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Zhao LW, Zhu YZ, Wu YW, Pi SB, Shen L, Fan HY. Nuclear poly(A) binding protein 1 (PABPN1) mediates zygotic genome activation-dependent maternal mRNA clearance during mouse early embryonic development. Nucleic Acids Res 2021; 50:458-472. [PMID: 34904664 PMCID: PMC8855302 DOI: 10.1093/nar/gkab1213] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 11/14/2022] Open
Abstract
An embryo starts its life with maternal mRNA clearance, which is crucial for embryonic development. The elimination of maternal transcripts occurs by the joint action of two pathways: the maternally encoded mRNA decay pathway (M-decay) and the zygotic genome activation (ZGA)-dependent pathway (Z-decay). However, zygotic factors triggering maternal mRNA decay in early mammalian embryos remain largely unknown. In this study, we identified the zygotically encoded nuclear poly(A) binding protein 1 (PABPN1) as a factor required for maternal mRNA turnover, with a previously undescribed cytoplasmic function. Cytoplasmic PABPN1 docks on 3'-uridylated transcripts, downstream of terminal uridylyl transferases TUT4 and TUT7, and recruits 3'-5' exoribonuclease DIS3L2 to its targets, facilitating maternal mRNA decay. Pabpn1-knockout in mice resulted in preimplantation stage mortality due to early developmental arrest at the morula stage. Maternal mRNAs to be eliminated via the Z-decay pathway failed to be removed from Pabpn1-depleted embryos. Furthermore, PABPN1-mediated Z-decay is essential for major ZGA and regulates the expression of cell fate-determining factors in mouse preimplantation embryos. This study revealed an unforeseen cytoplasmic function of PABPN1 coupled with early embryonic development, characterized the presence of a zygotic destabilizer of maternal mRNA, and elucidated the Z-decay process mechanisms, which potentially contribute to human fertility.
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Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuai-Bo Pi
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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2
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Lin CY, Lu MYJ, Yue JX, Li KL, Le Pétillon Y, Yong LW, Chen YH, Tsai FY, Lyu YF, Chen CY, Hwang SPL, Su YH, Yu JK. Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling. PLoS Genet 2021; 16:e1009294. [PMID: 33382716 PMCID: PMC7806126 DOI: 10.1371/journal.pgen.1009294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 01/13/2021] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
Studies in various animals have shown that asymmetrically localized maternal transcripts play important roles in axial patterning and cell fate specification in early embryos. However, comprehensive analyses of the maternal transcriptomes with spatial information are scarce and limited to a handful of model organisms. In cephalochordates (amphioxus), an early branching chordate group, maternal transcripts of germline determinants form a compact granule that is inherited by a single blastomere during cleavage stages. Further blastomere separation experiments suggest that other transcripts associated with the granule are likely responsible for organizing the posterior structure in amphioxus; however, the identities of these determinants remain unknown. In this study, we used high-throughput RNA sequencing of separated blastomeres to examine asymmetrically localized transcripts in two-cell and eight-cell stage embryos of the amphioxus Branchiostoma floridae. We identified 111 and 391 differentially enriched transcripts at the 2-cell stage and the 8-cell stage, respectively, and used in situ hybridization to validate the spatial distribution patterns for a subset of these transcripts. The identified transcripts could be categorized into two major groups: (1) vegetal tier/germ granule-enriched and (2) animal tier/anterior-enriched transcripts. Using zebrafish as a surrogate model system, we showed that overexpression of one animal tier/anterior-localized amphioxus transcript, zfp665, causes a dorsalization/anteriorization phenotype in zebrafish embryos by downregulating the expression of the ventral gene, eve1, suggesting a potential function of zfp665 in early axial patterning. Our results provide a global transcriptomic blueprint for early-stage amphioxus embryos. This dataset represents a rich platform to guide future characterization of molecular players in early amphioxus development and to elucidate conservation and divergence of developmental programs during chordate evolution.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kun-Lung Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yann Le Pétillon
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Luok Wen Yong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Fu-Yu Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Feng Lyu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yi Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Sheng-Ping L. Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- * E-mail: (Y-HS); (J-KY)
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
- * E-mail: (Y-HS); (J-KY)
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Vastenhouw NL, Cao WX, Lipshitz HD. The maternal-to-zygotic transition revisited. Development 2019; 146:146/11/dev161471. [PMID: 31189646 DOI: 10.1242/dev.161471] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The development of animal embryos is initially directed by maternal gene products. Then, during the maternal-to-zygotic transition (MZT), developmental control is handed to the zygotic genome. Extensive research in both vertebrate and invertebrate model organisms has revealed that the MZT can be subdivided into two phases, during which very different modes of gene regulation are implemented: initially, regulation is exclusively post-transcriptional and post-translational, following which gradual activation of the zygotic genome leads to predominance of transcriptional regulation. These changes in the gene expression program of embryos are precisely controlled and highly interconnected. Here, we review current understanding of the mechanisms that underlie handover of developmental control during the MZT.
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Affiliation(s)
- Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wen Xi Cao
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
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4
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Fukushima M, Hosoda N, Chifu K, Hoshino SI. TDP-43 accelerates deadenylation of target mRNAs by recruiting Caf1 deadenylase. FEBS Lett 2019; 593:277-287. [PMID: 30520513 DOI: 10.1002/1873-3468.13310] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022]
Abstract
TAR DNA-binding protein 43 (TDP-43) is an RNA-binding protein, whose loss-of-function mutation causes amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration. Recent studies demonstrated that TDP-43 binds to the 3' untranslated region (UTR) of target mRNAs to promote mRNA instability. Here, we show that TDP-43 recruits Caf1 deadenylase to mRNA targets and accelerates their deadenylation. Tethering TDP-43 to the mRNA 3'UTR recapitulates destabilization of the mRNA, and TDP-43 accelerates their deadenylation. This accelerated deadenylation is inhibited by a dominant negative mutant of Caf1. We find that TDP-43 physically interacts with Caf1. In addition, we provide evidence that TDP-43 regulates poly(A) tail length of endogenous Progranulin (GRN) mRNA. These results may shed light on the link between dysregulation of TDP-43-mediated mRNA deadenylation and pathogenesis of neurodegenerative diseases.
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Affiliation(s)
- Makoto Fukushima
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
| | - Nao Hosoda
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
| | - Kotaro Chifu
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
| | - Shin-Ichi Hoshino
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
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CNOT6 regulates a novel pattern of mRNA deadenylation during oocyte meiotic maturation. Sci Rep 2018; 8:6812. [PMID: 29717177 PMCID: PMC5931610 DOI: 10.1038/s41598-018-25187-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 04/13/2018] [Indexed: 01/16/2023] Open
Abstract
In many cell types, the length of the poly(A) tail of an mRNA is closely linked to its fate - a long tail is associated with active translation, a short tail with silencing and degradation. During mammalian oocyte development, two contrasting patterns of polyadenylation have been identified. Some mRNAs carry a long poly(A) tail during the growth stage and are actively translated, then become deadenylated and down-regulated during the subsequent stage, termed meiotic maturation. Other mRNAs carry a short tail poly(A) tail and are translationally repressed during growth, and their poly(A) tail lengthens and they become translationally activated during maturation. As well, a program of elimination of this ‘maternal’ mRNA is initiated during oocyte maturation. Here we describe a third pattern of polyadenylation: mRNAs are deadenylated in growing oocytes, become polyadenylated during early maturation and then deadenylated during late maturation. We show that the deadenylase, CNOT6, is present in cortical foci of oocytes and regulates deadenylation of these mRNAs, and that PUF-binding elements (PBEs) regulate deadenylation in mature oocytes. Unexpectedly, maintaining a long poly(A) tail neither enhances translation nor inhibits degradation of these mRNAs. Our findings implicate multiple machineries, more complex than previously thought, in regulating mRNA activity in oocytes.
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Despic V, Neugebauer KM. RNA tales – how embryos read and discard messages from mom. J Cell Sci 2018; 131:jcs.201996. [DOI: 10.1242/jcs.201996] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Following fertilization, embryos develop for a substantial amount of time with a transcriptionally silent genome. Thus, early development is maternally programmed, as it solely relies on RNAs and proteins that are provided by the female gamete. However, these maternal instructions are not sufficient to support later steps of embryogenesis and are therefore gradually replaced by novel products synthesized from the zygotic genome. This switch in the origin of molecular players that drive early development is known as the maternal-to-zygotic transition (MZT). MZT is a universal phenomenon among all metazoans and comprises two interconnected processes: maternal mRNA degradation and the transcriptional awakening of the zygotic genome. The recent adaptation of high-throughput methods for use in embryos has deepened our knowledge of the molecular principles underlying MZT. These mechanisms comprise conserved strategies for RNA regulation that operate in many well-studied cellular contexts but that have adapted differently to early development. In this Review, we will discuss advances in our understanding of post-transcriptional regulatory pathways that drive maternal mRNA clearance during MZT, with an emphasis on recent data in zebrafish embryos on codon-mediated mRNA decay, the contributions of microRNAs (miRNAs) and RNA-binding proteins to this process, and the roles of RNA modifications in the stability control of maternal mRNAs.
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Affiliation(s)
- Vladimir Despic
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Karla M. Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Tokmakov AA, Iguchi S, Iwasaki T, Fukami Y, Sato KI. Global decay of mRNA is a hallmark of apoptosis in aging Xenopus eggs. RNA Biol 2017; 14:339-346. [PMID: 28045588 PMCID: PMC5367254 DOI: 10.1080/15476286.2016.1276695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Cytoplasmic mRNAs are specifically degraded in somatic cells as a part of early apoptotic response. However, no reports have been presented so far concerning mRNA fate in apoptotic gametes. In the present study, we analyzed the content of various cytoplasmic mRNAs in aging oocytes and eggs of the African clawed frog, Xenopus laevis. To circumvent large gene expression variation among the individual oocytes and eggs, single-cell monitoring of transcript levels has been implemented, using multiple cytoplasmic collections and reverse transcriptase quantitative PCR. It was found that numerous cytoplasmic mRNAs, coding for proteins classified in different functional types, are robustly degraded in apoptotic Xenopus eggs, but not in aging oocytes. mRNA degradation becomes evident in the eggs after meiotic exit at the time of cytochrome c release. A strong correlation between the length of PCR amplicon and specific transcript content was observed, suggesting endonucleolytic cleavage of mRNA. In addition, it was found that mRNA deadenylation also contributes to apoptotic mRNA degradation. Altogether, these findings indicate that the global decay of mRNA represents a hallmark of apoptosis in aging Xenopus eggs. To our knowledge, this is the first description of mRNA degradation in apoptotic gamete cells.
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Affiliation(s)
- Alexander A Tokmakov
- a Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama , Kita ku , Kyoto , Japan.,b Graduate School of Science, Kobe University, Rokko dai , Nada , Kobe , Japan
| | - Sho Iguchi
- b Graduate School of Science, Kobe University, Rokko dai , Nada , Kobe , Japan
| | - Tetsushi Iwasaki
- b Graduate School of Science, Kobe University, Rokko dai , Nada , Kobe , Japan
| | - Yasuo Fukami
- b Graduate School of Science, Kobe University, Rokko dai , Nada , Kobe , Japan
| | - Ken-Ichi Sato
- a Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama , Kita ku , Kyoto , Japan
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8
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Zhang M, Skirkanich J, Lampson MA, Klein PS. Cell Cycle Remodeling and Zygotic Gene Activation at the Midblastula Transition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 953:441-487. [DOI: 10.1007/978-3-319-46095-6_9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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9
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Jiang P, Nelson JD, Leng N, Collins M, Swanson S, Dewey CN, Thomson JA, Stewart R. Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability. Dev Biol 2016; 426:143-154. [PMID: 27475628 DOI: 10.1016/j.ydbio.2016.05.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 05/20/2016] [Accepted: 05/21/2016] [Indexed: 12/14/2022]
Abstract
The axolotl (Ambystoma mexicanum) has long been the subject of biological research, primarily owing to its outstanding regenerative capabilities. However, the gene expression programs governing its embryonic development are particularly underexplored, especially when compared to other amphibian model species. Therefore, we performed whole transcriptome polyA+ RNA sequencing experiments on 17 stages of embryonic development. As the axolotl genome is unsequenced and its gene annotation is incomplete, we built de novo transcriptome assemblies for each stage and garnered functional annotation by comparing expressed contigs with known genes in other organisms. In evaluating the number of differentially expressed genes over time, we identify three waves of substantial transcriptome upheaval each followed by a period of relative transcriptome stability. The first wave of upheaval is between the one and two cell stage. We show that the number of differentially expressed genes per unit time is higher between the one and two cell stage than it is across the mid-blastula transition (MBT), the period of zygotic genome activation. We use total RNA sequencing to demonstrate that the vast majority of genes with increasing polyA+ signal between the one and two cell stage result from polyadenylation rather than de novo transcription. The first stable phase begins after the two cell stage and continues until the mid-blastula transition, corresponding with the pre-MBT phase of transcriptional quiescence in amphibian development. Following this is a peak of differential gene expression corresponding with the activation of the zygotic genome and a phase of transcriptomic stability from stages 9-11. We observe a third wave of transcriptomic change between stages 11 and 14, followed by a final stable period. The last two stable phases have not been documented in amphibians previously and correspond to times of major morphogenic change in the axolotl embryo: gastrulation and neurulation. These results yield new insights into global gene expression during early stages of amphibian embryogenesis and will help to further develop the axolotl as a model species for developmental and regenerative biology.
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Affiliation(s)
- Peng Jiang
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Jeffrey D Nelson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Ning Leng
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Michael Collins
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Scott Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States; Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, United States; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, United States
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States.
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Yartseva V, Giraldez AJ. The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming. Curr Top Dev Biol 2015; 113:191-232. [PMID: 26358874 DOI: 10.1016/bs.ctdb.2015.07.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cellular transitions occur at all stages of organismal life from conception to adult regeneration. Changing cellular state involves three main features: activating gene expression necessary to install the new cellular state, modifying the chromatin status to stabilize the new gene expression program, and removing existing gene products to clear out the previous cellular program. The maternal-to-zygotic transition (MZT) is one of the most profound changes in the life of an organism. It involves gene expression remodeling at all levels, including the active clearance of the maternal oocyte program to adopt the embryonic totipotency. In this chapter, we provide an overview of molecular mechanisms driving maternal mRNA clearance during the MZT, describe the developmental consequences of losing components of this gene regulation, and illustrate how remodeling of gene expression during the MZT is common to other cellular transitions with parallels to cellular reprogramming.
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Affiliation(s)
- Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.
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11
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Ma J, Fukuda Y, Schultz RM. Mobilization of Dormant Cnot7 mRNA Promotes Deadenylation of Maternal Transcripts During Mouse Oocyte Maturation. Biol Reprod 2015; 93:48. [PMID: 26134871 DOI: 10.1095/biolreprod.115.130344] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/10/2015] [Indexed: 11/01/2022] Open
Abstract
Maternal mRNAs in oocytes are remarkably stable. In mouse, oocyte maturation triggers a transition from mRNA stability to instability. This transition is a critical event in the oocyte-to-embryo transition in which a differentiated oocyte loses its identity as it is transformed into totipotent blastomeres. We previously demonstrated that phosphorylation of MSY2, an RNA-binding protein, and mobilization of mRNAs encoding the DCP1A-DCP2 decapping complex contribute to maternal mRNA destruction during meiotic maturation. We report here that Cnot7, Cnot6l, and Pan2, key components of deadenylation machinery, are also dormant maternal mRNAs that are recruited during oocyte maturation. Inhibiting the maturation-associated increase in CNOT7 (or CNOT6L) using a small interference RNA approach inhibits mRNA deadenylation, whereas inhibiting the increase in PAN2 has little effect. Reciprocally, expressing CNOT7 (or CNOT6L) in oocytes prevented from resuming meiosis initiates deadenylation of mRNAs. These effects on deadenylation are also observed when the total amount of poly (A) is quantified. Last, inhibiting the increase in CNOT7 protein results in an ~70% decrease in transcription in 2-cell embryos.
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Affiliation(s)
- Jun Ma
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yusuke Fukuda
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
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12
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Labrecque R, Lodde V, Dieci C, Tessaro I, Luciano AM, Sirard MA. Chromatin remodelling and histone m RNA accumulation in bovine germinal vesicle oocytes. Mol Reprod Dev 2015; 82:450-62. [PMID: 25940597 DOI: 10.1002/mrd.22494] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/14/2015] [Indexed: 01/24/2023]
Abstract
Major remodelling of the chromatin enclosed within the germinal vesicle occurs towards the end of oocyte growth in mammals, but the mechanisms involved in this process are not completely understood. In bovine, four distinct stages of chromatin compaction-ranging from a diffused state (GV0) to a fully compacted configuration (GV3)-are linked to the gradual acquisition of developmental potential. To better understand the molecular events and to identify mRNA modulations occurring in the oocyte during the GV0-to-GV3 transition, transcriptomic analysis was performed with the EmbryoGENE microarray platform. The mRNA abundance of several genes decreased as chromatin compaction increased, which correlates with progressive transcriptional silencing that is characteristic of the end of oocyte growth. On the other hand, the abundance of some transcripts increased during the same period, particularly several histone gene transcripts from the H2A, H2B, H3, H4, and linker H1 family. In silico analysis predicted RNA-protein interactions between specific histone transcripts and the bovine stem-loop binding protein 2 (SLBP2), which helps regulate the translation of histone mRNA during oogenesis. These results suggest that some histone-encoding transcripts are actively stored, possibly to sustain the needs of the embryo before genome activation. This dataset offers a unique opportunity to survey which histone mRNAs are needed to complete chromatin compaction during oocyte maturation and which are stockpiled for the first three cell cycles following fertilization.
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Affiliation(s)
- R Labrecque
- Département des Sciences Animales, Centre de Recherche en Biologie de la Reproduction, Université Laval, Québec, Québec, Canada
| | - V Lodde
- Reproductive and Developmental Biology Laboratory, Department of Health, Animal Sciences and Food Safety, University of Milan, Milan, Italy
| | - C Dieci
- Reproductive and Developmental Biology Laboratory, Department of Health, Animal Sciences and Food Safety, University of Milan, Milan, Italy
| | - I Tessaro
- Reproductive and Developmental Biology Laboratory, Department of Health, Animal Sciences and Food Safety, University of Milan, Milan, Italy
| | - A M Luciano
- Reproductive and Developmental Biology Laboratory, Department of Health, Animal Sciences and Food Safety, University of Milan, Milan, Italy
| | - M A Sirard
- Département des Sciences Animales, Centre de Recherche en Biologie de la Reproduction, Université Laval, Québec, Québec, Canada
- Department of Animal Sciences, Laval University, Québec, Québec, Canada
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13
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Angulo L, Guyader-Joly C, Auclair S, Hennequet-Antier C, Papillier P, Boussaha M, Fritz S, Hugot K, Moreews F, Ponsart C, Humblot P, Dalbies-Tran R. An integrated approach to bovine oocyte quality: from phenotype to genes. Reprod Fertil Dev 2015; 28:RD14353. [PMID: 25689671 DOI: 10.1071/rd14353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 01/07/2015] [Indexed: 11/23/2022] Open
Abstract
In cattle, early embryonic failure plays a major role in the limitation of reproductive performance and is influenced by genetic effects. Suboptimal oocyte quality, including an inadequate store of maternal factors, is suspected to contribute to this phenomenon. In the present study, 13 Montbeliarde cows were phenotyped on oocyte quality, based on their ability to produce viable embryos after in vitro maturation, fertilisation and culture for 7 days. This discriminated two groups of animals, exhibiting developmental rates below 18.8% or above 40.9% (relative to cleaved embryos). Using microarrays, transcriptomic profiles were compared between oocytes collected in vivo from these two groups of animals. The difference in oocyte development potential was associated with changes in transcripts from 60 genes in immature oocytes and 135 genes in mature oocytes (following Bonferroni 5% correction). Of these, 16 and 32 genes were located in previously identified fertility quantitative trait loci. A subset of differential genes was investigated on distinct samples by reverse transcription-quantitative polymerase chain reaction. For SLC25A16, PPP1R14C, ROBO1, AMDHD1 and MEAF6 transcripts, differential expression was confirmed between high and low oocyte potential animals. Further sequencing and searches for polymorphisms will pave the way for implementing their use in genomic selection.
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14
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Reyes JM, Chitwood JL, Ross PJ. RNA-Seq profiling of single bovine oocyte transcript abundance and its modulation by cytoplasmic polyadenylation. Mol Reprod Dev 2015; 82:103-14. [PMID: 25560149 DOI: 10.1002/mrd.22445] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/11/2014] [Indexed: 12/29/2022]
Abstract
Molecular changes occurring during mammalian oocyte maturation are partly regulated by cytoplasmic polyadenylation (CP) and affect oocyte quality, yet the extent of CP activity during oocyte maturation remains unknown. Single bovine oocyte RNA sequencing (RNA-Seq) was performed to examine changes in transcript abundance during in vitro oocyte maturation in cattle. Polyadenylated RNA from individual germinal-vesicle and metaphase-II oocytes was amplified and processed for Illumina sequencing, producing approximately 30 million reads per replicate for each sample type. A total of 10,494 genes were found to be expressed, of which 2,455 were differentially expressed (adjusted P < 0.05 and fold change >2) between stages, with 503 and 1,952 genes respectively increasing and decreasing in abundance. Differentially expressed genes with complete 3'-untranslated-region sequence (279 increasing and 918 decreasing in polyadenylated transcript abundance) were examined for the presence, position, and distribution of motifs mediating CP, revealing enrichment (85%) and lack thereof (18%) in up- and down-regulated genes, respectively. Examination of total and polyadenylated RNA abundance by quantitative PCR validated these RNA-Seq findings. The observed increases in polyadenylated transcript abundance within the RNA-Seq data are likely due to CP, providing novel insight into targeted transcripts and resultant differential gene expression profiles that contribute to oocyte maturation.
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Affiliation(s)
- Juan M Reyes
- Department of Animal Science, University of California, Davis, CA
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Smits AH, Lindeboom RGH, Perino M, van Heeringen SJ, Veenstra GJC, Vermeulen M. Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs. Nucleic Acids Res 2014; 42:9880-91. [PMID: 25056316 PMCID: PMC4150773 DOI: 10.1093/nar/gku661] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies. Here, we perform global absolute protein quantification of fertilized Xenopus laevis eggs using mass spectrometry-based proteomics, quantifying over 5800 proteins in the largest single cell proteome characterized to date. Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance. Protein copy numbers in single eggs range from tens of thousands to ten trillion copies per cell. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identify 439 proteins that significantly change in abundance during early embryogenesis. Downregulated proteins include ribosomal proteins and upregulated proteins include basal transcription factors, among others. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in X. laevis eggs.
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Affiliation(s)
- Arne H Smits
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands Cancer Genomics Netherlands, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands Cancer Genomics Netherlands, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Matteo Perino
- Department of Developmental Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Simon J van Heeringen
- Department of Developmental Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Department of Developmental Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands Cancer Genomics Netherlands, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
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Collart C, Owens NDL, Bhaw-Rosun L, Cooper B, De Domenico E, Patrushev I, Sesay AK, Smith JN, Smith JC, Gilchrist MJ. High-resolution analysis of gene activity during the Xenopus mid-blastula transition. Development 2014; 141:1927-39. [PMID: 24757007 PMCID: PMC3994770 DOI: 10.1242/dev.102012] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here, we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilisation wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the seventh cleavage and extending beyond the MBT at the twelfth cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal mRNAs that are deadenylated shortly after fertilisation, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organisation of gene regulatory networks in the early Xenopus embryo.
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Affiliation(s)
- Clara Collart
- Division of Systems Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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18
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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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19
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Paranjpe SS, Jacobi UG, van Heeringen SJ, Veenstra GJC. A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. BMC Genomics 2013; 14:762. [PMID: 24195446 PMCID: PMC3907017 DOI: 10.1186/1471-2164-14-762] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 10/26/2013] [Indexed: 12/21/2022] Open
Abstract
Background Dynamics of polyadenylation vs. deadenylation determine the fate of several developmentally regulated genes. Decay of a subset of maternal mRNAs and new transcription define the maternal-to-zygotic transition, but the full complement of polyadenylated and deadenylated coding and non-coding transcripts has not yet been assessed in Xenopus embryos. Results To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts and putative long non-coding RNAs (lncRNA). These lncRNA transcripts were stringently selected as spliced transcripts generated from independent promoters, with limited coding potential and a codon bias characteristic of noncoding sequences. Many lncRNAs are conserved and expressed in a developmental stage-specific fashion. Conclusions These data reveal dynamics of transcriptome polyadenylation and abundance and provides a high-confidence catalogue of novel and long non-coding RNAs.
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Affiliation(s)
- Sarita S Paranjpe
- Radboud University Nijmegen, Dept, of Molecular Developmental Biology, Faculty of Science, Nijmegen Center for Molecular Life Sciences, The Netherlands.
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20
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Curanovic D, Cohen M, Singh I, Slagle CE, Leslie CS, Jaffrey SR. Global profiling of stimulus-induced polyadenylation in cells using a poly(A) trap. Nat Chem Biol 2013; 9:671-3. [PMID: 23995769 PMCID: PMC3805764 DOI: 10.1038/nchembio.1334] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 08/05/2013] [Indexed: 11/25/2022]
Abstract
Polyadenylation of mRNA leads to increased protein expression in response to diverse stimuli, but it is difficult to identify mRNAs that become polyadenylated in living cells. Here we describe a click chemistry-compatible nucleoside analog that is selectively incorporated into poly(A) tails of transcripts in cells. Next-generation sequencing of labeled mRNAs enables a transcriptome-wide profile of polyadenylation and provides insights into the mRNA sequence elements that are correlated with polyadenylation.
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Affiliation(s)
- Dusica Curanovic
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
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21
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Dhorne-Pollet S, Thélie A, Pollet N. Validation of novel reference genes for RT-qPCR studies of gene expression in Xenopus tropicalis during embryonic and post-embryonic development. Dev Dyn 2013; 242:709-17. [PMID: 23559567 DOI: 10.1002/dvdy.23972] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 02/04/2013] [Accepted: 03/26/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Accurate interpretation of transcriptome profiling by quantitative PCR requires the establishment of species-specific standards. However, the selection of reference genes for assessing RNA expression profiles in Xenopus laevis and Xenopus tropicalis was mostly based on historical reasons and they often only reflect the traditions of a laboratory. RESULTS We investigated the expression stability of 10 genes (dicer1, drosha, eef1a1, elavl3, gsc, h4, odc1, rpl8, smn2, tbp), 8 of which are commonly used as internal controls in published RT-qPCR experiments. We defined specific primer pairs and evaluated their suitability as reference genes by performing RT-qPCR expression profiling in Xenopus tropicalis. Gene expression stability was assayed in a set of 15 developmental stages from the egg to the froglet, and in dissected embryos. CONCLUSIONS Overall, we determined a set of qualified reference genes for distinct developmental periods. We recommend the use of dicer1, drosha, eef1a1, and smn2 from early embryonic development up to the end of metamorphosis. During early embryogenesis drosha, eef1a1, smn2 are suitable. For the whole post-embryonic development and for metamorphic stages including pro-metamorphosis and metamorphic climax, we recommend the use of drosha and smn2. These reference genes should prove their usefulness for data comparison across studies.
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Mei W, Jin Z, Lai F, Schwend T, Houston DW, King ML, Yang J. Maternal Dead-End1 is required for vegetal cortical microtubule assembly during Xenopus axis specification. Development 2013; 140:2334-44. [PMID: 23615278 DOI: 10.1242/dev.094748] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Vertebrate axis specification is an evolutionarily conserved developmental process that relies on asymmetric activation of Wnt signaling and subsequent organizer formation on the future dorsal side of the embryo. Although roles of Wnt signaling during organizer formation have been studied extensively, it is unclear how the Wnt pathway is asymmetrically activated. In Xenopus and zebrafish, the Wnt pathway is triggered by dorsal determinants, which are translocated from the vegetal pole to the future dorsal side of the embryo shortly after fertilization. The transport of dorsal determinants requires a unique microtubule network formed in the vegetal cortex shortly after fertilization. However, molecular mechanisms governing the formation of vegetal cortical microtubule arrays are not fully understood. Here we report that Dead-End 1 (Dnd1), an RNA-binding protein required for primordial germ cell development during later stages of embryogenesis, is essential for Xenopus axis specification. We show that knockdown of maternal Dnd1 specifically interferes with the formation of vegetal cortical microtubules. This, in turn, impairs translocation of dorsal determinants, the initiation of Wnt signaling, organizer formation, and ultimately results in ventralized embryos. Furthermore, we found that Dnd1 binds to a uridine-rich sequence in the 3'-UTR of trim36, a vegetally localized maternal RNA essential for vegetal cortical microtubule assembly. Dnd1 anchors trim36 to the vegetal cortex in the egg, promoting high concentrations of Trim36 protein there. Our work thus demonstrates a novel and surprising function for Dnd1 during early development and provides an important link between Dnd1, mRNA localization, the microtubule cytoskeleton and axis specification.
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Affiliation(s)
- Wenyan Mei
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 2001 South Lincoln Avenue, 3411 Veterinary Medicine Basic Sciences Building, Urbana, IL 61802, USA
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23
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Barckmann B, Simonelig M. Control of maternal mRNA stability in germ cells and early embryos. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:714-24. [PMID: 23298642 DOI: 10.1016/j.bbagrm.2012.12.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 12/21/2012] [Accepted: 12/28/2012] [Indexed: 10/27/2022]
Abstract
mRNA regulation is essential in germ cells and early embryos. In particular, late oogenesis and early embryogenesis occur in the absence of transcription and rely on maternal mRNAs stored in oocytes. These maternal mRNAs subsequently undergo a general decay in embryos during the maternal-to-zygotic transition in which the control of development switches from the maternal to the zygotic genome. Regulation of mRNA stability thus plays a key role during these early stages of development and is tightly interconnected with translational regulation and mRNA localization. A common mechanism in these three types of regulation implicates variations in mRNA poly(A) tail length. Recent advances in the control of mRNA stability include the widespread and essential role of regulated deadenylation in early developmental processes, as well as the mechanisms regulating mRNA stability which involve RNA binding proteins, microRNAs and interplay between the two. Also emerging are the roles that other classes of small non-coding RNAs, endo-siRNAs and piRNAs play in the control of mRNA decay, including connections between the regulation of transposable elements and cellular mRNA regulation through the piRNA pathway. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Bridlin Barckmann
- mRNA Regulation and Development, Institute of Human Genetics, Montpellier Cedex 5, France
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24
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Weill L, Belloc E, Bava FA, Méndez R. Translational control by changes in poly(A) tail length: recycling mRNAs. Nat Struct Mol Biol 2012; 19:577-85. [PMID: 22664985 DOI: 10.1038/nsmb.2311] [Citation(s) in RCA: 233] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Beyond the well-known function of poly(A) tail length in mRNA stability, recent years have witnessed an explosion of information about how changes in tail length and the selection of alternative polyadenylation sites contribute to the translational regulation of a large portion of the genome. The mechanisms and factors mediating nuclear and cytoplasmic changes in poly(A) tail length have been studied in great detail, the targets of these mechanisms have been identified--in some cases by genome-wide screenings--and changes in poly(A) tail length are now implicated in a number of physiological and pathological processes. However, in very few cases have all three levels--mechanisms, targets and functions--been studied together.
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Affiliation(s)
- Laure Weill
- Institute for Research in Biomedicine-IRB Barcelona, Barcelona, Spain
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25
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Le Goff C, Laurent V, Le Bon K, Tanguy G, Couturier A, Le Goff X, Le Guellec R. pEg6, a Spire family member, is a maternal gene encoding a vegetally localized mRNA in Xenopus embryos. Biol Cell 2012; 98:697-708. [PMID: 16789907 DOI: 10.1042/bc20050095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND INFORMATION In Xenopus, during oocyte maturation and the segmentation period, cell cycle progression is independent of new transcription, but requires de novo translation. This suggests that the completion of oocyte maturation and then the rapid cell division period is controlled exclusively at a post-transcriptional level by specific gene products. To isolate these maternal genes, a differential screening of a Xenopus egg cDNA library was performed. Several cDNAs were isolated which correspond to mRNA polyadenylated in eggs and deadenylated in embryos, and these constitute the founders members of the Eg family of mRNAs. RESULTS We report here the characterization of Eg6 mRNA as a novel maternal gene expressed in Xenopus egg until gastrula stage. The Eg6 transcript is initially concentrated in the vegetal cytoplasm of the egg, and later the distribution of the transcript marks the posterior vegetal end of developing embryos. pEg6 is a multidomain protein with a kinase non-catalytic C-lobe domain of unknown function, a cluster of four WH2 (Wiskott-Aldrich syndrome protein homology 2) domains and a modified FYVE zinc-finger motif. The amino acid sequence of pEg6 is related to PEM-5 (posterior end mark-5), from an ascidian maternal mRNA, and spire, a Drosophila protein required to establish dorsal-ventral and anterior-posterior axes of polarity and recently described as an actin nucleation factor. In Xenopus and Schizosaccharomyces pombe cells pEg6 expression induces filamentous actin clusters and is associated with vesicular structure. CONCLUSION These data suggest that pEg6 acts as a vegetally localized factor contributing to the actin nucleation process during Xenopus early development.
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Affiliation(s)
- Catherine Le Goff
- CNRS UMR6061 Génétique et Développement, Université de Rennes 1, Groupe Développement Précoce, IFR140 GFAS, Faculté de Médecine, 2 avenue du Pr Léon Bernard, CS 34317, 35043 Rennes cedex, France.
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Méreau A, Le Sommer C, Lerivray H, Lesimple M, Hardy S. Xenopus as a model to study alternative splicing in vivo. Biol Cell 2012; 99:55-65. [PMID: 17155935 DOI: 10.1042/bc20060073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An increasing number of genes are being identified for which the corresponding mRNAs contain different combinations of the encoded exons. This highly regulated exon choice, or alternative splicing, is often tissue-specific and potentially could differentially affect cellular functions. Alternative splicing is therefore not only a means to increase the coding capacity of the genome, but also to regulate gene expression during differentiation or development. To both evaluate the importance for cellular functions and define the regulatory pathways of alternative splicing, it is necessary to progress from the in vitro or ex vivo experimental models actually used towards in vivo whole-animal studies. We present here the amphibian, Xenopus, as an experimental model highly amenable for such studies. The various experimental approaches that can be used with Xenopus oocytes and embryos to characterize regulatory sequence elements and factors are presented and the advantages and drawbacks of these approaches are discussed. Finally, the real possibilities for large-scale identification of mRNAs containing alternatively spliced exons, the tissue-specific patterns of exon usage and the way in which these patterns are modified by perturbing the relative amount of splicing factors are discussed.
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Affiliation(s)
- Agnes Méreau
- UMR 6061 CNRS-Université de Rennes 1, IFR 140 Génétique Fonctionnelle, Agronomie et Santé, Faculté de Médecine, 2 avenue de Pr. Léon Bernard, 35043 Rennes cedex, France
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27
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Walser CB, Lipshitz HD. Transcript clearance during the maternal-to-zygotic transition. Curr Opin Genet Dev 2011; 21:431-43. [PMID: 21497081 DOI: 10.1016/j.gde.2011.03.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 03/21/2011] [Indexed: 02/04/2023]
Abstract
In all animals, a key event in the transition from maternal control of development to control by products of the zygotic genome is the elimination of a significant fraction of the mRNAs loaded into the egg by the mother. Clearance of these maternal mRNAs is accomplished by two activities: the first is maternally encoded while the second requires zygotic transcription. Recent advances include identification of RNA-binding proteins that function as specificity factors to direct the maternal degradation machinery to its target mRNAs; small RNAs-most notably microRNAs-that function as components of the zygotically encoded activity; signaling pathways that trigger production and/or activation of the clearance mechanism in early embryos; and mechanisms for spatial control of transcript clearance.
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Affiliation(s)
- Claudia B Walser
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
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Marracci S, Michelotti V, Casola C, Giacoma C, Ragghianti M. Daz- and pumilio-like genes are asymmetrically localized in Pelophylax (Rana) oocytes and are expressed during early spermatogenesis. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 316:330-8. [PMID: 21344644 DOI: 10.1002/jez.b.21405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Revised: 12/22/2010] [Accepted: 01/01/2011] [Indexed: 12/14/2022]
Abstract
In many organisms, the specification of cell fate and the formation of embryonic axes depend on a proper distribution of maternal mRNAs during oogenesis. Asymmetrically localized determinants are required both for embryonic axes and germline determination in anuran amphibians. As a model system of these processes, we have used a species complex of the genus Pelophylax (Rana), characterized by a hybridogenetic reproduction that involves events of genome exclusion and endoreduplication during meiosis in both sexes. With the aim of characterizing the still largely unknown molecular events regulating Pelophylax gametogenesis, we have isolated in this animal model homologues of the deleted in AZoospermia-like (DAZl) and pumilio gene families (named RlDazl and RlPum1, respectively), which encode posttranscriptional regulators. Expression pattern analysis of these genes showed that RlDazl is exclusively expressed in gonadal tissues, whereas RlPum1 is expressed in both somatic tissues and gonads. In situ hybridization carried out on gonads revealed that the two transcripts were asymmetrically localized along the animal-vegetal (A-V) axis of oocytes. In particular, the RlDazl transcript progressively collected to the vegetal pole during oogenesis, whereas the RlPum1 mRNA was preferentially enriched at the animal hemisphere. In adult testes, RlDazl and RlPum1 were expressed in specific phases of spermatogenetic divisions as shown by immunostaining with anti-H3 phosphohistone antibody. Our results indicate that RlDazl and RlPum1 represent two early indicators of oocyte polarity in this hybridogenetic vertebrate model. Additionally, RlDazl share with vertebrate DAZ- like genes a germ cell-specific expression pattern.
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Affiliation(s)
- Silvia Marracci
- Laboratory of Cell and Developmental Biology, Department of Biology, University of Pisa, Pisa, Italy.
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29
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Abstract
Nearly all eukaryotic mRNAs terminate in a poly(A) tail that serves important roles in mRNA utilization. In the cytoplasm, the poly(A) tail promotes both mRNA stability and translation, and these functions are frequently regulated through changes in tail length. To identify the scope of poly(A) tail length control in a transcriptome, we developed the polyadenylation state microarray (PASTA) method. It involves the purification of mRNA based on poly(A) tail length using thermal elution from poly(U) sepharose, followed by microarray analysis of the resulting fractions. In this chapter we detail our PASTA approach and describe some methods for bulk and mRNA-specific poly(A) tail length measurements of use to monitor the procedure and independently verify the microarray data.
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Affiliation(s)
- Traude H Beilharz
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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30
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Kosubek A, Klein-Hitpass L, Rademacher K, Horsthemke B, Ryffel GU. Aging of Xenopus tropicalis eggs leads to deadenylation of a specific set of maternal mRNAs and loss of developmental potential. PLoS One 2010; 5:e13532. [PMID: 21042572 PMCID: PMC2962626 DOI: 10.1371/journal.pone.0013532] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 09/18/2010] [Indexed: 01/19/2023] Open
Abstract
As first shown more than 100 years ago, fertilization of an aged (overripe) egg increases the rate of malformations and embryonic loss in several vertebrates, including possibly humans as well. Since the molecular events in aging eggs may be similar in these species, we established in the frog Xenopus tropicalis a defined protocol for delayed fertilization of eggs. A three-hour delayed fertilization led to a dramatic increase in malformation and mortality. Gene expression profiling revealed that 14% of the polyadenylated maternal transcripts were downregulated upon aging. These transcripts were not degraded, but rather deadenylated as shown for specific maternal mRNAs. The affected transcripts are characterized by a relatively short 3′UTR and a paucity of cytoplasmic polyadenylation elements (CPE) and polyadenylation signals (PAS). Furthermore, maternal mRNAs known to be deadenylated during egg maturation as well as after fertilization were preferentially deadenylated in aged eggs. Taken together our analysis of aging eggs reveals that unfertilized eggs are in a dynamic state that was previously not realized. On the one hand deadenylation of transcripts that are typically deadenylated during egg maturation continues and this implies overripeness of the aged egg in the truest sense of the word. On the other hand transcripts that normally are deadenylated after fertilization loose their poly(A) in the aged egg and this implies that the egg awaiting fertilization starts processes that are normally only observed after fertilization. Based on our novel finding we postulate that the imbalance of the polyadenylated maternal transcripts upon egg aging contributes to the loss of developmental potential. Based on this hypothesis the developmental consequences of downregulation of specific transcripts can be analyzed in future.
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Affiliation(s)
- Anna Kosubek
- Institut für Zellbiologie (Tumorforschung), Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Ludger Klein-Hitpass
- Institut für Zellbiologie (Tumorforschung), Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Katrin Rademacher
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Gerhart U. Ryffel
- Institut für Zellbiologie (Tumorforschung), Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- * E-mail:
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Ribas L, Li MS, Doddington BJ, Robert J, Seidel JA, Kroll JS, Zimmerman LB, Grassly NC, Garner TWJ, Fisher MC. Expression profiling the temperature-dependent amphibian response to infection by Batrachochytrium dendrobatidis. PLoS One 2009; 4:e8408. [PMID: 20027316 PMCID: PMC2794374 DOI: 10.1371/journal.pone.0008408] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 11/20/2009] [Indexed: 01/31/2023] Open
Abstract
Amphibians are experiencing a panzootic of unprecedented proportions caused by the emergence of Batrachochytrium dendrobatidis (Bd). However, all species are not equally at risk of infection, and risk is further modified by environmental variables, specifically temperature. In order to understand how, and when, hosts mount a response to Bd we analysed infection dynamics and patterns of gene expression in the model amphibian species Silurana (Xenopus) tropicalis. Mathematical modelling of infection dynamics demonstrate the existence of a temperature-dependent protective response that is largely independent of the intrinsic growth-rate of Bd. Using temporal expression-profiling by microarrays and qRT-PCR, we characterise this response in the main amphibian lymphoid tissue, the spleen. We demonstrate that clearance of Bd at the host-optimal temperature is not clearly associated with an adaptive immune response, but rather is correlated with the induction of components of host innate immunity including the expression of genes that are associated with the production of the antimicrobial skin peptide preprocareulein (PPCP) as well as inflammatory responses. We find that adaptive immunity appears to be lacking at host-optimal temperatures. This suggests that either Bd does not stimulate, or suppresses, adaptive immunity, or that trade-offs exist between innate and adaptive limbs of the amphibian immune system. At cold temperatures, S. tropicalis loses the ability to mount a PPCP-based innate response, and instead manifests a more pronounced inflammatory reaction that is characterised by the production of proteases and higher pathogen burdens. This study demonstrates the temperature-dependency of the amphibian response to infection by Bd and indicates the influence that changing climates may exert on the ectothermic host response to pathogens.
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Affiliation(s)
- Laia Ribas
- Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom
| | - Ming-Shi Li
- Department of Paediatrics, Imperial College London, London, United Kingdom
| | | | - Jacques Robert
- University of Rochester Medical Centre, Rochester, New York, United States of America
| | - Judith A. Seidel
- Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom
| | - J. Simon Kroll
- Department of Paediatrics, Imperial College London, London, United Kingdom
| | - Lyle B. Zimmerman
- Developmental Biology, National Institute for Medical Research, London, United Kingdom
| | - Nicholas C. Grassly
- Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom
| | | | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom
- * E-mail:
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Collart C, Ramis JM, Down TA, Smith JC. Smicl is required for phosphorylation of RNA polymerase II and affects 3'-end processing of RNA at the midblastula transition in Xenopus. Development 2009; 136:3451-61. [PMID: 19783735 DOI: 10.1242/dev.027714] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Smicl (Smad-interacting CPSF 30-like) is an unusual protein that interacts with transcription factors as well as with the cleavage and polyadenylation specificity factor (CPSF). Previous work has shown that Smicl is expressed maternally in the Xenopus embryo and is later required for transcription of Chordin. In this paper we search for additional targets of Smicl. We identify many genes whose onset of expression at the midblastula transition (MBT) requires Smicl and is correlated with the translocation of Smicl from cytoplasm to nucleus. At least one such gene, Xiro1, is regulated via 3'-end processing. In searching for a general mechanism by which Smicl might regulate gene expression at the MBT, we have discovered that it interacts with the tail of Rpb1, the largest subunit of RNA polymerase II. Our results show that Smicl is required for the phosphorylation of the Rpb1 tail at serine 2 of the repeated heptapeptide YSPTSPS. This site becomes hyperphosphorylated at the MBT, thus allowing the docking of proteins required for elongation of transcription and RNA processing. Our work links the onset of zygotic gene expression in the Xenopus embryo with the translocation of Smicl from cytoplasm to nucleus, the phosphorylation of Rpb1 and the 3'-end processing of newly transcribed mRNAs.
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Affiliation(s)
- Clara Collart
- Wellcome Trust/CR-UK Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, UK
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Beilharz TH, Preiss T. Transcriptome-wide measurement of mRNA polyadenylation state. Methods 2009; 48:294-300. [PMID: 19233282 DOI: 10.1016/j.ymeth.2009.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 02/09/2009] [Accepted: 02/09/2009] [Indexed: 10/21/2022] Open
Abstract
The 3' poly(A) tail has important roles throughout the eukaryotic mRNA life cycle. A characteristic aspect of poly(A) tail function is furthermore that it can be modulated by changes in its length. This is in turn a well-recognised cellular means to regulate both, mRNA translation and stability, and a positive correlation has often been found between the efficiency of mRNA translation and the length of its poly(A) tail. Here we describe methodology to measure mRNA polyadenylation state in a transcriptome-wide manner, using separation of cellular mRNA populations on poly(U) sepharose in combination with microarray analysis of the resulting fractions. We further detail methods for bulk and mRNA-specific poly(A) tail length measurements to monitor the efficiency of initial mRNA separation and to verify candidates selected from the microarray data. Although detailed here for the study of yeast mRNAs, these methods are adaptable to the investigation of any cellular context in which poly(A) tail length control is known or suspected to operate.
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Affiliation(s)
- Traude H Beilharz
- Molecular Genetics Division, Victor Chang Cardiac Research Institute (VCCRI), Lowy Packer Building, 405 Liverpool Street, Darlinghurst (Sydney), NSW 2010, Australia.
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Faunes F, Sánchez N, Castellanos J, Vergara IA, Melo F, Larraín J. Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression. Genome Biol 2009; 10:R15. [PMID: 19210784 PMCID: PMC2688288 DOI: 10.1186/gb-2009-10-2-r15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 11/25/2008] [Accepted: 02/11/2009] [Indexed: 11/12/2022] Open
Abstract
Comparison of dorsal and ventral transcriptomes of Xenopus tropicalis gastrulae using serial analysis of gene expression provides at least 86 novel differentially expressed transcripts. Background Recent evidence from global studies of gene expression indicates that transcriptomes are more complex than expected. Xenopus has been typically used as a model organism to study early embryonic development, particularly dorso-ventral patterning. In order to identify novel transcripts involved in dorso-ventral patterning, we compared dorsal and ventral transcriptomes of Xenopus tropicalis at the gastrula stage using serial analysis of gene expression (SAGE). Results Of the experimental tags, 54.5% were confidently mapped to transcripts and 125 showed a significant difference in their frequency of occurrence between dorsal and ventral libraries. We selected 20 differentially expressed tags and assigned them to specific transcripts using bioinformatics and reverse SAGE. Five mapped to transcripts with known dorso-ventral expression and the frequency of appearance for these tags in each library is in agreement with the expression described by other methods. The other 15 tags mapped to transcripts with no previously described asymmetric expression along the dorso-ventral axis. The differential expression of ten of these novel transcripts was validated by in situ hybridization and/or RT-PCR. We can estimate that this SAGE experiment provides a list of at least 86 novel transcripts with differential expression along the dorso-ventral axis. Interestingly, the expression of some novel transcripts was independent of β-catenin. Conclusions Our SAGE analysis provides a list of novel transcripts with differential expression in the dorso-ventral axis and a large number of orphan tags that can be used to identify novel transcripts and to improve the current annotation of the X. tropicalis genome.
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Affiliation(s)
- Fernando Faunes
- Center for Cell Regulation and Pathology and Center for Aging and Regeneration, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, 8331150, Chile
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de Vries WN, Evsikov AV, Brogan LJ, Anderson CP, Graber JH, Knowles BB, Solter D. Reprogramming and differentiation in mammals: motifs and mechanisms. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2008; 73:33-8. [PMID: 19022741 DOI: 10.1101/sqb.2008.73.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The natural reprogramming of the mammalian egg and sperm genomes is an efficient process that takes place in less than 24 hours and gives rise to a totipotent zygote. Transfer of somatic nuclei to mammalian oocytes also leads to their reprogramming and formation of totipotent embryos, albeit very inefficiently and requiring an activation step. Reprogramming of differentiated cells to induced pluripotent stem (iPS) cells takes place during a period of time substantially longer than reprogramming of the egg and sperm nuclei and is significantly less efficient. The stochastic expression of endogenous proteins during this process would imply that controlled expression of specific proteins is crucial for reprogramming to take place. The fact that OCT4, NANOG, and SOX2 form the core components of the pluripotency circuitry would imply that control at the transcriptional level is important for reprogramming to iPS cells. In contradistinction, the much more efficient reprogramming of the mammalian egg and sperm genomes implies that other levels of control are necessary, such as chromatin remodeling, translational regulation, and efficient degradation of no longer needed proteins and RNAs.
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Affiliation(s)
- W N de Vries
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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Vlasova IA, Bohjanen PR. Posttranscriptional regulation of gene networks by GU-rich elements and CELF proteins. RNA Biol 2008; 5:201-7. [PMID: 18971639 DOI: 10.4161/rna.7056] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
GU-rich elements found in pre-mRNA and mRNA transcripts play diverse roles in the control of gene expression by regulating mRNA stability, translation and pre-mRNA processing. Regulatory GU-rich elements are highly conserved throughout evolution, and play major roles in development in diverse species from worms to mammals. The conservation of the GU-rich element allowed it to be identified as a sequence that was enriched in the 3' UTR of human transcripts that exhibited rapid mRNA decay. This element functions, at least in part, as a molecular target for members of the CELF family of RNA-binding proteins, which recruit other components of the cellular posttranscriptional gene regulatory machinery to the transcript. Depending on the context, binding to GU-rich sequences by CELF proteins direct a variety of posttranscriptional regulatory events, including deadenylation, mRNA decay, translation or pre-mRNA processing. Thus, GU-rich elements and CELF proteins serve multiple functions in gene expression regulation and define an important evolutionarily conserved posttranscriptional regulatory network.
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Affiliation(s)
- Irina A Vlasova
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, McGuire Translational Research Facility, Minneapolis, Minnesota 55455, USA
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37
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Farley BM, Ryder SP. Regulation of Maternal mRNAs in Early Development. Crit Rev Biochem Mol Biol 2008; 43:135-62. [PMID: 18365862 DOI: 10.1080/10409230801921338] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Vallee M, Aiba K, Piao Y, Palin MF, Ko MSH, Sirard MA. Comparative analysis of oocyte transcript profiles reveals a high degree of conservation among species. Reproduction 2008; 135:439-48. [DOI: 10.1530/rep-07-0342] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Translational control by cytoplasmic polyadenylation in Xenopus oocytes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:217-29. [PMID: 18316045 PMCID: PMC2323027 DOI: 10.1016/j.bbagrm.2008.02.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 01/30/2008] [Accepted: 02/04/2008] [Indexed: 12/21/2022]
Abstract
Elongation of the poly(A) tails of specific mRNAs in the cytoplasm is a crucial regulatory step in oogenesis and early development of many animal species. The best studied example is the regulation of translation by cytoplasmic polyadenylation elements (CPEs) in the 3′ untranslated region of mRNAs involved in Xenopus oocyte maturation. In this review we discuss the mechanism of translational control by the CPE binding protein (CPEB) in Xenopus oocytes as follows:The cytoplasmic polyadenylation machinery such as CPEB, the subunits of cleavage and polyadenylation specificity factor (CPSF), symplekin, Gld-2 and poly(A) polymerase (PAP). The signal transduction that leads to the activation of CPE-mediated polyadenylation during oocyte maturation, including the potential roles of kinases such as MAPK, Aurora A, CamKII, cdk1/Ringo and cdk1/cyclin B. The role of deadenylation and translational repression, including the potential involvement of PARN, CCR4/NOT, maskin, pumilio, Xp54 (Ddx6, Rck), other P-body components and isoforms of the cap binding initiation factor eIF4E.
Finally we discuss some of the remaining questions regarding the mechanisms of translational regulation by cytoplasmic polyadenylation and give our view on where our knowledge is likely to be expanded in the near future.
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Graindorge A, Le Tonquèze O, Thuret R, Pollet N, Osborne HB, Audic Y. Identification of CUG-BP1/EDEN-BP target mRNAs in Xenopus tropicalis. Nucleic Acids Res 2008; 36:1861-70. [PMID: 18267972 PMCID: PMC2330240 DOI: 10.1093/nar/gkn031] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The early development of many animals relies on the posttranscriptional regulations of maternally stored mRNAs. In particular, the translation of maternal mRNAs is tightly controlled during oocyte maturation and early mitotic cycles in Xenopus. The Embryonic Deadenylation ElemeNt (EDEN) and its associated protein EDEN-BP are known to trigger deadenylation and translational silencing to several mRNAs bearing an EDEN. This Xenopus RNA-binding protein is an ortholog of the human protein CUG-BP1/CELF1. Five mRNAs, encoding cell cycle regulators and a protein involved in the notch pathway, have been identified as being deadenylated by EDEN/EDEN-BP. To identify new EDEN-BP targets, we immunoprecipitated EDEN-BP/mRNA complexes from Xenopus tropicalis egg extracts. We identified 153 mRNAs as new binding targets for EDEN-BP using microarrays. Sequence analyses of the 3′ untranslated regions of the newly identified EDEN-BP targets reveal an enrichment in putative EDEN sequences. EDEN-BP binding to a subset of the targets was confirmed both in vitro and in vivo. Among the newly identified targets, Cdk1, a key player of oocyte maturation and cell cycle progression, is specifically targeted by its 3′ UTR for an EDEN-BP-dependent deadenylation after fertilization.
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Affiliation(s)
- Antoine Graindorge
- CNRS, UMR 6061 Génétique et Développement, Université de Rennes 1, IFR 140 GFAS, 2 avenue du Pr Léon Bernard, CS 34317, 35043 Rennes Cedex and CNRS UMR 8080, Université Paris Sud, Orsay, France
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41
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Thélie A, Papillier P, Pennetier S, Perreau C, Traverso JM, Uzbekova S, Mermillod P, Joly C, Humblot P, Dalbiès-Tran R. Differential regulation of abundance and deadenylation of maternal transcripts during bovine oocyte maturation in vitro and in vivo. BMC DEVELOPMENTAL BIOLOGY 2007; 7:125. [PMID: 17988387 PMCID: PMC2211488 DOI: 10.1186/1471-213x-7-125] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Accepted: 11/07/2007] [Indexed: 12/03/2022]
Abstract
Background In bovine maturing oocytes and cleavage stage embryos, gene expression is mostly controlled at the post-transcriptional level, through degradation and deadenylation/polyadenylation. We have investigated how post transcriptional control of maternal transcripts was affected during in vitro and in vivo maturation, as a model of differential developmental competence. Results Using real time PCR, we have analyzed variation of maternal transcripts, in terms of abundance and polyadenylation, during in vitro or in vivo oocyte maturation and in vitro embryo development. Four genes are characterized here for the first time in bovine: ring finger protein 18 (RNF18) and breast cancer anti-estrogen resistance 4 (BCAR4), whose oocyte preferential expression was not previously reported in any species, as well as Maternal embryonic leucine zipper kinase (MELK) and STELLA. We included three known oocyte marker genes (Maternal antigen that embryos require (MATER), Zygote arrest 1 (ZAR1), NACHT, leucine rich repeat and PYD containing 9 (NALP9)). In addition, we selected transcripts previously identified as differentially regulated during maturation, peroxiredoxin 1 and 2 (PRDX1, PRDX2), inhibitor of DNA binding 2 and 3 (ID2, ID3), cyclin B1 (CCNB1), cell division cycle 2 (CDC2), as well as Aurora A (AURKA). Most transcripts underwent a moderate degradation during maturation. But they displayed sharply contrasted deadenylation patterns that account for variations observed previously by DNA array and correlated with the presence of a putative cytoplasmic polyadenylation element in their 3' untranslated region. Similar variations in abundance and polyadenylation status were observed during in vitro maturation or in vivo maturation, except for PRDX1, that appears as a marker of in vivo maturation. Throughout in vitro development, oocyte restricted transcripts were progressively degraded until the morula stage, except for MELK ; and the corresponding genes remained silent after major embryonic genome activation. Conclusion Altogether, our data emphasize the extent of post-transcriptional regulation during oocyte maturation. They do not evidence a general alteration of this phenomenon after in vitro maturation as compared to in vivo maturation, but indicate that some individual messenger RNA can be affected.
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Affiliation(s)
- Aurore Thélie
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France.
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Meijer HA, Bushell M, Hill K, Gant TW, Willis AE, Jones P, de Moor CH. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 2007; 35:e132. [PMID: 17933768 PMCID: PMC2095794 DOI: 10.1093/nar/gkm830] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The length of the poly(A) tail of an mRNA plays an important role in translational efficiency, mRNA stability and mRNA degradation. Regulated polyadenylation and deadenylation of specific mRNAs is involved in oogenesis, embryonic development, spermatogenesis, cell cycle progression and synaptic plasticity. Here we report a new technique to analyse the length of poly(A) tails and to separate a mixed population of mRNAs into fractions dependent on the length of their poly(A) tails. The method can be performed on crude lysate or total RNA, is fast, highly reproducible and minor changes in poly(A) tail length distribution are easily detected. We validated the method by analysing mRNAs known to undergo cytoplasmic polyadenylation during Xenopus laevis oocyte maturation. We then separated RNA from NIH3T3 cells into two fractions with short and long poly(A) tails and compared them by microarray analysis. In combination with the validation experiments, the results indicate that ∼25% of the expressed genes have a poly(A) tail of less than 30 residues in a significant percentage of their transcripts.
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Affiliation(s)
- Hedda A Meijer
- RNA Biology Group, Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham, UK
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43
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Jacobi UG, Akkers RC, Pierson ES, Weeks DL, Dagle JM, Veenstra GJC. TBP paralogs accommodate metazoan- and vertebrate-specific developmental gene regulation. EMBO J 2007; 26:3900-9. [PMID: 17703192 PMCID: PMC1994123 DOI: 10.1038/sj.emboj.7601822] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 07/16/2007] [Indexed: 11/08/2022] Open
Abstract
In addition to TATA-binding protein (TBP), a key factor for transcription initiation, the metazoan-specific TBP-like factor TLF/TRF2 and the vertebrate-specific factor TBP2/TRF3 are known to be required for transcription of specific subsets of genes. We have combined an antisense-knockdown approach with transcriptome profiling to determine the significance and biological role of TBP-independent transcription in early gastrula-stage Xenopus laevis embryos. Here, we report that, although each of the TBP family members is essential for embryonic development, relatively few genes depend on TBP in the embryo. Most of the transcripts that depend on TBP in the embryo are also expressed maternally and in adult stages, and show no functional specialization. In contrast, TLF is linked to preferential expression in embryos and shows functional specialization in catabolism. A requirement for TBP2 is linked to vertebrate-specific embryonic genes and ventral-specific expression. Therefore TBP paralogs are essential for the gene-regulatory repertoire that is directly linked to early embryogenesis.
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Affiliation(s)
- Ulrike G Jacobi
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Robert C Akkers
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Elisabeth S Pierson
- Department of General Instruments, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Daniel L Weeks
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | - John M Dagle
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Gert Jan C Veenstra
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Mol.Biol. M850/3.79, PO Box 9101, Nijmegen 6500, The Netherlands. Tel.: +31 24 3610541; Fax: +31 24 3610520; E-mail:
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Beilharz TH, Preiss T. Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA (NEW YORK, N.Y.) 2007; 13:982-97. [PMID: 17586758 PMCID: PMC1894919 DOI: 10.1261/rna.569407] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Control of poly(A) tail length can affect translation and stability of eukaryotic mRNAs. Although well established for individual cases, it was not known to what extent this type of adjustable gene control is used to shape expression of eukaryotic transcriptomes. Here we report on microarray-based measurements of mRNA poly(A) tail lengths and association with the poly(A)-binding protein Pab1 in S. cerevisiae, revealing extensive correlation between tail length and other physical and functional mRNA characteristics. Gene ontology analyses and further directed experiments indicate coregulation of tail length on functionally and cytotopically related mRNAs to coordinate cell-cycle progression, ribosome biogenesis, and retrotransposon expression. We show that the 3'-untranslated region drives transcript-specific adenylation control and translational efficiency of multiple mRNAs. Our findings suggest a wide-spread interdependence between 3'-untranslated region-mediated poly(A) tail length control, Pab1 binding, and mRNA translation in budding yeast. They further provide a molecular explanation for deadenylase function in the cell cycle and suggest additional cellular processes that depend on control of mRNA polyadenylation.
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Affiliation(s)
- Traude H Beilharz
- Molecular Genetics Program, Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW, Australia
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Danner S, Kajahn J, Geismann C, Klink E, Kruse C. Derivation of oocyte-like cells from a clonal pancreatic stem cell line. Mol Hum Reprod 2006; 13:11-20. [PMID: 17114208 DOI: 10.1093/molehr/gal096] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Adult pancreatic stem cells (PSCs) are able to differentiate spontaneously in vitro into various somatic cell types. Stem cells isolated from rat pancreas show extensive self-renewal ability and grow in highly viable long-term cultures. Additionally, these cells express typical stem cell markers such as Oct-4, nestin and SSEA-1. Although differentiation potential is slightly decreasing in long-term cultures, it is possible to keep cell lines up to passage 140. Clonal cell lines could be established from different passages and showed similar characteristics. Remarkably, one clonal cell line, generated from passage 75, showed deviant properties during further culture. Clonal cells formed aggregates, which built tissue-like structures in suspension culture. These generated 3D aggregates produced permanently new cells at the outside margin. Released cells had remarkable size, and closer examination by light microscopy analysis revealed oocyte-like morphology. A comparison of the gene expression patterns between primary cultures of passages 8 and 75, the clonal cell line and the produced oocyte-like cells (OLCs) from tissue-like structures demonstrated some differences. Expression of various germ cell markers, such as Vasa, growth differentiation marker 9 and SSEA-1, increased in the clonal cell line, and OLCs showed additionally expression of meiosis-specific markers SCP3 and DMC1. We here present a first pilot study investigating the putative germ line potential of adult PSCs.
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Affiliation(s)
- S Danner
- Fraunhofer-Institute of Biomedical Engineering, Group of Cell Differentiation and Cell Technology at the University of Luebeck, Luebeck, Germany
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