51
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Roles of MicroRNAs in Establishing and Modulating Stem Cell Potential. Int J Mol Sci 2019; 20:ijms20153643. [PMID: 31349654 PMCID: PMC6696000 DOI: 10.3390/ijms20153643] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
Early embryonic development in mammals, from fertilization to implantation, can be viewed as a process in which stem cells alternate between self-renewal and differentiation. During this process, the fates of stem cells in embryos are gradually specified, from the totipotent state, through the segregation of embryonic and extraembryonic lineages, to the molecular and cellular defined progenitors. Most of those stem cells with different potencies in vivo can be propagated in vitro and recapitulate their differentiation abilities. Complex and coordinated regulations, such as epigenetic reprogramming, maternal RNA clearance, transcriptional and translational landscape changes, as well as the signal transduction, are required for the proper development of early embryos. Accumulated studies suggest that Dicer-dependent noncoding RNAs, including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs), are involved in those regulations and therefore modulate biological properties of stem cells in vitro and in vivo. Elucidating roles of these noncoding RNAs will give us a more comprehensive picture of mammalian embryonic development and enable us to modulate stem cell potencies. In this review, we will discuss roles of miRNAs in regulating the maintenance and cell fate potential of stem cells in/from mouse and human early embryos.
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Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ. Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Genome Res 2019; 29:1100-1114. [PMID: 31227602 PMCID: PMC6633259 DOI: 10.1101/gr.245159.118] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/07/2019] [Indexed: 12/16/2022]
Abstract
Posttranscriptional regulation plays a crucial role in shaping gene expression. During the maternal-to-zygotic transition (MZT), thousands of maternal transcripts are regulated. However, how different cis-elements and trans-factors are integrated to determine mRNA stability remains poorly understood. Here, we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. By using a massively parallel reporter assay, we identified cis-regulatory sequences in the 3' UTR, including U-rich motifs that are associated with increased mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC, and CUGC elements emerged as destabilizing motifs, with miR-430 and AREs causing mRNA deadenylation upon genome activation. We identified trans-factors by profiling RNA-protein interactions and found that poly(U)-binding proteins are preferentially associated with 3' UTR sequences and stabilizing motifs. We show that this activity is antagonized by C-rich motifs and correlated with protein binding. Finally, we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.
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Affiliation(s)
- Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Mario Abdel Messih
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- University of New Haven, West Haven, Connecticut 06516, USA
| | - Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neuroscience, Genentech, Incorporated, South San Francisco, California 94080, USA
| | - Panos Oikonomou
- Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Romain Christiano
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Marlon Stoeckius
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- New York Genome Center, New York, New York 10013, USA
| | - Stephanie Lau
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Jean-Denis Beaudoin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Damir Musaev
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Hiba Darwich-Codore
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Tobias C Walther
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02124, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Saeed Tavazoie
- Department of Biochemistry and Molecular Biophysics, and Department of Systems Biology, Columbia University, New York, New York 10032, USA
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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53
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Ning J, Liu Y, Gao F, Song C, Cui Z. Two alpha-2 macroglobulin from Portunus trituberculatus involved in the prophenoloxidase system, phagocytosis and regulation of antimicrobial peptides. FISH & SHELLFISH IMMUNOLOGY 2019; 89:574-585. [PMID: 30995541 DOI: 10.1016/j.fsi.2019.04.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 03/06/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Alpha-2 macroglobulin (A2M) is a ubiquitous protease inhibitor involved in the innate host defense system. Herein, two distinct A2M genes (designated as PtA2M-1 and PtA2M-2, respectively) were isolated from the swimming crab Portunus trituberculatus. PtA2M-1 and PtA2M-2 encoded proteins with 1541 or 1516 amino acids, respectively, containing the typically functional domains of A2M. Unlike highly expressed in hemocytes of most arthropods, PtA2M-1 and PtA2M-2 were predominantly detected in gill, eyestalk and digestive tracks. During the embryonic stages, PtA2Ms were found to be expressed most highly in fertilized eggs, suggesting their maternal origin. After challenged with Vibrio alginolyticus, the transcripts of PtA2Ms showed similar time-dependent response expression pattern, while PtA2M-1 was more sensitive to Micrococcus luteus and Pichia pastoris infection than PtA2M-2. Knockdown of PtA2M-1 or PtA2M-2 could significantly enhance the expression of prophenoloxidase (proPO) associated genes (PtproPO and PtPPAF) and serine protease related genes (PtcSP1-3 and PtSPH), however, PtLSZ and the phagocytosis-related genes (PtMyosin and PtRab5) were effectively inhibited. These results were further supported by the PO and lysozyme activities in hemolymph of the PtA2M-1- or PtA2M-2-silenced crabs. In addition, PtA2M-1 and PtA2M-2 could regulate the expression of antimicrobial peptide (AMP) genes (PtALF1-3, PtCrustin1 and PtCrustin3) through the Toll and NF-κB pathways. Our findings together suggest that PtA2Ms might function in crab host defense via regulating the proPO system, phagocytosis and the expression of AMP genes.
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Affiliation(s)
- Junhao Ning
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fengtao Gao
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chengwen Song
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhaoxia Cui
- School of Marine Science, Ningbo University, Zhejiang, Ningbo, 315211, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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54
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6mA-DNA-binding factor Jumu controls maternal-to-zygotic transition upstream of Zelda. Nat Commun 2019; 10:2219. [PMID: 31101825 PMCID: PMC6525185 DOI: 10.1038/s41467-019-10202-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/19/2019] [Indexed: 12/21/2022] Open
Abstract
A long-standing question in the field of embryogenesis is how the zygotic genome is precisely activated by maternal factors, allowing normal early embryonic development. We have previously shown that N6-methyladenine (6mA) DNA modification is highly dynamic in early Drosophila embryos and forms an epigenetic mark. However, little is known about how 6mA-formed epigenetic information is decoded. Here we report that the Fox-family protein Jumu binds 6mA-marked DNA and acts as a maternal factor to regulate the maternal-to-zygotic transition. We find that zelda encoding the pioneer factor Zelda is marked by 6mA. Our genetic assays suggest that Jumu controls the proper zygotic genome activation (ZGA) in early embryos, at least in part, by regulating zelda expression. Thus, our findings not only support that the 6mA-formed epigenetic marks can be read by specific transcription factors, but also uncover a mechanism by which the Jumu regulates ZGA partially through Zelda in early embryos. N6-methyladenine (6mA) DNA modification is a dynamic epigenetic mark in Drosophila embryos, but how 6mA is decoded is unclear. Here, the authors show that the protein Jumu binds 6mA-marked DNA to regulate the maternal-to-zygotic transition, partly through regulation the expression of the 6mA marked pioneer factor zelda.
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55
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Hanyu-Nakamura K, Matsuda K, Cohen SM, Nakamura A. Pgc suppresses the zygotically acting RNA decay pathway to protect germ plasm RNAs in the Drosophila embryo. Development 2019; 146:dev.167056. [PMID: 30890569 DOI: 10.1242/dev.167056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 03/11/2019] [Indexed: 11/20/2022]
Abstract
Specification of germ cells is pivotal to ensure continuation of animal species. In many animal embryos, germ cell specification depends on maternally supplied determinants in the germ plasm. Drosophila polar granule component (pgc) mRNA is a component of the germ plasm. pgc encodes a small protein that is transiently expressed in newly formed pole cells, the germline progenitors, where it globally represses mRNA transcription. pgc is also required for pole cell survival, but the mechanism linking transcriptional repression to pole cell survival remains elusive. We report that pole cells lacking pgc show premature loss of germ plasm mRNAs, including the germ cell survival factor nanos, and undergo apoptosis. We found that pgc- pole cells misexpress multiple miRNA genes. Reduction of miRNA pathway activity in pgc- embryos partially suppressed germ plasm mRNA degradation and pole cell death, suggesting that Pgc represses zygotic miRNA transcription in pole cells to protect germ plasm mRNAs. Interestingly, germ plasm mRNAs are protected from miRNA-mediated degradation in vertebrates, albeit by a different mechanism. Thus, independently evolved mechanisms are used to silence miRNAs during germ cell specification.
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Affiliation(s)
- Kazuko Hanyu-Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan.,Laboratory for Germline Development, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan
| | - Kazuki Matsuda
- Laboratory for Germline Development, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan
| | - Stephen M Cohen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Akira Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan .,Laboratory for Germline Development, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan.,Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
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56
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Comparative transcriptome analysis explores maternal to zygotic transition during Eriocheir sinensis early embryogenesis. Gene 2019; 685:12-20. [PMID: 30321661 DOI: 10.1016/j.gene.2018.10.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 09/27/2018] [Accepted: 10/11/2018] [Indexed: 11/21/2022]
Abstract
The maternal genome directs almost all aspects of early animal development. As development proceeds, the elimination of maternal gene products and zygotic genome activation (ZGA) occur during the maternal to zygotic transition (MZT). To study the molecular mechanisms regulating this developmental event in Eriocheir sinensis, RNA-Seq technology was applied to generate comprehensive information on transcriptome dynamics during early embryonic stages. In total, 32,088 annotated unigenes were obtained from the transcriptomes of fertilized eggs and embryos at the cleavage (2-4 cell) and blastula stage. A total of 566 maternal genes and 1165 zygotic genes were isolated, among which 103 and 266 genes were predicted conserved maternal transcripts (COMATs) and conserved zygotic transcripts (COZYTs), respectively. The COMATs performed housekeeping gene functions and may be essential for initiating early embryogenesis of the Bilateria. Furthermore, 87, 76 and 117 differentially expressed genes associated with the MZT, morphogenesis and immunity were identified when compared the three transcriptomic datasets. We also unmask that the MZT takes place around the cleavage stage, when the genes involved in the clearance of maternal gene products and the ZGA were significantly up-regulated. Taken together, these datasets provide a valuable resource for understanding the mechanisms of early developmental events in E. sinensis, and facilitate further studies on molecular mechanisms of asynchronous development in crabs.
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57
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Chang H, Yeo J, Kim JG, Kim H, Lim J, Lee M, Kim HH, Ohk J, Jeon HY, Lee H, Jung H, Kim KW, Kim VN. Terminal Uridylyltransferases Execute Programmed Clearance of Maternal Transcriptome in Vertebrate Embryos. Mol Cell 2019; 70:72-82.e7. [PMID: 29625039 DOI: 10.1016/j.molcel.2018.03.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/07/2018] [Accepted: 03/01/2018] [Indexed: 12/26/2022]
Abstract
During the maternal-to-zygotic transition (MZT), maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However, it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here, through genome-wide profiling of RNA abundance and 3' modification, we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 (TUT4/7) are depleted in zebrafish and Xenopus, maternal mRNA clearance is significantly delayed, leading to developmental defects during gastrulation. Short-tailed mRNAs are selectively uridylated by TUT4/7, with the highly uridylated transcripts degraded faster during the MZT than those with unmodified poly(A) tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation, thereby allowing the progression of early development.
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Affiliation(s)
- Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Jinah Yeo
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Jeong-Gyun Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Seoul National University, Seoul 08826, Korea
| | - Hyunjoon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Hyun Ho Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Seoul National University, Seoul 08826, Korea
| | - Jiyeon Ohk
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hee-Yeon Jeon
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyunsook Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hosung Jung
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Kyu-Won Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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58
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Initiation of the zygotic genetic program in the ascidian embryo. Semin Cell Dev Biol 2018; 84:111-117. [DOI: 10.1016/j.semcdb.2018.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 12/26/2022]
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59
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Ahi EP, Singh P, Lecaudey LA, Gessl W, Sturmbauer C. Maternal mRNA input of growth and stress-response-related genes in cichlids in relation to egg size and trophic specialization. EvoDevo 2018; 9:23. [PMID: 30519389 PMCID: PMC6271631 DOI: 10.1186/s13227-018-0112-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/22/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Egg size represents an important form of maternal effect determined by a complex interplay of long-term adaptation and short-term plasticity balancing egg size with brood size. Haplochromine cichlids are maternal mouthbrooders showing differential parental investment in different species, manifested in great variation in egg size, brood size and duration of maternal care. Little is known about maternally determined molecular characters of eggs in fishes and their relation to egg size and trophic specialization. Here we investigate maternal mRNA inputs of selected growth- and stress-related genes in eggs of mouthbrooding cichlid fishes adapted to different trophic niches from Lake Tanganyika, Lake Malawi, Lake Victoria and compare them to their riverine allies. RESULTS We first identified two reference genes, atf7ip and mid1ip1, to be suitable for cross-species quantification of mRNA abundance via qRT-PCR in the cichlid eggs. Using these reference genes, we found substantial variation in maternal mRNA input for a set of candidate genes related to growth and stress response across species and lakes. We observed negative correlation of mRNA abundance between two of growth hormone receptor paralogs (ghr1 and ghr2) across all haplochromine cichlid species which also differentiate the species in the two younger lakes, Malawi and Lake Victoria, from those in Lake Tanganyika and ancestral riverine species. Furthermore, we found correlations between egg size and maternal mRNA abundance of two growth-related genes igf2 and ghr2 across the haplochromine cichlids as well as distinct clustering of the species based on their trophic specialization using maternal mRNA abundance of five genes (ghr1, ghr2, igf2, gr and sgk1). CONCLUSIONS These findings indicate that variations in egg size in closely related cichlid species can be linked to differences in maternal RNA deposition of key growth-related genes. In addition, the cichlid species with contrasting trophic specialization deposit different levels of maternal mRNAs in their eggs for particular growth-related genes; however, it is unclear whether such differences contribute to differential morphogenesis at later stages of development. Our results provide first insights into this aspect of gene activation, as a basis for future studies targeting their role during ecomorphological specialization and adaptive radiation.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
- Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, 75236 Uppsala, Sweden
| | - Pooja Singh
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | | | - Wolfgang Gessl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
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60
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Sato A. Chaperones, Canalization, and Evolution of Animal Forms. Int J Mol Sci 2018; 19:E3029. [PMID: 30287767 PMCID: PMC6213012 DOI: 10.3390/ijms19103029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 12/18/2022] Open
Abstract
Over half a century ago, British developmental biologist Conrad Hal Waddington proposed the idea of canalization, that is, homeostasis in development. Since the breakthrough that was made by Rutherford and Lindquist (1998), who proposed a role of Hsp90 in developmental buffering, chaperones have gained much attention in the study of canalization. However, recent studies have revealed that a number of other molecules are also potentially involved in canalization. Here, I introduce the emerging role of DnaJ chaperones in canalization. I also discuss how the expression levels of such buffering molecules can be altered, thereby altering organismal development. Since developmental robustness is maternally inherited in various organisms, I propose that dynamic bet hedging, an increase in within-clutch variation in offspring phenotypes that is caused by unpredictable environmental challenges to the mothers, plays a key role in altering the expression levels of buffering molecules. Investigating dynamic bet hedging at the molecular level and how it impacts upon morphological phenotypes will help our understanding of the molecular mechanisms of canalization and evolutionary processes.
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Affiliation(s)
- Atsuko Sato
- Department of Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-0012, Japan.
- Marine Biological Association of the UK, The Laboratory, Plymouth PL1 2PB, UK.
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61
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Godini R, Fallahi H. Dynamics changes in the transcription factors during early human embryonic development. J Cell Physiol 2018; 234:6489-6502. [PMID: 30246428 DOI: 10.1002/jcp.27386] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/17/2018] [Indexed: 12/30/2022]
Abstract
Development of an embryo from a single cell, zygote, to multicellular morulae requires activation of hundreds of genes that were mostly inactivated before fertilization. Inevitably, transcription factors (TFs) would be involved in modulating the drastic changes in gene expression pattern observed at all preimplantation stages. Despite many ongoing efforts to uncover the role of TFs at the early stages of embryogenesis, still many unanswered questions remained that need to be explored. This could be done by studying the expression pattern of multiple genes obtained by high-throughput techniques. In the current study, we have identified a set of TFs that are involved in the progression of the zygote to blastocyst. Global gene expression patterns of consecutive stages were compared and differences documented. Expectedly, at the early stages of development, only a few sets of TFs differentially expressed while at the later stages hundreds of TFs appear to be upregulated. Interestingly, the expression levels of many TFs show an oscillation pattern during development indicating a need for their precise expression. A significant shift in gene expression was observed during the transition from four- to eight-cell stages, an indication of zygote genome activation. Additionally, we have found 11 TFs that were common in all stages including ATF3, EN1, IFI16, IKZF3, KLF3, NPAS3, NR2F2, RUNX1, SOX2, ZBTB20, and ZSCAN4. However, their expression patterns did not follow similar trends in the steps studied. Besides, our findings showed that both upregulation and active downregulation of the TFs expression is required for successful embryogenesis. Furthermore, our detailed network analysis identified the hub TFs for each transition. We found that HNF4A, FOXA2, and EP300 are the three most important elements for the first division of zygote.
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Affiliation(s)
- Rasoul Godini
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
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62
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Li XX, Cao PH, Han WX, Xu YK, Wu H, Yu XL, Chen JY, Zhang F, Li YH. Non-invasive metabolomic profiling of culture media of ICSI- and IVF-derived early developmental cattle embryos via Raman spectroscopy. Anim Reprod Sci 2018; 196:99-110. [DOI: 10.1016/j.anireprosci.2018.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/18/2018] [Accepted: 07/02/2018] [Indexed: 10/28/2022]
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63
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Winata CL, Korzh V. The translational regulation of maternal mRNAs in time and space. FEBS Lett 2018; 592:3007-3023. [PMID: 29972882 PMCID: PMC6175449 DOI: 10.1002/1873-3468.13183] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/29/2018] [Accepted: 06/29/2018] [Indexed: 12/16/2022]
Abstract
Since their discovery, the study of maternal mRNAs has led to the identification of mechanisms underlying their spatiotemporal regulation within the context of oogenesis and early embryogenesis. Following synthesis in the oocyte, maternal mRNAs are translationally silenced and sequestered into storage in cytoplasmic granules. At the same time, their unique distribution patterns throughout the oocyte and embryo are tightly controlled and connected to their functions in downstream embryonic processes. At certain points in oogenesis and early embryogenesis, maternal mRNAs are translationally activated to perform their functions in a timely manner. The cytoplasmic polyadenylation machinery is responsible for the translational activation of maternal mRNAs, and its role in initiating the maternal to zygotic transition events has recently come to light. Here, we summarize the current knowledge on maternal mRNA regulation, with particular focus on cytoplasmic polyadenylation as a mechanism for translational regulation.
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Affiliation(s)
- Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, Poland.,Max-Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, Poland
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64
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Masala L, Ariu F, Bogliolo L, Bellu E, Ledda S, Bebbere D. Delay in maternal transcript degradation in ovine embryos derived from low competence oocytes. Mol Reprod Dev 2018; 85:427-439. [PMID: 29542856 DOI: 10.1002/mrd.22977] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 02/14/2018] [Accepted: 02/18/2018] [Indexed: 01/06/2023]
Abstract
Oocytes from prepubertal animals have a reduced ability to undergo embryo development and produce viable offspring. The present work used an ovine model consisting of oocytes derived from adult and prepubertal donors to assess the molecular status of oocytes and preimplantation embryos with different developmental competence. The lower potential of oocytes of young donors was confirmed in terms of in vitro developmental capabilities and kinetics. A panel of genes including maternal effect (DPPA3, GDF9, NMP2, ZAR1) and housekeeping genes (ACTB, RPL19, SDHA, YWHAZ, ATP1A1), genes involved in DNA methylation (DNMT1, DNMT3A, DNMT3B), genomic imprinting (IGF2R), pluripotency (NANOG, POU5F1) and cell cycle regulation (CCNB1, CDK1, MELK) was relatively quantified. Temporal analysis during oocyte maturation and preimplantation embryo development evidenced patterns associated with donor age. With a few gene-specific exceptions, the differential model showed a reduced transcript abundance in immature prepubertal oocytes that completely reversed trend after fertilization, when higher mRNA levels were consistently observed in early embryos, indicating a delay in maternal transcript degradation. We propose that the molecular shortage in the prepubertal oocyte may affect its developmental potential and impair the early pathways of maternal mRNA clearance in the embryo. While confirming the different potential of oocytes derived from adult and prepubertal donors, our work showed for the first time a consistent delay in maternal transcript degradation in embryos derived from low competence oocytes that interestingly recalls the delayed developmental kinetics. Such abnormal transcript persistence may hinder further development and represents a novel perspective on the complexity of developmental competence.
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Affiliation(s)
- Laura Masala
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Federica Ariu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Luisa Bogliolo
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Emanuela Bellu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Sergio Ledda
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daniela Bebbere
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
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65
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Liu C, Ma Y, Shang Y, Huo R, Li W. Post-translational regulation of the maternal-to-zygotic transition. Cell Mol Life Sci 2018; 75:1707-1722. [PMID: 29427077 PMCID: PMC11105290 DOI: 10.1007/s00018-018-2750-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/24/2017] [Accepted: 01/08/2018] [Indexed: 02/07/2023]
Abstract
The maternal-to-zygotic transition (MZT) is essential for the developmental control handed from maternal products to newly synthesized zygotic genome in the earliest stages of embryogenesis, including maternal component (mRNAs and proteins) degradation and zygotic genome activation (ZGA). Various protein post-translational modifications have been identified during the MZT, such as phosphorylation, methylation and ubiquitination. Precise post-translational regulation mechanisms are essential for the timely transition of early embryonic development. In this review, we summarize recent progress regarding the molecular mechanisms underlying post-translational regulation of maternal component degradation and ZGA during the MZT and discuss some important issues in the field.
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Affiliation(s)
- Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanjie Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- Department of Animal Science and Technology, Northeast Agricultural University, Haerbin, 150030, People's Republic of China
| | - Yongliang Shang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029, People's Republic of China.
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, People's Republic of China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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66
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Eckersley-Maslin MA, Alda-Catalinas C, Reik W. Dynamics of the epigenetic landscape during the maternal-to-zygotic transition. Nat Rev Mol Cell Biol 2018; 19:436-450. [DOI: 10.1038/s41580-018-0008-z] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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67
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Adrian-Kalchhauser I, Walser JC, Schwaiger M, Burkhardt-Holm P. RNA sequencing of early round goby embryos reveals that maternal experiences can shape the maternal RNA contribution in a wild vertebrate. BMC Evol Biol 2018; 18:34. [PMID: 29566669 PMCID: PMC5863367 DOI: 10.1186/s12862-018-1132-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/29/2018] [Indexed: 01/01/2023] Open
Abstract
Background It has been proposed that non-genetic inheritance could promote species fitness. Non-genetic inheritance could allow offspring to benefit from the experience of their parents, and could advocate pre-adaptation to prevailing and potentially selective conditions. Indeed, adaptive parental effects have been modeled and observed, but the molecular mechanisms behind them are far from understood. Results In the present study, we investigated whether maternal RNA can carry information about environmental conditions experienced by the mother in a wild vertebrate. Maternal RNA directs the development of the early embryo in many non-mammalian vertebrates and invertebrates. However, it is not known whether vertebrate maternal RNA integrates information about the parental environment. We sequenced the maternal RNA contribution from a model that we expected to rely on parental effects: the invasive benthic fish species Neogobius melanostomus (Round Goby). We found that maternal RNA expression levels correlated with the water temperature experienced by the mother before oviposition, and identified temperature-responsive gene groups such as core nucleosome components or the microtubule cytoskeleton. Conclusions Our findings suggest that the maternal RNA contribution may incorporate environmental information. Maternal RNA should therefore be considered a potentially relevant pathway for non-genetic inheritance. Also, the ability of a species to integrate environmental information in the maternal RNA contribution could potentially contribute to species fitness and may also play a role in extraordinary adaptive success stories of invasive species such as the round goby. Electronic supplementary material The online version of this article (10.1186/s12862-018-1132-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
| | - Jean-Claude Walser
- Department of Environmental Systems Science, Genetic Diversity Centre Zurich, ETH Zurich, Universitätstrasse 16, CH-8092, Zurich, Switzerland
| | - Michaela Schwaiger
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Patricia Burkhardt-Holm
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
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68
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Zhang M, Qin S, Xu P, Zhang G. Identifying potential maternal genes of Bombyx mori using digital gene expression profiling. PLoS One 2018; 13:e0192745. [PMID: 29462160 PMCID: PMC5819784 DOI: 10.1371/journal.pone.0192745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/30/2018] [Indexed: 01/16/2023] Open
Abstract
Maternal genes present in mature oocytes play a crucial role in the early development of silkworm. Although maternal genes have been widely studied in many other species, there has been limited research in Bombyx mori. High-throughput next generation sequencing provides a practical method for gene discovery on a genome-wide level. Herein, a transcriptome study was used to identify maternal-related genes from silkworm eggs. Unfertilized eggs from five different stages of early development were used to detect the changing situation of gene expression. The expressed genes showed different patterns over time. Seventy-six maternal genes were annotated according to homology analysis with Drosophila melanogaster. More than half of the differentially expressed maternal genes fell into four expression patterns, while the expression patterns showed a downward trend over time. The functional annotation of these material genes was mainly related to transcription factor activity, growth factor activity, nucleic acid binding, RNA binding, ATP binding, and ion binding. Additionally, twenty-two gene clusters including maternal genes were identified from 18 scaffolds. Altogether, we plotted a profile for the maternal genes of Bombyx mori using a digital gene expression profiling method. This will provide the basis for maternal-specific signature research and improve the understanding of the early development of silkworm.
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Affiliation(s)
- Meirong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang Jiangsu, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang Jiangsu, China
| | - Sheng Qin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang Jiangsu, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang Jiangsu, China
| | - Pingzhen Xu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang Jiangsu, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang Jiangsu, China
| | - Guozheng Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang Jiangsu, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang Jiangsu, China
- * E-mail:
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69
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Abstract
The activation of the zygotic genome and onset of transcription in blastula embryos is linked to changes in cell behavior and remodeling of the cell cycle and constitutes a transition from exclusive maternal to zygotic control of development. This step in development is referred to as mid-blastula transition and has served as a paradigm for the link between developmental program and cell behavior and morphology. Here, we discuss the mechanism and functional relationships between the zygotic genome activation and cell cycle control during mid-blastula transition with a focus on Drosophila embryos.
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Affiliation(s)
- Boyang Liu
- Institute for Developmental Biochemistry, Medical School, University of Göttingen, Justus-von-Liebig-Weg11, Göttingen 37077, Germany
| | - Jörg Grosshans
- Institute for Developmental Biochemistry, Medical School, University of Göttingen, Justus-von-Liebig-Weg11, Göttingen 37077, Germany.
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70
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Bohn JA, Van Etten JL, Schagat TL, Bowman BM, McEachin RC, Freddolino PL, Goldstrohm AC. Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins. Nucleic Acids Res 2018; 46:362-386. [PMID: 29165587 PMCID: PMC5758885 DOI: 10.1093/nar/gkx1120] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/21/2017] [Accepted: 10/25/2017] [Indexed: 12/20/2022] Open
Abstract
Human Pumilio proteins, PUM1 and PUM2, are sequence specific RNA-binding proteins that regulate protein expression. We used RNA-seq, rigorous statistical testing and an experimentally derived fold change cut-off to identify nearly 1000 target RNAs-including mRNAs and non-coding RNAs-that are functionally regulated by PUMs. Bioinformatic analysis defined a PUM Response Element (PRE) that was significantly enriched in transcripts that increased in abundance and matches the PUM RNA-binding consensus. We created a computational model that incorporates PRE position and frequency within an RNA relative to the magnitude of regulation. The model reveals significant correlation of PUM regulation with PREs in 3' untranslated regions (UTRs), coding sequences and non-coding RNAs, but not 5' UTRs. To define direct, high confidence PUM targets, we cross-referenced PUM-regulated RNAs with all PRE-containing RNAs and experimentally defined PUM-bound RNAs. The results define nearly 300 direct targets that include both PUM-repressed and, surprisingly, PUM-activated target RNAs. Annotation enrichment analysis reveal that PUMs regulate genes from multiple signaling pathways and developmental and neurological processes. Moreover, PUM target mRNAs impinge on human disease genes linked to cancer, neurological disorders and cardiovascular disease. These discoveries pave the way for determining how the PUM-dependent regulatory network impacts biological functions and disease states.
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Affiliation(s)
- Jennifer A Bohn
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jamie L Van Etten
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Trista L Schagat
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Promega Corporation, Madison, WI 53711, USA
| | - Brittany M Bowman
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard C McEachin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Aaron C Goldstrohm
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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71
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Winata CL, Łapiński M, Pryszcz L, Vaz C, Bin Ismail MH, Nama S, Hajan HS, Lee SGP, Korzh V, Sampath P, Tanavde V, Mathavan S. Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal-to-zygotic transition. Development 2018; 145:dev.159566. [PMID: 29229769 DOI: 10.1242/dev.159566] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/20/2017] [Indexed: 10/18/2022]
Abstract
In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to the point of zygotic genome activation (ZGA). These maternal mRNAs undergo cytoplasmic polyadenylation (CPA), suggesting translational control of their activation. To elucidate the biological role of CPA during embryogenesis, we performed genome-wide polysome profiling at several stages of zebrafish development. Our analysis revealed a correlation between CPA and polysome-association dynamics, demonstrating a coupling of translation to the CPA of maternal mRNAs. Pan-embryonic CPA inhibition disrupted the maternal-to-zygotic transition (MZT), causing a failure of developmental progression beyond the mid-blastula transition and changes in global gene expression that indicated a failure of ZGA and maternal mRNA clearance. Among the genes that were differentially expressed were those encoding chromatin modifiers and key transcription factors involved in ZGA, including nanog, pou5f3 and sox19b, which have distinct CPA dynamics. Our results establish the necessity of CPA for ensuring progression of the MZT. The RNA-seq data generated in this study represent a valuable zebrafish resource for the discovery of novel elements of the early embryonic transcriptome.
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Affiliation(s)
- Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland .,Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Leszek Pryszcz
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Candida Vaz
- Bioinformatics Institute, Agency for Science Technology and Research, 138671 Singapore
| | | | - Srikanth Nama
- Institute of Medical Biology, Agency of Science Technology and Research, 138648 Singapore
| | - Hajira Shreen Hajan
- Genome Institute of Singapore, Agency of Science Technology and Research, 138672 Singapore
| | - Serene Gek Ping Lee
- Genome Institute of Singapore, Agency of Science Technology and Research, 138672 Singapore
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.,Institute of Molecular and Cell Biology, Agency of Science Technology and Research, 138673 Singapore
| | - Prabha Sampath
- Institute of Medical Biology, Agency of Science Technology and Research, 138648 Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, 117596 Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857 Singapore
| | - Vivek Tanavde
- Bioinformatics Institute, Agency for Science Technology and Research, 138671 Singapore.,Institute of Medical Biology, Agency of Science Technology and Research, 138648 Singapore
| | - Sinnakaruppan Mathavan
- Genome Institute of Singapore, Agency of Science Technology and Research, 138672 Singapore .,Vision Research Foundation, Sankara Nethralaya, 600 006 Chennai, India
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72
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Cell Fate Maintenance and Reprogramming During the Oocyte-to-Embryo Transition. Results Probl Cell Differ 2017; 59:269-286. [PMID: 28247053 DOI: 10.1007/978-3-319-44820-6_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
This chapter reviews our current understanding of the mechanisms that regulate reprogramming during the oocyte-to-embryo transition (OET). There are two major events reshaping the transcriptome during OET. One is the clearance of maternal transcripts in the early embryo, extensively reviewed by others. The other event, which is the focus of this chapter, is the embryonic (or zygotic) genome activation (EGA). The mechanisms controlling EGA can be broadly divided into transcriptional and posttranscriptional. The former includes the regulation of the basal transcription machinery, the regulation by specific transcription factors and chromatin modifications. The latter is performed mostly via specific RNA-binding proteins (RBPs). Different animal models have been used to decipher the regulation of EGA. These models are often biased for the specific type of regulation, which is why we discuss the models ranging from invertebrates to mammals. Whether these biases stem from incomplete understanding of EGA in these models, or reflect evolutionarily distinct solutions to EGA regulation, is a key unresolved problem in developmental biology. As the mechanisms controlling developmental reprogramming can, and in some cases have been shown to, function in differentiated cells subjected to induced reprogramming, our understanding of EGA regulation may have implications for the efficiency of induced reprogramming and, thus, for regenerative medicine.
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73
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Rauwerda H, Pagano JFB, de Leeuw WC, Ensink W, Nehrdich U, de Jong M, Jonker M, Spaink HP, Breit TM. Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos. BMC Genomics 2017; 18:287. [PMID: 28399811 PMCID: PMC5387192 DOI: 10.1186/s12864-017-3672-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 03/29/2017] [Indexed: 02/08/2023] Open
Abstract
Background Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression time series with 180 individual zebrafish embryos, obtained from nine different spawns, developmentally ordered and profiled from late blastula to mid-gastrula stage. On average one embryo per minute was analysed. The focus was on identification and description of the transcriptome dynamics of the expressed genes in this embryonic stage, rather than to biologically interpret profiles in cellular processes and pathways. Results In the late blastula to mid-gastrula stage, we found 6,734 genes being expressed with low variability and rather gradual changes. Ten types of dynamic behaviour were defined, such as genes with continuously increasing or decreasing expression, and all expressed genes were grouped into these types. Also, the exact expression starting and stopping points of several hundred genes during this developmental period could be pinpointed. Although the resolution of the experiment was so high, that we were able to clearly identify four known oscillating genes, no genes were observed with a peaking expression. Additionally, several genes showed expression at two or three distinct levels that strongly related to the spawn an embryo originated from. Conclusion Our unique experimental set-up of whole-transcriptome analysis of 180 individual embryos, provided an unparalleled in-depth insight into the dynamics of early zebrafish embryogenesis. The existence of a tightly regulated embryonic transcriptome program, even between individuals from different spawns is shown. We have made the expression profile of all genes available for domain experts. The fact that we were able to separate the different spawns by their gene-expression variance over all expressed genes, underlines the importance of spawn specificity, as well as the unexpectedly tight gene-expression regulation in early zebrafish embryogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3672-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han Rauwerda
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Johanna F B Pagano
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Wim C de Leeuw
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Wim Ensink
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Ulrike Nehrdich
- Institute Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Mark de Jong
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.,Present address: GenomeScan B.V., Plesmanlaan, Leiden, The Netherlands
| | - Martijs Jonker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Herman P Spaink
- Institute Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Timo M Breit
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands. .,Institute Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands. .,MAD/AB&RB, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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74
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m 6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature 2017; 542:475-478. [PMID: 28192787 PMCID: PMC5323276 DOI: 10.1038/nature21355] [Citation(s) in RCA: 404] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 12/22/2016] [Indexed: 12/23/2022]
Abstract
The maternal-to-zygotic transition (MZT) is one of the most profound and orchestrated processes during the early life of embryos, yet factors that shape the temporal pattern of vertebrate MZT are largely unknown. Here we show that over one-third of zebrafish maternal messenger RNAs (mRNAs) can be N6-methyladenosine (m6A) modified, and the clearance of these maternal mRNAs is facilitated by an m6A-binding protein, Ythdf2. Removal of Ythdf2 in zebrafish embryos decelerates the decay of m6A-modified maternal mRNAs and impedes zygotic genome activation. These embryos fail to initiate timely MZT, undergo cell cycle pause, and remain developmentally delayed throughout larval life. Our study reveals m6A-dependent RNA decay as a previously unidentified maternally driven mechanism that regulates maternal mRNA clearance during zebrafish MZT, highlighting the critical role of m6A mRNA methylation in transcriptome switching and animal development.
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75
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Yang Y, Zhou C, Wang Y, Liu W, Liu C, Wang L, Liu Y, Shang Y, Li M, Zhou S, Wang Y, Zeng W, Zhou J, Huo R, Li W. The E3 ubiquitin ligase RNF114 and TAB1 degradation are required for maternal-to-zygotic transition. EMBO Rep 2017; 18:205-216. [PMID: 28073917 DOI: 10.15252/embr.201642573] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 11/20/2016] [Accepted: 11/25/2016] [Indexed: 11/09/2022] Open
Abstract
The functional role of the ubiquitin-proteasome pathway during maternal-to-zygotic transition (MZT) remains to be elucidated. Here we show that the E3 ubiquitin ligase, Rnf114, is highly expressed in mouse oocytes and that knockdown of Rnf114 inhibits development beyond the two-cell stage. To study the underlying mechanism, we identify its candidate substrates using a 9,000-protein microarray and validate them using an in vitro ubiquitination system. We show that five substrates could be degraded by RNF114-mediated ubiquitination, including TAB1. Furthermore, the degradation of TAB1 in mouse early embryos is required for MZT, most likely because it activates the NF-κB pathway. Taken together, our study uncovers that RNF114-mediated ubiquitination and degradation of TAB1 activate the NF-κB pathway during MZT, and thus directly link maternal clearance to early embryo development.
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Affiliation(s)
- Ye Yang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.,Department of Reproduction, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Cheng Zhou
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Ying Wang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.,Department of Reproduction, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Weixiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, the Chinese Academy of Science, Beijing, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, the Chinese Academy of Science, Beijing, China
| | - Liying Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, the Chinese Academy of Science, Beijing, China
| | - Yujiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, the Chinese Academy of Science, Beijing, China
| | - Yongliang Shang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, the Chinese Academy of Science, Beijing, China
| | - Mingrui Li
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Shuai Zhou
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yuanting Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, the Chinese Academy of Science, Beijing, China
| | - Wentao Zeng
- Animal Core Facility, Nanjing Medical University, Nanjing, China
| | - Jianli Zhou
- Animal Core Facility, Nanjing Medical University, Nanjing, China
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, the Chinese Academy of Science, Beijing, China
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76
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Abstract
The recent discovery of reversible mRNA methylation has opened a new realm of post-transcriptional gene regulation in eukaryotes. The identification and functional characterization of proteins that specifically recognize RNA N6-methyladenosine (m6A) unveiled it as a modification that cells utilize to accelerate mRNA metabolism and translation. N6-adenosine methylation directs mRNAs to distinct fates by grouping them for differential processing, translation and decay in processes such as cell differentiation, embryonic development and stress responses. Other mRNA modifications, including N1-methyladenosine (m1A), 5-methylcytosine (m5C) and pseudouridine, together with m6A form the epitranscriptome and collectively code a new layer of information that controls protein synthesis.
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Affiliation(s)
- Boxuan Simen Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Ian A Roundtree
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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77
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Abstract
Until the zygotic genome is activated, early development relies on the products deposited by the mother. Once the zygotic genome starts to be transcribed, most maternal products are not needed anymore by the developing embryo. This emancipation from the maternal genome occurs during the Zygotic Genome Activation (ZGA). Although the process by which the maternal content is replaced with zygotic products differs from species to species, there is a common theme to all of them: maternal transcripts are actively degraded. Here, a review of how the degradation of maternal RNAs is regulated during early development and discussions on some computational tools that may be of use in this research area are outlined.
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Affiliation(s)
- Antonio Marco
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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78
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Li J, Gao Z, Wang X, Liu H, Zhang Y, Liu Z. Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development. Sci Rep 2016; 6:38333. [PMID: 27922056 PMCID: PMC5138625 DOI: 10.1038/srep38333] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/08/2016] [Indexed: 12/21/2022] Open
Abstract
Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species. By weighted co-expression network analysis, we identified 5 developmental stages specific co-expression modules. Gene ontology enrichment analysis of these specific co-expression modules suggested that many lincRNAs are associated with cell cycle regulation, transcription and metabolism to regulate the process of zygotic genome activation. Futhermore, we identified hub lincRNAs in each co-expression modules, and found two lincRNAs TCONS_00166370 and TCONS_00020255 may play a vital role in porcine PED. This study systematically analyze lincRNAs in pig and provides the first catalog of lincRNAs that might function as gene regulatory factors of porcine PED.
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Affiliation(s)
- Jingyu Li
- College of Life Science, North-east Agricultural University, Harbin, 150030, China.,Chong Qing Reproductive and Genetics Institute, Chongqing Obstetrics and Gynecology Hospital, 64 Jing Tang ST, Yu Zhong District, Chongqing, 400013, China
| | - Zhengling Gao
- College of Life Science, North-east Agricultural University, Harbin, 150030, China
| | - Xingyu Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150080, China
| | - Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150080, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150080, China
| | - Zhonghua Liu
- College of Life Science, North-east Agricultural University, Harbin, 150030, China
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79
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Trofimova I, Krasikova A. Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts. RNA Biol 2016; 13:1246-1257. [PMID: 27763817 PMCID: PMC5207375 DOI: 10.1080/15476286.2016.1240142] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/13/2016] [Accepted: 09/20/2016] [Indexed: 10/20/2022] Open
Abstract
Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.
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Affiliation(s)
| | - Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg, Russia
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80
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The Smaug RNA-Binding Protein Is Essential for microRNA Synthesis During the Drosophila Maternal-to-Zygotic Transition. G3-GENES GENOMES GENETICS 2016; 6:3541-3551. [PMID: 27591754 PMCID: PMC5100853 DOI: 10.1534/g3.116.034199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Metazoan embryos undergo a maternal-to-zygotic transition (MZT) during which maternal gene products are eliminated and the zygotic genome becomes transcriptionally active. During this process, RNA-binding proteins (RBPs) and the microRNA-induced silencing complex (miRISC) target maternal mRNAs for degradation. In Drosophila, the Smaug (SMG), Brain tumor (BRAT), and Pumilio (PUM) RBPs bind to and direct the degradation of largely distinct subsets of maternal mRNAs. SMG has also been shown to be required for zygotic synthesis of mRNAs and several members of the miR-309 family of microRNAs (miRNAs) during the MZT. Here, we have carried out global analysis of small RNAs both in wild-type and in smg mutants. Our results show that 85% of all miRNA species encoded by the genome are present during the MZT. Whereas loss of SMG has no detectable effect on Piwi-interacting RNAs (piRNAs) or small interfering RNAs (siRNAs), zygotic production of more than 70 species of miRNAs fails or is delayed in smg mutants. SMG is also required for the synthesis and stability of a key miRISC component, Argonaute 1 (AGO1), but plays no role in accumulation of the Argonaute family proteins associated with piRNAs or siRNAs. In smg mutants, maternal mRNAs that are predicted targets of the SMG-dependent zygotic miRNAs fail to be cleared. BRAT and PUM share target mRNAs with these miRNAs but not with SMG itself. We hypothesize that SMG controls the MZT, not only through direct targeting of a subset of maternal mRNAs for degradation but, indirectly, through production and function of miRNAs and miRISC, which act together with BRAT and/or PUM to control clearance of a distinct subset of maternal mRNAs.
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81
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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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82
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Mature maternal mRNAs are longer than zygotic ones and have complex degradation kinetics in sea urchin. Dev Biol 2016; 414:121-31. [PMID: 27085752 DOI: 10.1016/j.ydbio.2016.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/16/2016] [Accepted: 04/10/2016] [Indexed: 11/22/2022]
Abstract
Early in embryogenesis, maternally deposited transcripts are degraded and new zygotic transcripts are generated during the maternal to zygotic transition. Recent works have shown that early zygotic transcripts are short compared to maternal transcripts, in zebrafish and Drosophila species. The reduced zygotic transcript length was attributed to the short cell cycle in these organisms that prevents the transcription of long primary transcripts (intron delay). Here we study the length of maternal mRNAs and their degradation kinetics in two sea urchin species to further the understanding of maternal gene usage and processing. Early zygotic primary transcripts and mRNAs are shorter than maternal ones in the sea urchin, Strongylocentrotus purpuratus. Yet, while primary transcripts length increases when cell cycle lengthens, typical for intron delay, the relatively short length of zygotic mRNAs is consistent. The enhanced mRNA length is due to significantly longer maternal open reading frames and 3'UTRs compared to the zygotic lengths, a ratio that does not change with developmental time. This implies unique usage of both coding sequences and regulatory information in the maternal stage compared to the zygotic stages. We extracted the half-lifetimes due to maternal and zygotic degradation mechanisms from high-density time course of a set of maternal mRNAs in Paracentrotus lividus. The degradation rates due to maternal and zygotic degradation mechanisms are not correlated, indicating that these mechanisms are independent and relay on different regulatory information. Our studies illuminate specific structural and kinetic properties of sea urchin maternal mRNAs that might be broadly shared by other organisms.
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83
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Yang Q, Lin J, Liu M, Li R, Tian B, Zhang X, Xu B, Liu M, Zhang X, Li Y, Shi H, Wu L. Highly sensitive sequencing reveals dynamic modifications and activities of small RNAs in mouse oocytes and early embryos. SCIENCE ADVANCES 2016; 2:e1501482. [PMID: 27500274 PMCID: PMC4974095 DOI: 10.1126/sciadv.1501482] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 05/20/2016] [Indexed: 05/03/2023]
Abstract
Small RNAs play important roles in early embryonic development. However, their expression dynamics and modifications are poorly understood because of the scarcity of RNA that is obtainable for sequencing analysis. Using an improved deep sequencing method that requires as little as 10 ng of total RNA or 50 oocytes, we profile small RNAs in mouse oocytes and early embryos. We find that microRNA (miRNA) expression starts soon after fertilization, and the mature miRNAs carried into the zygote by sperm during fertilization are relatively rare compared to the oocyte miRNAs. Intriguingly, the zygotic miRNAs display a marked increase in 3' mono- and oligoadenylation in one- to two-cell embryos, which may protect the miRNAs from the massive degradation taking place during that time. Moreover, bioinformatics analyses show that the function of miRNA is suppressed from the oocyte to the two-cell stage and appears to be reactivated after the two-cell stage to regulate genes important in embryonic development. Our study thus provides a highly sensitive profiling method and valuable data sets for further examination of small RNAs in early embryos.
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Affiliation(s)
- Qiyuan Yang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jimin Lin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Miao Liu
- China National Population and Family Planning Key Laboratory of Contraceptive Drugs and Devices, Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China
| | - Ronghong Li
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Xue Zhang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Beiying Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mofang Liu
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xuan Zhang
- China National Population and Family Planning Key Laboratory of Contraceptive Drugs and Devices, Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China
| | - Yiping Li
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huijuan Shi
- China National Population and Family Planning Key Laboratory of Contraceptive Drugs and Devices, Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
- Corresponding author. (H.S.); (L.W.)
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Corresponding author. (H.S.); (L.W.)
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84
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BTG4 is a meiotic cell cycle-coupled maternal-zygotic-transition licensing factor in oocytes. Nat Struct Mol Biol 2016; 23:387-94. [PMID: 27065194 DOI: 10.1038/nsmb.3204] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/11/2016] [Indexed: 12/29/2022]
Abstract
The mRNAs stored in oocytes undergo general decay during the maternal-zygotic transition (MZT), and their stability is tightly interconnected with meiotic cell-cycle progression. However, the factors that trigger decay of maternal mRNA and couple this event to oocyte meiotic maturation remain elusive. Here, we identified B-cell translocation gene-4 (BTG4) as an MZT licensing factor in mice. BTG4 bridged CNOT7, a catalytic subunit of the CCR4-NOT deadenylase, to eIF4E, a key translation initiation factor, and facilitated decay of maternal mRNA. Btg4-null females produced morphologically normal oocytes but were infertile, owing to early developmental arrest. The intrinsic MAP kinase cascade in oocytes triggered translation of Btg4 mRNA stored in fully grown oocytes by targeting the 3' untranslated region, thereby coupling CCR4-NOT deadenylase-mediated decay of maternal mRNA with oocyte maturation and fertilization. This is a key step in oocyte cytoplasmic maturation that determines the developmental potential of mammalian embryos.
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85
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A Smaug2-Based Translational Repression Complex Determines the Balance between Precursor Maintenance versus Differentiation during Mammalian Neurogenesis. J Neurosci 2016; 35:15666-81. [PMID: 26609159 DOI: 10.1523/jneurosci.2172-15.2015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED Here, we have asked about post-transcriptional mechanisms regulating murine developmental neurogenesis, focusing upon the RNA-binding proteins Smaug2 and Nanos1. We identify, in embryonic neural precursors of the murine cortex, a Smaug2 protein/nanos1 mRNA complex that is present in cytoplasmic granules with the translational repression proteins Dcp1 and 4E-T. We show that Smaug2 inhibits and Nanos1 promotes neurogenesis, with Smaug2 knockdown enhancing neurogenesis and depleting precursors, and Nanos1 knockdown inhibiting neurogenesis and maintaining precursors. Moreover, we show that Smaug2 likely regulates neurogenesis by silencing nanos1 mRNA. Specifically, Smaug2 knockdown inappropriately increases Nanos1 protein, and the Smaug2 knockdown-mediated neurogenesis is rescued by preventing this increase. Thus, Smaug2 and Nanos1 function as a bimodal translational repression switch to control neurogenesis, with Smaug2 acting in transcriptionally primed precursors to silence mRNAs important for neurogenesis, including nanos1 mRNA, and Nanos1 acting during the transition to neurons to repress the precursor state. SIGNIFICANCE STATEMENT The mechanisms instructing neural stem cells to generate the appropriate progeny are still poorly understood. Here, we show that the RNA-binding proteins Smaug2 and Nanos1 are critical regulators of this balance and provide evidence supporting the idea that neural precursors are transcriptionally primed to generate neurons but translational regulation maintains these precursors in a stem cell state until the appropriate developmental time.
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86
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Oocyte-expressed yes-associated protein is a key activator of the early zygotic genome in mouse. Cell Res 2016; 26:275-87. [PMID: 26902285 PMCID: PMC4783469 DOI: 10.1038/cr.2016.20] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/20/2022] Open
Abstract
In early mammalian embryos, the genome is transcriptionally quiescent until the zygotic genome activation (ZGA) which occurs 2-3 days after fertilization. Despite a long-standing effort, maternal transcription factors regulating this crucial developmental event remain largely elusive. Here, using maternal and paternal mouse models of Yap1 deletion, we show that maternally accumulated yes-associated protein (YAP) in oocyte is essential for ZGA. Maternal Yap1-knockout embryos exhibit a prolonged two-cell stage and develop into the four-cell stage at a much slower pace than the wild-type controls. Transcriptome analyses identify YAP target genes in early blastomeres; two of which, Rpl13 and Rrm2, are required to mediate maternal YAP's effect in conferring developmental competence on preimplantation embryos. Furthermore, the physiological YAP activator, lysophosphatidic acid, can substantially improve early development of wild-type, but not maternal Yap1-knockout embryos in both oviduct and culture. These observations provide insights into the mechanisms of ZGA, and suggest potentials of YAP activators in improving the developmental competence of cultured embryos in assisted human reproduction and animal biotechnology.
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87
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Jedrusik A. Making the first decision: lessons from the mouse. Reprod Med Biol 2015; 14:135-150. [PMID: 29259411 PMCID: PMC5715835 DOI: 10.1007/s12522-015-0206-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/31/2015] [Indexed: 01/06/2023] Open
Abstract
Pre-implantation development encompasses a period of 3-4 days over which the mammalian embryo has to make its first decision: to separate the pluripotent inner cell mass (ICM) from the extra-embryonic epithelial tissue, the trophectoderm (TE). The ICM gives rise to tissues mainly building the body of the future organism, while the TE contributes to the extra-embryonic tissues that support embryo development after implantation. This review provides an overview of the cellular and molecular mechanisms that control the critical aspects of this first decision, and highlights the role of critical events, namely zytotic genome activation, compaction, polarization, asymmetric cell divisions, formation of the blastocyst cavity and expression of key transcription factors.
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Affiliation(s)
- Agnieszka Jedrusik
- Wellcome Trust/CR UK Gurdon InstituteTennis Court RoadCB2 1QNCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeDowning StreetCB2 3DYCambridgeUK
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88
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Sullivan CV, Chapman RW, Reading BJ, Anderson PE. Transcriptomics of mRNA and egg quality in farmed fish: Some recent developments and future directions. Gen Comp Endocrinol 2015; 221:23-30. [PMID: 25725305 DOI: 10.1016/j.ygcen.2015.02.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 02/14/2015] [Accepted: 02/18/2015] [Indexed: 11/29/2022]
Abstract
Maternal mRNA transcripts deposited in growing oocytes regulate early development and are under intensive investigation as determinants of egg quality. The research has evolved from single gene studies to microarray and now RNA-Seq analyses in which mRNA expression by virtually every gene can be assessed and related to gamete quality. Such studies have mainly focused on genes changing two- to several-fold in expression between biological states, and have identified scores of candidate genes and a few gene networks whose functioning is related to successful development. However, ever-increasing yields of information from high throughput methods for detecting transcript abundance have far outpaced progress in methods for analyzing the massive quantities of gene expression data, and especially for meaningful relation of whole transcriptome profiles to gamete quality. We have developed a new approach to this problem employing artificial neural networks and supervised machine learning with other novel bioinformatics procedures to discover a previously unknown level of ovarian transcriptome function at which minute changes in expression of a few hundred genes is highly predictive of egg quality. In this paper, we briefly review the progress in transcriptomics of fish egg quality and discuss some future directions for this field of study.
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Affiliation(s)
- Craig V Sullivan
- Department of Biology, North Carolina State University, Raleigh, NC 27695-7617, USA; Carolina AquaGyn, P.O. Box 12914, Raleigh, NC 27605, USA(1).
| | - Robert W Chapman
- Marine Resources Division, South Carolina Department of Natural Resources, Charleston, SC 29412, USA
| | - Benjamin J Reading
- Department of Biology, North Carolina State University, Raleigh, NC 27695-7617, USA; Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695-7617, USA(1)
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, SC 29424, USA
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89
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Laver JD, Marsolais AJ, Smibert CA, Lipshitz HD. Regulation and Function of Maternal Gene Products During the Maternal-to-Zygotic Transition in Drosophila. Curr Top Dev Biol 2015; 113:43-84. [PMID: 26358870 DOI: 10.1016/bs.ctdb.2015.06.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Drosophila late-stage oocytes and early embryos are transcriptionally silent. Thus, control of gene expression during these developmental periods is posttranscriptional and posttranslational. Global changes in the transcriptome and proteome occur during oocyte maturation, after egg activation and fertilization, and upon zygotic genome activation. We review the scale, content, and dynamics of these global changes; the factors that regulate these changes; and the mechanisms by which they are accomplished. We highlight the intimate relationship between the clearance of maternal gene products and the activation of the embryo's own genome, and discuss the fact that each of these complementary components of the maternal-to-zygotic transition can be subdivided into several phases that serve different biological roles and are regulated by distinct factors.
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Affiliation(s)
- John D Laver
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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90
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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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91
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Zhao P, Sun MX. The Maternal-to-Zygotic Transition in Higher Plants: Available Approaches, Critical Limitations, and Technical Requirements. Curr Top Dev Biol 2015; 113:373-98. [PMID: 26358879 DOI: 10.1016/bs.ctdb.2015.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fertilization marks the turnover from the gametophyte to sporophyte generation in higher plants. After fertilization, sporophytic development undergoes genetic turnover from maternal to zygotic control: the maternal-to-zygotic transition (MZT). The MZT is thought to be critical for early embryogenesis; however, little is known about the time course or developmental impact of the MZT in higher plants. Here, we discuss what is known in the field and focus on techniques used in relevant studies and their limitations. Some significant questions and technical requirements for further investigations are also discussed.
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Affiliation(s)
- Peng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
| | - Meng-Xiang Sun
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China.
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92
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Ruiz N, de Abreu LA, Parizi LF, Kim TK, Mulenga A, Braz GRC, Vaz IDS, Logullo C. Non-Invasive Delivery of dsRNA into De-Waxed Tick Eggs by Electroporation. PLoS One 2015; 10:e0130008. [PMID: 26091260 PMCID: PMC4474930 DOI: 10.1371/journal.pone.0130008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 05/15/2015] [Indexed: 11/18/2022] Open
Abstract
RNA interference-mediated gene silencing was shown to be an efficient tool for validation of targets that may become anti-tick vaccine components. Here, we demonstrate the application of this approach in the validation of components of molecular signaling cascades, such as the Protein Kinase B (AKT)/Glycogen Synthase Kinase (GSK) axis during tick embryogenesis. It was shown that heptane and hypochlorite treatment of tick eggs can remove wax, affecting corium integrity and but not embryo development. Evidence of AKT and GSK dsRNA delivery into de-waxed eggs of via electroporation is provided. Primers designed to amplify part of the dsRNA delivered into the electroporated eggs dsRNA confirmed its entry in eggs. In addition, it was shown that electroporation is able to deliver the fluorescent stain, 4',6-diamidino-2-phenylindole (DAPI). To confirm gene silencing, a second set of primers was designed outside the dsRNA sequence of target gene. In this assay, the suppression of AKT and GSK transcripts (approximately 50% reduction in both genes) was demonstrated in 7-day-old eggs. Interestingly, silencing of GSK in 7-day-old eggs caused 25% reduction in hatching. Additionally, the effect of silencing AKT and GSK on embryo energy metabolism was evaluated. As expected, knockdown of AKT, which down regulates GSK, the suppressor of glycogen synthesis, decreased glycogen content in electroporated eggs. These data demonstrate that electroporation of de-waxed R. microplus eggs could be used for gene silencing in tick embryos, and improve the knowledge about arthropod embryogenesis.
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Affiliation(s)
- Newton Ruiz
- Unidade de Experimentação Animal and Laboratório de Química e Função de Proteínas—Universidade Estadual Norte Fluminense–Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Leonardo Araujo de Abreu
- Laboratório Integrado de Bioquímica Hatisaburo Masuda—Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM/UFRJ), Macaé, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Ilha do Fundão, RJ, Brazil
| | - Luís Fernando Parizi
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, United States of America
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, United States of America
| | - Gloria Regina Cardoso Braz
- Departamento de Bioquímica–Instituto de Química, Universidade Federal do Rio de Janeiro, Ilha do Fundão, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Ilha do Fundão, RJ, Brazil
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Ilha do Fundão, RJ, Brazil
| | - Carlos Logullo
- Unidade de Experimentação Animal and Laboratório de Química e Função de Proteínas—Universidade Estadual Norte Fluminense–Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Ilha do Fundão, RJ, Brazil
- * E-mail:
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93
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Laver JD, Li X, Ray D, Cook KB, Hahn NA, Nabeel-Shah S, Kekis M, Luo H, Marsolais AJ, Fung KY, Hughes TR, Westwood JT, Sidhu SS, Morris Q, Lipshitz HD, Smibert CA. Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition. Genome Biol 2015; 16:94. [PMID: 25962635 PMCID: PMC4460960 DOI: 10.1186/s13059-015-0659-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/22/2015] [Indexed: 11/30/2022] Open
Abstract
Background Brain tumor (BRAT) is a Drosophila member of the TRIM-NHL protein family. This family is conserved among metazoans and its members function as post-transcriptional regulators. BRAT was thought to be recruited to mRNAs indirectly through interaction with the RNA-binding protein Pumilio (PUM). However, it has recently been demonstrated that BRAT directly binds to RNA. The precise sequence recognized by BRAT, the extent of BRAT-mediated regulation, and the exact roles of PUM and BRAT in post-transcriptional regulation are unknown. Results Genome-wide identification of transcripts associated with BRAT or with PUM in Drosophila embryos shows that they bind largely non-overlapping sets of mRNAs. BRAT binds mRNAs that encode proteins associated with a variety of functions, many of which are distinct from those implemented by PUM-associated transcripts. Computational analysis of in vitro and in vivo data identified a novel RNA motif recognized by BRAT that confers BRAT-mediated regulation in tissue culture cells. The regulatory status of BRAT-associated mRNAs suggests a prominent role for BRAT in post-transcriptional regulation, including a previously unidentified role in transcript degradation. Transcriptomic analysis of embryos lacking functional BRAT reveals an important role in mediating the decay of hundreds of maternal mRNAs during the maternal-to-zygotic transition. Conclusions Our results represent the first genome-wide analysis of the mRNAs associated with a TRIM-NHL protein and the first identification of an RNA motif bound by this protein family. BRAT is a prominent post-transcriptional regulator in the early embryo through mechanisms that are largely independent of PUM. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0659-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John D Laver
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Xiao Li
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Debashish Ray
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Kate B Cook
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Noah A Hahn
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Mariana Kekis
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Hua Luo
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Alexander J Marsolais
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Karen Yy Fung
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - J Timothy Westwood
- Department of Biology, University of Toronto, Mississauga, 3359 Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada.
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada.
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, M5S 3E1, Canada. .,Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario, M5S 3G4, Canada. .,Department of Computer Science, University of Toronto, 40 St. George Street, Toronto, Ontario, M5S 2E4, Canada.
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada. .,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
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94
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Qamar S, Kramer K, Urlaub H. Studying RNA-Protein Interactions of Pre-mRNA Complexes by Mass Spectrometry. Methods Enzymol 2015; 558:417-463. [PMID: 26068749 DOI: 10.1016/bs.mie.2015.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RNA-protein interactions play a crucial role in gene expression. These interactions take place in so-called ribonucleoprotein (RNP) complexes. To investigate which proteins interact with RNA in these complexes, and how they do so, UV-light-induced cross-linking has proven to be a valuable, yet straightforward technique. UV irradiation induces a covalent bond between the RNA and the proteins, whereafter cross-linked proteins can be identified by mass spectrometric (MS) approaches. Moreover, the cross-linked region of the protein, and often the actual cross-linked amino acid, can be identified by state-of-the-art MS, as can the cross-linked RNA moiety. This protocol describes in detail how to isolate peptide-RNA oligonucleotide cross-links from UV-irradiated human pre-mRNA RNPs and to perform the subsequent MS investigation of these peptide-RNA conjugates in combination with a dedicated computational analysis, in order to obtain sequence information about the cross-linked peptide and oligoribonucleotide. The described workflow can be applied to any RNP, irrespective of its origin, e.g., RNPs assembled in vitro (as described here) or RNPs isolated from UV-irradiated cells, either ex vivo or in vivo.
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Affiliation(s)
- Saadia Qamar
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Katharina Kramer
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany.
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95
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Garcia SM, Marinho LSR, Lunardelli PA, Seneda MM, Meirelles FV. Developmental block and programmed cell death in Bos indicus embryos: effects of protein supplementation source and developmental kinetics. PLoS One 2015; 10:e0119463. [PMID: 25760989 PMCID: PMC4356560 DOI: 10.1371/journal.pone.0119463] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/21/2015] [Indexed: 11/18/2022] Open
Abstract
The aims of this study were to determine if the protein source of the medium influences zebu embryo development and if developmental kinetics, developmental block and programmed cell death are related. The culture medium was supplemented with either fetal calf serum or bovine serum albumin. The embryos were classified as Fast (n = 1,235) or Slow (n = 485) based on the time required to reach the fourth cell cycle (48 h and 90 h post insemination - hpi -, respectively). The Slow group was further separated into two groups: those presenting exactly 4 cells at 48 hpi (Slow/4 cells) and those that reached the fourth cell cycle at 90 hpi (Slow). Blastocyst quality, DNA fragmentation, mitochondrial membrane potential and signs of apoptosis or necrosis were evaluated. The Slow group had higher incidence of developmental block than the Fast group. The embryos supplemented with fetal calf serum had lower quality. DNA fragmentation and mitochondrial membrane potential were absent in embryos at 48 hpi but present at 90 hpi. Early signs of apoptosis were more frequent in the Slow and Slow/4 cell groups than in the Fast group. We concluded that fetal calf serum reduces blastocyst development and quality, but the mechanism appears to be independent of DNA fragmentation. The apoptotic cells detected at 48 hpi reveal a possible mechanism of programmed cell death activation prior to genome activation. The apoptotic cells observed in the slow-developing embryos suggested a relationship between programmed cell death and embryonic developmental kinetics in zebu in vitro-produced embryos.
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Affiliation(s)
- Sheila Merlo Garcia
- São Paulo University (USP), Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brazil
| | | | - Paula Alvares Lunardelli
- State University of Londrina (UEL), Laboratório de Reprodução Animal, DCV, CCA, Londrina, PR, Brazil
| | - Marcelo Marcondes Seneda
- State University of Londrina (UEL), Laboratório de Reprodução Animal, DCV, CCA, Londrina, PR, Brazil
- * E-mail:
| | - Flávio Vieira Meirelles
- São Paulo University (USP), Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brazil
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96
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Jiang P, Coller H. Functional interactions between microRNAs and RNA binding proteins. Microrna 2014; 1:70-9. [PMID: 25048093 DOI: 10.2174/2211536611201010070] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 10/11/2011] [Accepted: 11/05/2011] [Indexed: 01/19/2023]
Abstract
Ensuring the appropriate spatial-temporal control of protein abundance requires careful control of transcript levels. This process is regulated at many steps, including the rate at which transcripts decay. microRNAs (miRNAs) and RNA Binding Proteins (RBPs) represent two important regulators of transcript degradation. We review here recent literature that suggests these two regulators of transcript decay may functionally interact. Some studies have reported an excess of miRNA binding sites surrounding the positions at which RBPs bind. Experimental reports focusing on a particular transcript have identified instances in which RBPs and miRNAs compete for the same target sites, and instances in which the binding of a RBP makes a miRNA recognition site more accessible to the RISC complex. Further, miRNAs and RBPs use similar enzymes for degradation of target transcripts and the degradation of the target transcripts occurs in similar subcellular compartments. In addition to miRNA-RBP interactions involving transcript decay, RBPs have also been reported to facilitate the processing of pri-miRNAs to their final form. We summarize here several possible mechanisms through which miRNA-RBP interactions may occur.
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Affiliation(s)
| | - Hilary Coller
- Department of Molecular Biology, Lewis Thomas Laboratory, Room 140, Princeton University Princeton, NJ 08544
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97
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Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development. Mol Genet Genomics 2014; 290:685-97. [DOI: 10.1007/s00438-014-0952-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/10/2014] [Indexed: 12/20/2022]
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98
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Bebbere D, Ariu F, Bogliolo L, Masala L, Murrone O, Fattorini M, Falchi L, Ledda S. Expression of maternally derived KHDC3, NLRP5, OOEP and TLE6 is associated with oocyte developmental competence in the ovine species. BMC DEVELOPMENTAL BIOLOGY 2014; 14:40. [PMID: 25420964 PMCID: PMC4247878 DOI: 10.1186/s12861-014-0040-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 11/11/2014] [Indexed: 12/30/2022]
Abstract
BACKGROUND The sub-cortical maternal complex (SCMC), located in the subcortex of mouse oocytes and preimplantation embryos, is composed of at least four proteins encoded by maternal effect genes: OOEP, NLRP5/MATER, TLE6 and KHDC3/FILIA. The SCMC assembles during oocyte growth and was seen to be essential for murine zygote progression beyond the first embryonic cell divisions; although roles in chromatin reprogramming and embryonic genome activation were hypothesized, the full range of functions of the complex in preimplantation development remains largely unknown. RESULTS Here we report the expression of the SCMC genes in ovine oocytes and pre-implantation embryos, describing for the first time its expression in a large mammalian species. We report sheep-specific patterns of expression and a relationship with the oocyte developmental potential in terms of delayed degradation of maternal SCMC transcripts in pre-implantation embryos derived from developmentally incompetent oocytes. In addition, by determining OOEP full length cDNA by Rapid Amplification of cDNA Ends (RACE) we identified two different transcript variants (OOEP1 and OOEP2), both expressed in oocytes and early embryos, but with different somatic tissue distributions. In silico translation showed that 140 aminoacid peptide OOEP1 shares an identity with orthologous proteins ranging from 95% with the bovine to 45% with mouse. Conversely, OOEP2 contains a premature termination codon, thus representing an alternative noncoding transcript and supporting the existence of aberrant splicing during ovine oogenesis. CONCLUSIONS These findings confirm the existence of the SCMC in sheep and its key role for the oocyte developmental potential, deepening our understanding on the molecular differences underlying cytoplasmic vs nuclear maturation of the oocytes. Describing differences and overlaps in transcriptome composition between model organisms advance our comprehension of the diversity/uniformity between mammalian species during early embryonic development and provide information on genes that play important regulatory roles in fertility in nonmurine models, including the human.
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Affiliation(s)
- Daniela Bebbere
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100, Sassari, Italy.
| | - Federica Ariu
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100, Sassari, Italy.
| | - Luisa Bogliolo
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100, Sassari, Italy.
| | - Laura Masala
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100, Sassari, Italy.
| | - Ombretta Murrone
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100, Sassari, Italy.
| | - Mauro Fattorini
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100, Sassari, Italy.
| | - Laura Falchi
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100, Sassari, Italy.
| | - Sergio Ledda
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100, Sassari, Italy.
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99
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Lee M, Choi Y, Kim K, Jin H, Lim J, Nguyen TA, Yang J, Jeong M, Giraldez AJ, Yang H, Patel DJ, Kim VN. Adenylation of maternally inherited microRNAs by Wispy. Mol Cell 2014; 56:696-707. [PMID: 25454948 DOI: 10.1016/j.molcel.2014.10.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/03/2014] [Accepted: 10/10/2014] [Indexed: 12/31/2022]
Abstract
Early development depends heavily on accurate control of maternally inherited mRNAs, and yet it remains unknown how maternal microRNAs are regulated during maternal-to-zygotic transition (MZT). We here find that maternal microRNAs are highly adenylated at their 3' ends in mature oocytes and early embryos. Maternal microRNA adenylation is widely conserved in fly, sea urchin, and mouse. We identify Wispy, a noncanonical poly(A) polymerase, as the enzyme responsible for microRNA adenylation in flies. Knockout of wispy abrogates adenylation and results in microRNA accumulation in eggs, whereas overexpression of Wispy increases adenylation and reduces microRNA levels in S2 cells. Wispy interacts with Ago1 through protein-protein interaction, which may allow the effective and selective adenylation of microRNAs. Thus, adenylation may contribute to the clearance of maternally deposited microRNAs during MZT. Our work provides mechanistic insights into the regulation of maternal microRNAs and illustrates the importance of RNA tailing in development.
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Affiliation(s)
- Mihye Lee
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Hua Jin
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Tuan Anh Nguyen
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Minsun Jeong
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hui Yang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.
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100
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Deutsch DR, Fröhlich T, Otte KA, Beck A, Habermann FA, Wolf E, Arnold GJ. Stage-Specific Proteome Signatures in Early Bovine Embryo Development. J Proteome Res 2014; 13:4363-76. [DOI: 10.1021/pr500550t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Daniela R. Deutsch
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Kathrin A. Otte
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Andrea Beck
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Felix A. Habermann
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Georg J. Arnold
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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