation complex in the uterine luminal epithelium at the time of implantation. In accordance with the closed loop model of translational initiation, this review focuses on the regulatory impact of 5'-mRNA end associated proteins (components of the mRNA-cap binding complex) and 3'-end associated proteins (components of the poly(A) binding complex) during in vitro maturation of cattle and pig oocytes, early embryonic development and in the pig uterine epithelia.
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Affiliation(s)
- Wolfgang Tomek
- Leibniz Institute for Farm Animal Biology, Dep. of Reproductive Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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Demant M, Trapphoff T, Fröhlich T, Arnold GJ, Eichenlaub-Ritter U. Vitrification at the pre-antral stage transiently alters inner mitochondrial membrane potential but proteome of in vitro grown and matured mouse oocytes appears unaffected. Hum Reprod 2012; 27:1096-111. [PMID: 22258663 DOI: 10.1093/humrep/der453] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Vitrification is a fast and effective method to cryopreserve ovarian tissue, but it might influence mitochondrial activity and affect gene expression to cause persistent alterations in the proteome of oocytes that grow and mature following cryopreservation. METHODS In part one of the study, the inner mitochondrial membrane potential (Ψ(mit)) of JC-1 stained oocytes from control and CryoTop vitrified pre-antral follicles was analyzed by confocal microscopy at Day 0, or after culture of follicles for 1 or 12 days. In part two, proteins of in vivo grown germinal vesicle (GV) oocytes were subjected to proteome analysis by SDS polyacrylamide gel electrophoresis, tryptic in-gel digestion of gel slices, and one-dimensional-nano-liquid chromatography of peptides on a multi-dimensional-nano-liquid chromatography system followed by mass spectrometry (LC-MS/MS) and Uniprot Gene Ontology (GO) analysis. In part three, samples containing the protein amount of 40 GV and metaphase II (MII) oocytes, respectively, from control and vitrified pre-antral follicles cultured for 12 or 13 days were subjected to 2D DIGE saturation labeling and separated by isoelectric focusing and SDS gel electrophoresis (2D DIGE), followed by DeCyder(Tm) analysis of spot patterns in three independent biological replicates. Statistical and hierarchical cluster analysis was employed to compare control and vitrified groups. RESULTS (i) Mitochondrial inner membrane potential differs significantly between control and vitrified GV oocytes at Day 0 and Day 1, but is similar at Day 12 of culture. (ii) LC-MS/MS analysis of SDS gel fractionated protein lysates of 988 mouse GV oocytes revealed identification of 1123 different proteins with a false discovery rate of <1%. GO analysis assigned 811 proteins to the 'biological process' subset. Thirty-five percent of the proteins corresponded to metabolic processes, about 15% to mitochondrion and transport, each, and close to 8% to oxidation-reduction processes. (iii) From the 2D-saturation DIGE analysis 1891 matched spots for GV-stage and 1718 for MII oocyte proteins were detected and the related protein abundances in vitrified and control oocytes were quantified. None of the spots was significantly altered in intensity, and hierarchical cluster analysis as well as histograms of p and q values suggest that vitrification at the pre-antral stage does not significantly alter the proteome of GV or MII oocytes compared with controls. CONCLUSIONS Vitrification appears to be associated with a significant transient increase in Ψ(mit) in oocyte mitochondria, which disappears when oocyte/cumulus cell apposition is restored upon development to the antral stage. The nano-LC-MS/MS analysis of low numbers of oocytes is useful to obtain information on relevant biological signaling pathways based on protein identifications. For quantitative comparisons, saturation 2D DIGE analysis is superior to LC-MS/MS due to its high sensitivity in cases where the biological material is very limited. Genetic background, age of the female, and/or stimulation protocol appear to influence the proteome pattern. However, the quantitative 2D DIGE approach provides evidence that vitrification does not affect the oocyte proteome after recovery from transient loss of cell-cell interactions, in vitro growth and in vitro maturation under tested conditions. Therefore, transient changes in mitochondrial activity by vitrification do not appear causal to persistent alterations in the mitochondrial or overall oocyte proteome.
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Affiliation(s)
- Myriam Demant
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-Universität, München 81377, Germany
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16
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Robinson JF, Pennings JLA, Piersma AH. A review of toxicogenomic approaches in developmental toxicology. Methods Mol Biol 2012; 889:347-371. [PMID: 22669676 DOI: 10.1007/978-1-61779-867-2_22] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Over the past decade, the use of gene expression profiling (i.e., toxicogenomics or transcriptomics) has been established as the vanguard "omics" technology to investigate exposure-induced molecular changes that underlie the development of disease. As this technology quickly advances, researchers are striving to keep pace in grasping the complexity of toxicogenomic response while at the same time determine its applicability for the field of developmental toxicology. Initial studies suggest toxicogenomics to be a promising tool for multiple types of study designs, including exposure-response investigations (dose and duration), chemical classification, and model comparisons. In this review, we examine the use of toxicogenomics in developmental toxicology, discussing biological and technical factors that influence response and interpretation. Additionally, we provide a framework to guide toxicogenomic investigations in the field of developmental toxicology.
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Affiliation(s)
- Joshua F Robinson
- National Institute for Public Health and the Environment-RIVM, Bilthoven, The Netherlands
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