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Blengini CS, Vaskovicova M, Schier J, Drutovic D, Schindler K. Spatio-temporal requirements of Aurora kinase A in mouse oocyte meiotic spindle building. iScience 2024; 27:110451. [PMID: 39081293 PMCID: PMC11284559 DOI: 10.1016/j.isci.2024.110451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/30/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Meiotic spindles are critical to ensure chromosome segregation during gamete formation. Oocytes lack centrosomes and use alternative microtubule-nucleation mechanisms for spindle building. How these mechanisms are regulated is still unknown. Aurora kinase A (AURKA) is essential for mouse oocyte meiosis because in pro-metaphase I it triggers microtubule organizing-center fragmentation and its expression compensates for the loss of the two other Aurora kinases (AURKB/AURKC). Although knockout mouse models were useful for foundational studies, AURK spatial and temporal functions are not yet resolved. We provide high-resolution analyses of AURKA/AURKC requirements during meiotic spindle-building and identify the subcellular populations that carry out these functions: 1) AURKA is required in early spindle assembly and later for spindle stability, whereas 2) AURKC is required in late pro-metaphase, and 3) Targeted AURKA constructs expressed in triple AURK knockout oocytes reveal that spindle pole-localized AURKA is the most important population controlling spindle building and stability mechanisms.
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Affiliation(s)
- Cecilia S. Blengini
- Department of Genetics, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Michaela Vaskovicova
- Laboratory of DNA Integrity, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Schier
- The Czech Academy of Sciences, Institute of Information Theory and Automation, Piscataway, NJ 08854, USA
| | - David Drutovic
- Laboratory of DNA Integrity, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Karen Schindler
- Department of Genetics, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
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2
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Tang F, Hummitzsch K, Rodgers RJ. RNAseq analysis of oocyte maturation from the germinal vesicle stage to metaphase II in pig and human. PLoS One 2024; 19:e0305893. [PMID: 39121087 PMCID: PMC11315340 DOI: 10.1371/journal.pone.0305893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/06/2024] [Indexed: 08/11/2024] Open
Abstract
During maturation oocytes at the germinal vesicle (GV) stage progress to metaphase II (MII). However, during in vitro maturation a proportion often fail to progress. To understand these processes, we employed RNA sequencing to examine the transcriptome profile of these three groups of oocytes from the pig. We compared our findings with similar public oocyte data from humans. The transcriptomes in oocytes that failed to progress was similar to those that did. We found in both species, the most upregulated genes in MII oocytes were associated with chromosome segregation and cell cycle processes, while the most down regulated genes were relevant to ribosomal and mitochondrial pathways. Moreover, those genes involved in chromosome segregation during GV to MII transition were conserved in pig and human. We also compared MII and GV oocyte transcriptomes at the isoform transcript level in both species. Several thousands of genes (including DTNBP1, MAPK1, RAB35, GOLGA7, ATP1A1 and ATP2B1) identified as not different in expression at a gene transcript level were found to have differences in isoform transcript levels. Many of these genes were involved in ATPase-dependent or GTPase-dependent intracellular transport in pig and human, respectively. In conclusion, our study suggests the failure to progress to MII in vitro may not be regulated at the level of the genome and that many genes are differentially regulated at the isoform level, particular those involved ATPase- or GTPase-dependent intracellular transport.
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Affiliation(s)
- Feng Tang
- School of Biomedicine, Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Katja Hummitzsch
- School of Biomedicine, Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Raymond J. Rodgers
- School of Biomedicine, Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
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3
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Kunitomi C, Romero M, Daldello EM, Schindler K, Conti M. Multiple intersecting pathways are involved in CPEB1 phosphorylation and regulation of translation during mouse oocyte meiosis. Development 2024; 151:dev202712. [PMID: 38785133 PMCID: PMC11190569 DOI: 10.1242/dev.202712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024]
Abstract
The RNA-binding protein cytoplasmic polyadenylation element binding 1 (CPEB1) plays a fundamental role in regulating mRNA translation in oocytes. However, the specifics of how and which protein kinase cascades modulate CPEB1 activity are still controversial. Using genetic and pharmacological tools, and detailed time courses, we have re-evaluated the relationship between CPEB1 phosphorylation and translation activation during mouse oocyte maturation. We show that both the CDK1/MAPK and AURKA/PLK1 pathways converge on CPEB1 phosphorylation during prometaphase of meiosis I. Only inactivation of the CDK1/MAPK pathway disrupts translation, whereas inactivation of either pathway alone leads to CPEB1 stabilization. However, CPEB1 stabilization induced by inactivation of the AURKA/PLK1 pathway does not affect translation, indicating that destabilization and/or degradation is not linked to translational activation. The accumulation of endogenous CCNB1 protein closely recapitulates the translation data that use an exogenous template. These findings support the overarching hypothesis that the activation of translation during prometaphase in mouse oocytes relies on a CDK1/MAPK-dependent CPEB1 phosphorylation, and that translational activation precedes CPEB1 destabilization.
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Affiliation(s)
- Chisato Kunitomi
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Mayra Romero
- Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Enrico Maria Daldello
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, LBD - IBPS, F-75005 Paris, France
| | - Karen Schindler
- Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ 08854, USA
| | - Marco Conti
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
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Gajjar G, Huggins HP, Kim ES, Huang W, Bonnet FX, Updike DL, Keiper BD. Two germ granule eIF4E isoforms reside in different mRNPs to hand off C elegans mRNAs from translational repression to activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595216. [PMID: 38826235 PMCID: PMC11142241 DOI: 10.1101/2024.05.24.595216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
We studied the function of translation factor eIF4E isoforms in regulating mRNAs in germ cell granules/condensates. Translational control of mRNAs plays an essential role in germ cell gene regulation. Messenger ribonucleoprotein (mRNP) complexes assemble on mRNAs as they move from the nucleus into perinuclear germ granules to exert both positive and negative post-transcriptional regulation in the cytoplasm. In C. elegans , germ granules are surprisingly dynamic mRNP condensates that remodel during development. Two eIF4E isoforms (called IFE-1 and IFE-3), eIF4E-Interacting Proteins (4EIPs), RBPs, DEAD-box helicases, polyadenylated mRNAs, Argonautes and miRNAs all occupy positions in germ granules. Affinity purification of IFE-1 and IFE-3 allowed mass spectrometry and mRNA-Seq to identify the proteins and mRNAs that populate stable eIF4E mRNPs. We find translationally controlled mRNAs (e.g. pos-1, mex-3, spn-4, etc.) enriched in IFE-3 mRNPs, but excluded from IFE-1 mRNPs. These mRNAs also require IFE-1 for efficient translation. The findings support a model in which oocytes and embryos utilize the two eIF4Es for opposite purposes on critically regulated germline mRNAs. Careful colocalization of the eIF4Es with other germ granule components suggests an architecture in which GLH-1, PGL-1 and the IFEs are stratified to facilitate sequential interactions for mRNAs. Biochemical characterization demonstrates opposing yet cooperative roles for IFE-3 and IFE-1 to hand-off of translationally controlled mRNAs from the repressed to the activated state, respectively. The model involves eIF4E mRNPs shuttling mRNAs through nuclear pore-associated granules/condensates to cytoplasmic ribosomes.
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Xiang K, Ly J, Bartel DP. Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos. Dev Cell 2024; 59:1058-1074.e11. [PMID: 38460509 DOI: 10.1016/j.devcel.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/28/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
During oocyte maturation and early embryogenesis, changes in mRNA poly(A)-tail lengths strongly influence translation, but how these tail-length changes are orchestrated has been unclear. Here, we performed tail-length and translational profiling of mRNA reporter libraries (each with millions of 3' UTR sequence variants) in frog oocytes and embryos and in fish embryos. Contrasting to previously proposed cytoplasmic polyadenylation elements (CPEs), we found that a shorter element, UUUUA, together with the polyadenylation signal (PAS), specify cytoplasmic polyadenylation, and we identified contextual features that modulate the activity of both elements. In maturing oocytes, this tail lengthening occurs against a backdrop of global deadenylation and the action of C-rich elements that specify tail-length-independent translational repression. In embryos, cytoplasmic polyadenylation becomes more permissive, and additional elements specify waves of stage-specific deadenylation. Together, these findings largely explain the complex tapestry of tail-length changes observed in early frog and fish development, with strong evidence of conservation in both mice and humans.
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Affiliation(s)
- Kehui Xiang
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jimmy Ly
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Rios KT, McGee JP, Sebastian A, Moritz RL, Feric M, Absalon S, Swearingen KE, Lindner SE. Global Release of Translational Repression Across Plasmodium's Host-to-Vector Transmission Event. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577866. [PMID: 38352447 PMCID: PMC10862809 DOI: 10.1101/2024.02.01.577866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Malaria parasites must be able to respond quickly to changes in their environment, including during their transmission between mammalian hosts and mosquito vectors. Therefore, before transmission, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. This essential regulatory control requires the orthologues of DDX6 (DOZI), LSM14a (CITH), and ALBA proteins to form a translationally repressive complex in female gametocytes that associates with many of the affected mRNAs. However, while the release of translational repression of individual mRNAs has been documented, the details of the global release of translational repression have not. Moreover, the changes in spatial arrangement and composition of the DOZI/CITH/ALBA complex that contribute to translational control are also not known. Therefore, we have conducted the first quantitative, comparative transcriptomics and DIA-MS proteomics of Plasmodium parasites across the host-to-vector transmission event to document the global release of translational repression. Using female gametocytes and zygotes of P. yoelii, we found that nearly 200 transcripts are released for translation soon after fertilization, including those with essential functions for the zygote. However, we also observed that some transcripts remain repressed beyond this point. In addition, we have used TurboID-based proximity proteomics to interrogate the spatial and compositional changes in the DOZI/CITH/ALBA complex across this transmission event. Consistent with recent models of translational control, proteins that associate with either the 5' or 3' end of mRNAs are in close proximity to one another during translational repression in female gametocytes and then dissociate upon release of repression in zygotes. This observation is cross-validated for several protein colocalizations in female gametocytes via ultrastructure expansion microscopy and structured illumination microscopy. Moreover, DOZI exchanges its interaction from NOT1-G in female gametocytes to the canonical NOT1 in zygotes, providing a model for a trigger for the release of mRNAs from DOZI. Finally, unenriched phosphoproteomics revealed the modification of key translational control proteins in the zygote. Together, these data provide a model for the essential translational control mechanisms used by malaria parasites to promote their efficient transmission from their mammalian host to their mosquito vector.
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Affiliation(s)
- Kelly T. Rios
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
| | - James P. McGee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802
| | | | - Marina Feric
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Sabrina Absalon
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202
| | | | - Scott E. Lindner
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
- Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802
- Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
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Conti M, Kunitomi C. A genome-wide perspective of the maternal mRNA translation program during oocyte development. Semin Cell Dev Biol 2024; 154:88-98. [PMID: 36894378 PMCID: PMC11250054 DOI: 10.1016/j.semcdb.2023.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 02/01/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Transcriptional and post-transcriptional regulations control gene expression in most cells. However, critical transitions during the development of the female gamete relies exclusively on regulation of mRNA translation in the absence of de novo mRNA synthesis. Specific temporal patterns of maternal mRNA translation are essential for the oocyte progression through meiosis, for generation of a haploid gamete ready for fertilization and for embryo development. In this review, we will discuss how mRNAs are translated during oocyte growth and maturation using mostly a genome-wide perspective. This broad view on how translation is regulated reveals multiple divergent translational control mechanisms required to coordinate protein synthesis with progression through the meiotic cell cycle and with development of a totipotent zygote.
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Affiliation(s)
- Marco Conti
- Center for Reproductive Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA.
| | - Chisato Kunitomi
- Center for Reproductive Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
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8
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Guo H. A journey through translational control. Semin Cell Dev Biol 2024; 154:85-87. [PMID: 37661538 DOI: 10.1016/j.semcdb.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Affiliation(s)
- Huili Guo
- Bia-Echo Asia Centre for Reproductive Longevity and Equality, Healthy Longevity Translational Research Program, National University of Singapore, Singapore.
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9
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Wang X, Leung FS, Bush JO, Conti M. Alternative cleavage and polyadenylation of the Ccnb1 mRNA defines accumulation of cyclin protein during the meiotic cell cycle. Nucleic Acids Res 2024; 52:1258-1271. [PMID: 38048302 PMCID: PMC10853788 DOI: 10.1093/nar/gkad1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023] Open
Abstract
Progression through the mitotic and meiotic cell cycle is driven by fluctuations in the levels of cyclins, the regulatory subunits controlling the localization and activity of CDK1 kinases. Cyclin levels are regulated through a precise balance of synthesis and degradation. Here we demonstrate that the synthesis of Cyclin B1 during the oocyte meiotic cell cycle is defined by the selective translation of mRNA variants generated through alternative cleavage and polyadenylation (APA). Using gene editing in mice, we introduced mutations into the proximal and distal polyadenylation elements of the 3' untranslated region (UTR) of the Ccnb1 mRNA. Through in vivo loss-of-function experiments, we demonstrate that the translation of mRNA with a short 3' UTR specifies Cyclin B1 protein levels that set the timing of meiotic re-entry. In contrast, translation directed by a long 3' UTR is necessary to direct Cyclin B1 protein accumulation during the MI/MII transition. These findings establish that the progression through the cell cycle is dependent on the selective translation of multiple mRNA variants generated by APA.
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Affiliation(s)
- Xiaotian Wang
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Fang-Shiuan Leung
- USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA 94143, USA
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey O Bush
- USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA 94143, USA
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Marco Conti
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
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O'Connor EC, Kambara K, Bertrand D. Advancements in the use of xenopus oocytes for modelling neurological disease for novel drug discovery. Expert Opin Drug Discov 2024; 19:173-187. [PMID: 37850233 DOI: 10.1080/17460441.2023.2270902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023]
Abstract
INTRODUCTION Introduced about 50 years ago, the model of Xenopus oocytes for the expression of recombinant proteins has gained a broad spectrum of applications. The authors herein review the benefits brought from using this model system, with a focus on modeling neurological disease mechanisms and application to drug discovery. AREAS COVERED Using multiple examples spanning from ligand gated ion channels to transporters, this review presents, in the light of the latest publications, the benefits offered from using Xenopus oocytes. Studies range from the characterization of gene mutations to the discovery of novel treatments for disorders of the central nervous system (CNS). EXPERT OPINION Development of new drugs targeting CNS disorders has been marked by failures in the translation from preclinical to clinical studies. As progress in genetics and molecular biology highlights large functional differences arising from a single to a few amino acid exchanges, the need for drug screening and functional testing against human proteins is increasing. The use of Xenopus oocytes to enable precise modeling and characterization of clinically relevant genetic variants constitutes a powerful model system that can be used to inform various aspects of CNS drug discovery and development.
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Affiliation(s)
- Eoin C O'Connor
- Roche Pharma Research and Early Development, Neuroscience & Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
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Kunitomi C, Romero M, Daldello EM, Schindler K, Conti M. Multiple intersecting pathways are involved in the phosphorylation of CPEB1 to activate translation during mouse oocyte meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.575938. [PMID: 38293116 PMCID: PMC10827138 DOI: 10.1101/2024.01.17.575938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The RNA-binding protein cytoplasmic polyadenylation element binding 1 (CPEB1) plays a fundamental role in the regulation of mRNA translation in oocytes. However, the nature of protein kinase cascades modulating the activity of CPEB1 is still a matter of controversy. Using genetic and pharmacological tools and detailed time courses, here we have reevaluated the relationship between CPEB1 phosphorylation and the activation of translation during mouse oocyte maturation. We show that both the CDK1/MAPK and AURKA/PLK1 pathways converge on the phosphorylation of CPEB1 during prometaphase. Only inactivation of the CDK1/MAPK pathway disrupts translation, while inactivation of either pathway leads to CPEB1 stabilization. However, stabilization of CPEB1 induced by inactivation of the AURKA/PLK1 does not affect translation, indicating that destabilization/degradation can be dissociated from translational activation. The accumulation of the endogenous CCNB1 protein closely recapitulates the translation data. These findings support the overarching hypothesis that the activation of translation in prometaphase in mouse oocytes relies on a CDK1-dependent CPEB1 phosphorylation, and this translational activation precedes CPEB1 destabilization.
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Affiliation(s)
- Chisato Kunitomi
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Mayra Romero
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Human Genetics Institute of New Jersey
| | - Enrico Maria Daldello
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, LBD - IBPS, F-75005 Paris, France
| | - Karen Schindler
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Human Genetics Institute of New Jersey
| | - Marco Conti
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
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12
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Konstantinidou F, Placidi M, Di Emidio G, Stuppia L, Tatone C, Gatta V, Artini PG. Maternal MicroRNA Profile Changes When LH Is Added to the Ovarian Stimulation Protocol: A Pilot Study. EPIGENOMES 2023; 7:25. [PMID: 37873810 PMCID: PMC10594432 DOI: 10.3390/epigenomes7040025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023] Open
Abstract
While the use of follicle-stimulating hormone (FSH) in ovarian stimulation for in vitro fertilization (IVF) is an established practice, the use of luteinizing hormone (LH) remains debatable. MicroRNAs (miRNAs) are short, endogenous, non-coding transcripts that control a variety of cellular functions, such as gonadotrophin production and follicular development. The goal of this pilot study was to investigate whether the employment of recombinant LH (rLH) in ovarian stimulation protocols results in changes in the miRNA profiles in human oocytes. Patients were divided into two groups: seven received recombinant FSH (rFSH, 225 IU), and six received rFSH (150 IU) plus rLH (75 IU). MiRNA predesigned panels and real-time PCR technology were used to analyze the oocytes retrieved from the follicular ovarian retrieval. Among the miRNAs evaluated, a series of them evidenced upregulation or downregulation in their expression in the FSH plus LH group compared to the FSH group. Considering the results obtained from the functional and network analysis, the different maternal miRNA profiles in the two groups revealed a differential modulation of pathways involved in numerous biological functions. Overall, based on the pathways associated with most of these maternal miRNAs, the presence of LH may result in a different modulation of pathways regulating survival under the control of a Tp53-related mechanism. Interestingly, among the miRNAs differentially expressed in oocytes of the two groups, we have found miRNAs already investigated at ovarian, follicular, oocyte, and embryonic levels: hsa-miR-484, hsa-miR-222, hsa-miR-520d-5p, hsa-miRNA-17, hsa-miR-548, and hsa-miR-140. Thus, investigation into the role of these miRNAs in oocyte molecular pathways may help determine how LH affects oocyte competence and eventually leads to the clinical improvement of IVF.
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Affiliation(s)
- Fani Konstantinidou
- Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (F.K.)
- Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Martina Placidi
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.P.); (G.D.E.); (C.T.)
| | - Giovanna Di Emidio
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.P.); (G.D.E.); (C.T.)
| | - Liborio Stuppia
- Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (F.K.)
- Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Carla Tatone
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (M.P.); (G.D.E.); (C.T.)
| | - Valentina Gatta
- Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy; (F.K.)
- Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University of Chieti-Pescara, 66100 Chieti, Italy
| | - Paolo Giovanni Artini
- Division of Gynecology and Obstetrics, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy;
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13
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Kalous J, Aleshkina D, Anger M. A Role of PI3K/Akt Signaling in Oocyte Maturation and Early Embryo Development. Cells 2023; 12:1830. [PMID: 37508495 PMCID: PMC10378481 DOI: 10.3390/cells12141830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/24/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
A serine/threonine-specific protein kinase B (PKB), also known as Akt, is a key factor in the phosphoinositide 3-kinase (PI3K)/Akt signaling pathway that regulates cell survival, metabolism and proliferation. Akt phosphorylates many downstream specific substrates, which subsequently control the nuclear envelope breakdown (NEBD), centrosome maturation, spindle assembly, chromosome segregation, and cytokinesis. In vertebrates, Akt is also an important player during oogenesis and preimplantation development. In the signaling pathways regulating mRNA translation, Akt is involved in the control of mammalian target of rapamycin complex 1 (mTORC1) and thereby regulates the activity of a translational repressor, the eukaryotic initiation factor 4E (eIF4E) binding protein 1 (4E-BP1). In this review, we summarize the functions of Akt in mitosis, meiosis and early embryonic development. Additionally, the role of Akt in the regulation of mRNA translation is addressed with respect to the significance of this process during early development.
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Affiliation(s)
- Jaroslav Kalous
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Libechov, Czech Republic
| | - Daria Aleshkina
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Libechov, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Albertov 6, 128 00 Praha, Czech Republic
| | - Martin Anger
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Libechov, Czech Republic
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14
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Rouhana L, Edgar A, Hugosson F, Dountcheva V, Martindale MQ, Ryan JF. Cytoplasmic Polyadenylation Is an Ancestral Hallmark of Early Development in Animals. Mol Biol Evol 2023; 40:msad137. [PMID: 37288606 PMCID: PMC10284499 DOI: 10.1093/molbev/msad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3'-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in nonanimal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, and cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs, and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.
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Affiliation(s)
- Labib Rouhana
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Fredrik Hugosson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Valeria Dountcheva
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
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15
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Liu Z, Jin X, Miao Y, Wang P, Gu Y, Shangguan X, Chen L, Wang G. Identification and Characterization of C-Mos in Pearl Mussel Hyriopsis cumingii and Its Role in Gonadal Development. Biomolecules 2023; 13:931. [PMID: 37371511 DOI: 10.3390/biom13060931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
C-Mos, a proto-oncogene, regulates oocyte maturation by activating the classical MAPK pathway in cells. To examine the function of C-Mos in Hyriopsis cumingii, C-Mos was identified in this study. The full-length cDNA of C-Mos was 2213 bp, including 144 bp in the 5' UTR, 923 bp in 3' the UTR, and 1146 bp in the open reading frame (ORF) region. During early gonad development, the expression of C-Mos from 4 to 6 months of age in H. cumingii was significantly higher than that in other months, with the highest expression in 6-month-old H. cumingii, suggesting that C-Mos may be involved in early gonadal development in H. cumingii. Clear hybridization signals were found by in situ hybridization in the oocytes, oocyte nucleus and oogonium, and a small number of hybridization signals were found in the follicular wall of the male gonads. In addition, the C-Mos RNA interference (RNAi) assay results showed that the knockdown of C-Mos caused a down-regulation of ERK and P90rsk. In summary, these results indicate that C-Mos has a crucial part to play in gonadal development in H. cumingii.
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Affiliation(s)
- Zongyu Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Xin Jin
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Yulin Miao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Ping Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Yang Gu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Xiaozhao Shangguan
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Lijing Chen
- Shanghai Vocational College of Agriculture and Forestry, Shanghai 201699, China
| | - Guiling Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
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16
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de Morree A, Rando TA. Regulation of adult stem cell quiescence and its functions in the maintenance of tissue integrity. Nat Rev Mol Cell Biol 2023; 24:334-354. [PMID: 36922629 PMCID: PMC10725182 DOI: 10.1038/s41580-022-00568-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 03/18/2023]
Abstract
Adult stem cells are important for mammalian tissues, where they act as a cell reserve that supports normal tissue turnover and can mount a regenerative response following acute injuries. Quiescent stem cells are well established in certain tissues, such as skeletal muscle, brain, and bone marrow. The quiescent state is actively controlled and is essential for long-term maintenance of stem cell pools. In this Review, we discuss the importance of maintaining a functional pool of quiescent adult stem cells, including haematopoietic stem cells, skeletal muscle stem cells, neural stem cells, hair follicle stem cells, and mesenchymal stem cells such as fibro-adipogenic progenitors, to ensure tissue maintenance and repair. We discuss the molecular mechanisms that regulate the entry into, maintenance of, and exit from the quiescent state in mice. Recent studies revealed that quiescent stem cells have a discordance between RNA and protein levels, indicating the importance of post-transcriptional mechanisms, such as alternative polyadenylation, alternative splicing, and translation repression, in the control of stem cell quiescence. Understanding how these mechanisms guide stem cell function during homeostasis and regeneration has important implications for regenerative medicine.
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Affiliation(s)
- Antoine de Morree
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Thomas A Rando
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA.
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17
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Song CR, Zhang RJ, Xue FR, Zhang XJ, Wang XY, Sun D, Ding K, Yang Q, Wang XY, Liang CG. mRNA 3' -UTR-mediate translational control through PAS and CPE in sheep oocyte. Theriogenology 2023; 201:30-40. [PMID: 36827867 DOI: 10.1016/j.theriogenology.2022.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 10/21/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022]
Abstract
In oocytes, the cytoplasmic polyadenylation and maternal mRNAs translation is regulated by cis-elements, including polyadenylation signal (PAS) and cytoplasmic polyadenylation element (CPE) in 3'-UTR. Recent studies illustrate non-canonical polyadenylation mechanisms of translational regulation in mouse oocytes, which is different from that in Xenopus oocytes. However, it is still unclear if this regulation in rodent oocytes functions in the domestic animal oocyte. Here, by using sheep as an animal model, we cloned the 3'-UTRs of Cpeb1 or Btg4 and ligated it into the pRK5-Flag-Gfp vector. Variant numbers and positions of PASs and CPEs within the 3'-UTRs were constructed to detect their effects on translational control. After in vitro-transcription and microinjection into sheep fully grown germinal vesicle stage oocytes, the expression efficiency of mRNAs was detected by the GFP and flag expression. Our results show that: (i) PAS located at the proximal end of 3'-UTR can mediate the translation of the maternal mRNAs, as long as they locate far from CPEs; (ii) The proximal PAS has higher efficiency in regulating transcription than the distal one; (iii) increase of PAS number can promote the translational activity more efficiently; (iv) a single CPE located close to PAS (<50 bp) in 3'-UTRs of Cpeb1 or Btg4 could partially repress translation. In 3'-UTRs of Btg4, two CPEs have a higher inhibitory effect, and three CPEs can completely inhibit mRNA translation. These results confirm the existence of the non-canonical mechanism in domestic animal oocytes.
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Affiliation(s)
- Chun-Ru Song
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China
| | - Ru-Jing Zhang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China
| | - Fang-Rui Xue
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China
| | - Xiao-Jie Zhang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China
| | - Xing-Yue Wang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China
| | - Dui Sun
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China
| | - Kang Ding
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China
| | - Qi Yang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China
| | - Xin-Yu Wang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China
| | - Cheng-Guang Liang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, People's Republic of China.
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18
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He M, Jiao S, Zhang R, Ye D, Wang H, Sun Y. Translational control by maternal Nanog promotes oogenesis and early embryonic development. Development 2022; 149:286111. [PMID: 36533583 DOI: 10.1242/dev.201213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022]
Abstract
Many maternal mRNAs are translationally repressed during oocyte development and spatio-temporally activated during early embryogenesis, which is crucial for oocyte and early embryo development. By analyzing maternal mutants of nanog (Mnanog) in zebrafish, we demonstrated that Nanog tightly controls translation of maternal mRNA during oogenesis via transcriptional repression of eukaryotic translation elongation factor 1 alpha 1, like 2 (eef1a1l2). Loss of maternal Nanog led to defects of egg maturation, increased endoplasmic reticulum stress, and an activated unfold protein response, which was caused by elevated translational activity. We further demonstrated that Nanog, as a transcriptional repressor, represses the transcription of eefl1a1l2 by directly binding to the eef1a1l2 promoter in oocytes. More importantly, depletion of eef1a1l2 in nanog mutant females effectively rescued the elevated translational activity in oocytes, oogenesis defects and embryonic defects of Mnanog embryos. Thus, our study demonstrates that maternal Nanog regulates oogenesis and early embryogenesis through translational control of maternal mRNA via a mechanism whereby Nanog acts as a transcriptional repressor to suppress transcription of eef1a1l2.
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Affiliation(s)
- Mudan He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengbo Jiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ru Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ding Ye
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Houpeng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,Hubei Hongshan Laboratory, Wuhan 430070, China
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19
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Peng Y, Gavis ER. The Drosophila hnRNP F/H homolog Glorund recruits dFMRP to inhibit nanos translation elongation. Nucleic Acids Res 2022; 50:7067-7083. [PMID: 35699205 PMCID: PMC9262583 DOI: 10.1093/nar/gkac500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
Translational control of maternal mRNAs generates spatial and temporal patterns of protein expression necessary to begin animal development. Translational repression of unlocalized nanos (nos) mRNA in late-stage Drosophila oocytes by the hnRNP F/H homolog, Glorund (Glo), is important for embryonic body patterning. While previous work has suggested that repression occurs at both the translation initiation and elongation phases, the molecular mechanism by which Glo regulates nos translation remains elusive. Here, we have identified the Drosophila fragile X mental retardation protein, dFMRP, as a Glo interaction partner with links to the translational machinery. Using an oocyte-based in vitro translation system, we confirmed that Glo regulates both initiation and elongation of a nos translational reporter and showed that dFMRP specifically represses translation elongation and promotes ribosome stalling. Furthermore, we combined mutational analysis and in vivo and in vitro binding assays to show that Glo's qRRM2 domain specifically and directly interacts with dFMRP. Our findings suggest that Glo regulates nos translation elongation by recruiting dFMRP and that Glo's RNA-binding domains can also function as protein-protein interaction interfaces critical for its regulatory functions. Additionally, they reveal a mechanism for targeting dFMRP to specific transcripts.
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Affiliation(s)
- Yingshi Peng
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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20
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Shannon J, Sundaresan A, Bukulmez O, Jiao Z, Doody K, Capelouto S, Carr B, Banaszynski LA. Chromatin Accessibility Analysis from Fresh and Cryopreserved Human Ovarian Follicles. Mol Hum Reprod 2022; 28:gaac020. [PMID: 35674368 DOI: 10.1093/molehr/gaac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/06/2022] [Indexed: 11/14/2022] Open
Abstract
Understanding how gene regulatory elements influence ovarian follicle development has important implications in clinically relevant settings. This includes understanding decreased fertility with age and understanding the short-lived graft function commonly observed after ovarian tissue cryopreservation and subsequent autologous transplantation as a fertility preservation treatment. The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is a powerful tool to identify distal and proximal regulatory elements important for activity-dependent gene regulation and hormonal and environmental responses such as those involved in germ cell maturation and human fertility. Original ATAC protocols were optimized for fresh cells, a major barrier to implementing this technique for clinical tissue samples which are more often than not frozen and stored. While recent advances have improved data obtained from stored samples, this technique has yet to be applied to human ovarian follicles, perhaps due to the difficulty in isolating follicles in sufficient quantities from stored clinical samples. Further, it remains unknown whether the process of cryopreservation affects the quality of the data obtained from ovarian follicles. Here, we generate ATAC-seq data sets from matched fresh and cryopreserved human ovarian follicles. We find that data obtained from cryopreserved samples are of reduced quality but consistent with data obtained from fresh samples, suggesting that the act of cryopreservation does not significantly affect biological interpretation of chromatin accessibility data. Our study encourages the use of this method to uncover the role of chromatin regulation in a number of clinical settings with the ultimate goal of improving fertility.
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Affiliation(s)
- Jennifer Shannon
- Department of Obstetrics and Gynecology: Division of Reproductive Endocrinology and Infertility, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Aishwarya Sundaresan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Orhan Bukulmez
- Department of Obstetrics and Gynecology: Division of Reproductive Endocrinology and Infertility, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zexu Jiao
- Department of Obstetrics and Gynecology: Division of Reproductive Endocrinology and Infertility, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kaitlin Doody
- Department of Obstetrics and Gynecology: Division of Reproductive Endocrinology and Infertility, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sarah Capelouto
- Department of Obstetrics and Gynecology: Division of Reproductive Endocrinology and Infertility, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bruce Carr
- Department of Obstetrics and Gynecology: Division of Reproductive Endocrinology and Infertility, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Laura A Banaszynski
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
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21
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Kretov DA. Role of Y-Box Binding Proteins in Ontogenesis. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S71-S74. [PMID: 35501987 DOI: 10.1134/s0006297922140061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/14/2023]
Abstract
Y-box binding proteins (YB proteins) are multifunctional DNA/RNA-binding proteins capable of regulating gene expression at multiple levels. At present, the most studied function of these proteins is the regulation of protein synthesis. Special attention in this review has been paid to the role of YB proteins in the control of mRNA translation and stability at the earliest stages of organism formation, from fertilization to gastrulation. Furthermore, the functions of YB proteins in the formation of germ cells, in which they accumulate in large amounts, are summarized. The review then discusses the contribution of YB proteins to the regulation of gene expression during the differentiation of various types of somatic cells. Finally, future directions in the study of YB proteins and their role in ontogenesis are considered.
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Affiliation(s)
- Dmitry A Kretov
- Department of Biochemistry, School of Medicine, Boston University, Boston, USA, 02218.
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22
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Small RNA expression and miRNA modification dynamics in human oocytes and early embryos. Genome Res 2021; 31:1474-1485. [PMID: 34340992 PMCID: PMC8327922 DOI: 10.1101/gr.268193.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 05/05/2021] [Indexed: 12/13/2022]
Abstract
Small noncoding RNAs (sRNAs) play important roles during the oocyte-to-embryo transition (OET), when the maternal phenotype is reprogrammed and the embryo genome is gradually activated. The transcriptional program driving early human development has been studied with the focus mainly on protein-coding RNAs, and expression dynamics of sRNAs remain largely unexplored. We profiled sRNAs in human oocytes and early embryos using an RNA-sequencing (RNA-seq) method suitable for low inputs of material. We show that OET in humans is temporally coupled with the transition from predominant expression of oocyte short piRNAs (os-piRNAs) in oocytes, to activation of microRNA (miRNA) expression in cleavage stage embryos. Additionally, 3′ mono- and oligoadenylation of miRNAs is markedly increased in zygotes. We hypothesize that this may modulate the function or stability of maternal miRNAs, some of which are retained throughout the first cell divisions in embryos. This study is the first of its kind elucidating the dynamics of sRNA expression and miRNA modification along a continuous trajectory of early human development and provides a valuable data set for in-depth interpretative analyses.
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23
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Hopes T, Norris K, Agapiou M, McCarthy CGP, Lewis PA, O'Connell MJ, Fontana J, Aspden JL. Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching. Nucleic Acids Res 2021; 50:2240-2257. [PMID: 34283226 PMCID: PMC8887423 DOI: 10.1093/nar/gkab606] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/23/2021] [Accepted: 07/02/2021] [Indexed: 12/02/2022] Open
Abstract
Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tissues of Drosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through a combination of paralog-enrichment and paralog-switching. We have solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation.
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Affiliation(s)
- Tayah Hopes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,LeedsOmics, University of Leeds, Leeds, UK
| | - Karl Norris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,LeedsOmics, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Michaela Agapiou
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,LeedsOmics, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Charley G P McCarthy
- School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Philip A Lewis
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Mary J O'Connell
- School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Juan Fontana
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,LeedsOmics, University of Leeds, Leeds, UK
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24
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Xiang K, Bartel DP. The molecular basis of coupling between poly(A)-tail length and translational efficiency. eLife 2021; 10:66493. [PMID: 34213414 PMCID: PMC8253595 DOI: 10.7554/elife.66493] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/21/2021] [Indexed: 01/10/2023] Open
Abstract
In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in Xenopus oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. Thus, strong coupling requires limiting PABPC, implying that in coupled systems longer-tail mRNAs better compete for limiting PABPC. In addition to expressing excess PABPC, post-embryonic mammalian cell lines had two other properties that prevented strong coupling: terminal-uridylation-dependent destabilization of mRNAs lacking bound PABPC, and a regulatory regime wherein PABPC contributes minimally to TE. Thus, these results revealed three fundamental mechanistic requirements for coupling and defined the context-dependent functions for PABPC, which promotes TE but not mRNA stability in coupled systems and mRNA stability but not TE in uncoupled systems. Cells are microscopic biological factories that are constantly creating new proteins. To do so, a cell must first convert its master genetic blueprint, the DNA, into strands of messenger RNA or mRNA. These strands are subsequently translated to make proteins. Cells have two ways to adjust the number of proteins they generate so they do not produce too many or too few: by changing how many mRNA molecules are available for translation, and by regulating how efficiently they translate these mRNA molecules into proteins. In animals, both unfertilized eggs and early-stage embryos lack the ability to create or destroy mRNAs, and consequently cannot adjust the number of mRNA molecules available for translation. These cells can therefore only regulate how efficiently each mRNA is translated. They do this by changing the length of the so-called poly(A) tail at the end of each mRNA molecule, which is made up of a long stretch of repeating adenosine nucleotides. The mRNAs with longer poly(A) tails are translated more efficiently than those with shorter poly(A) tails. However, this difference disappears in older embryos, when both long and short poly(A) tails are translated with equal efficiency, and it is largely unknown why. To find out more, Xiang and Bartel studied frog eggs, and discovered that artificially raising levels of a protein that binds poly(A) tails, also known as PABPC, improved the translation of short-tailed mRNAs to create a situation in which both short- and long-tailed mRNAs were translated with near-equal efficiency. This suggested that short- and long-tailed mRNAs compete for limited amounts of the translation-enhancing PABPC, and that long-tailed mRNAs are better at it than short-tailed mRNAs. Further investigation revealed that eggs also had to establish the right conditions for PABPC to enhance translation and had to protect mRNAs not associated with PABPC from being destroyed before they could be translated. Overall, Xiang and Bartel found that in eggs and early embryos, PABPC and poly(A) tails enhanced the translation of mRNAs but did not influence their stability, whereas later in development, they enhanced mRNA stability but not translation. This research provides new insights into how protein production is controlled at different stages of animal development, from unfertilized eggs to older embryos. Understanding how this process is regulated during normal development is crucial for gaining insights into how it can become dysfunctional and cause disease. These findings may therefore have important implications for research into areas such as infertility, reproductive medicine and rare genetic diseases.
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Affiliation(s)
- Kehui Xiang
- Howard Hughes Medical Institute, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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25
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Voronina AS, Pshennikova ES. mRNPs: Structure and role in development. Cell Biochem Funct 2021; 39:832-843. [PMID: 34212408 DOI: 10.1002/cbf.3656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/05/2021] [Accepted: 06/17/2021] [Indexed: 11/11/2022]
Abstract
In eukaryotic cells, mRNA molecules are coated with numerous RNA-binding proteins and so exist in ribonucleoproteins (mRNPs). The proteins associated with the mRNA regulate the fate of mRNA, including its localization, translation and decay. Before activation of translation, the mRNA does not display any template functions-it is masked. The coordinated activity of certain RNA-binding proteins determines the future fate of each mRNA individually. In embryo development, the temporal and spatial regulation of translation can cause a situation when the mRNA and the encoded protein are localized in different compartments and so the differentiation of the cells can be determined. The fundamentals of regulation of the mRNAs fate and functioning in nerves are similar to those already described for oo- and embryogenesis. Disorders in the mRNA masking and demasking result in the emergence of various diseases, in particular cancers and neuro-degenerative diseases.
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Affiliation(s)
- Anna S Voronina
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena S Pshennikova
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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26
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Norris K, Hopes T, Aspden JL. Ribosome heterogeneity and specialization in development. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1644. [PMID: 33565275 PMCID: PMC8647923 DOI: 10.1002/wrna.1644] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Regulation of protein synthesis is a vital step in controlling gene expression, especially during development. Over the last 10 years, it has become clear that rather than being homogeneous machines responsible for mRNA translation, ribosomes are highly heterogeneous and can play an active part in translational regulation. These "specialized ribosomes" comprise of specific protein and/or rRNA components, which are required for the translation of particular mRNAs. However, while there is extensive evidence for ribosome heterogeneity, support for specialized functions is limited. Recent work in a variety of developmental model organisms has shed some light on the biological relevance of ribosome heterogeneity. Tissue-specific expression of ribosomal components along with phenotypic analysis of ribosomal gene mutations indicate that ribosome heterogeneity and potentially specialization are common in key development processes like embryogenesis, spermatogenesis, oogenesis, body patterning, and neurogenesis. Several examples of ribosome specialization have now been proposed but strong links between ribosome heterogeneity, translation of specific mRNAs by defined mechanisms, and role of these translation events remain elusive. Furthermore, several studies have indicated that heterogeneous ribosome populations are a product of tissue-specific expression rather than specialized function and that ribosomal protein phenotypes are the result of extra-ribosomal function or overall reduced ribosome levels. Many important questions still need to be addressed in order to determine the functional importance of ribosome heterogeneity to development and disease, which is likely to vary across systems. It will be essential to dissect these issues to fully understand diseases caused by disruptions to ribosomal composition, such as ribosomopathies. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Structure/Function RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Karl Norris
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Julie Louise Aspden
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
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27
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Na Y, Kim H, Choi Y, Shin S, Jung JH, Kwon SC, Kim VN, Kim JS. FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo. Nucleic Acids Res 2021; 49:e28. [PMID: 33332543 PMCID: PMC7968992 DOI: 10.1093/nar/gkaa1194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 11/11/2020] [Accepted: 11/24/2020] [Indexed: 02/05/2023] Open
Abstract
RNA-protein interaction is central to post-transcriptional gene regulation. Identification of RNA-binding proteins relies mainly on UV-induced crosslinking (UVX) followed by the enrichment of RNA-protein conjugates and LC-MS/MS analysis. However, UVX has limited applicability in tissues of multicellular organisms due to its low penetration depth. Here, we introduce formaldehyde crosslinking (FAX) as an alternative chemical crosslinking for RNA interactome capture (RIC). Mild FAX captures RNA-protein interaction with high specificity and efficiency in cell culture. Unlike UVX-RIC, FAX-RIC robustly detects proteins that bind to structured RNAs or uracil-poor RNAs (e.g. AGO1, STAU1, UPF1, NCBP2, EIF4E, YTHDF proteins and PABP), broadening the coverage. Applied to Xenopus laevis oocytes and embryos, FAX-RIC provided comprehensive and unbiased RNA interactome, revealing dynamic remodeling of RNA-protein complexes. Notably, translation machinery changes during oocyte-to-embryo transition, for instance, from canonical eIF4E to noncanonical eIF4E3. Furthermore, using Mus musculus liver, we demonstrate that FAX-RIC is applicable to mammalian tissue samples. Taken together, we report that FAX can extend the RNA interactome profiling into multicellular organisms.
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Affiliation(s)
- Yongwoo Na
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyunjoon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jae Hun Jung
- Department of Applied Chemistry, Kyung Hee University, Yongin 17104, Korea
| | - S Chul Kwon
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea.,School of Biological Sciences, 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
| | - Jong-Seo 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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28
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Ma XY, Zhang H, Feng JX, Hu JL, Yu B, Luo L, Cao YL, Liao S, Wang J, Gao S. Structures of mammalian GLD-2 proteins reveal molecular basis of their functional diversity in mRNA and microRNA processing. Nucleic Acids Res 2020; 48:8782-8795. [PMID: 32633758 PMCID: PMC7470959 DOI: 10.1093/nar/gkaa578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/20/2020] [Accepted: 07/03/2020] [Indexed: 11/12/2022] Open
Abstract
The stability and processing of cellular RNA transcripts are efficiently controlled via non-templated addition of single or multiple nucleotides, which is catalyzed by various nucleotidyltransferases including poly(A) polymerases (PAPs). Germline development defective 2 (GLD-2) is among the first reported cytoplasmic non-canonical PAPs that promotes the translation of germline-specific mRNAs by extending their short poly(A) tails in metazoan, such as Caenorhabditis elegans and Xenopus. On the other hand, the function of mammalian GLD-2 seems more diverse, which includes monoadenylation of certain microRNAs. To understand the structural basis that underlies the difference between mammalian and non-mammalian GLD-2 proteins, we determine crystal structures of two rodent GLD-2s. Different from C. elegans GLD-2, mammalian GLD-2 is an intrinsically robust PAP with an extensively positively charged surface. Rodent and C. elegans GLD-2s have a topological difference in the β-sheet region of the central domain. Whereas C. elegans GLD-2 prefers adenosine-rich RNA substrates, mammalian GLD-2 can work on RNA oligos with various sequences. Coincident with its activity on microRNAs, mammalian GLD-2 structurally resembles the mRNA and miRNA processor terminal uridylyltransferase 7 (TUT7). Our study reveals how GLD-2 structurally evolves to a more versatile nucleotidyltransferase, and provides important clues in understanding its biological function in mammals.
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Affiliation(s)
- Xiao-Yan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Hong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Jian-Xiong Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Jia-Li Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Bing Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Li Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Yu-Lu Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Shuang Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Jichang Wang
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.,Department of histology and embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510530, China
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29
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Yan YB. Diverse functions of deadenylases in DNA damage response and genomic integrity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1621. [PMID: 32790161 DOI: 10.1002/wrna.1621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022]
Abstract
DNA damage response (DDR) is a coordinated network of diverse cellular processes including the detection, signaling, and repair of DNA lesions, the adjustment of metabolic network and cell fate determination. To deal with the unavoidable DNA damage caused by either endogenous or exogenous stresses, the cells need to reshape the gene expression profile to allow efficient transcription and translation of DDR-responsive messenger RNAs (mRNAs) and to repress the nonessential mRNAs. A predominant method to adjust RNA fate is achieved by modulating the 3'-end oligo(A) or poly(A) length via the opposing actions of polyadenylation and deadenylation. Poly(A)-specific ribonuclease (PARN) and the carbon catabolite repressor 4 (CCR4)-Not complex, the major executors of deadenylation, are indispensable to DDR and genomic integrity in eukaryotic cells. PARN modulates cell cycle progression by regulating the stabilities of mRNAs and microRNA (miRNAs) involved in the p53 pathway and contributes to genomic stability by affecting the biogenesis of noncoding RNAs including miRNAs and telomeric RNA. The CCR4-Not complex is involved in diverse pathways of DDR including transcriptional regulation, signaling pathways, mRNA stabilities, translation regulation, and protein degradation. The RNA targets of deadenylases are tuned by the DDR signaling pathways, while in turn the deadenylases can regulate the levels of DNA damage-responsive proteins. The mutual feedback between deadenylases and the DDR signaling pathways allows the cells to precisely control DDR by dynamically adjusting the levels of sensors and effectors of the DDR signaling pathways. Here, the diverse functions of deadenylases in DDR are summarized and the underlying mechanisms are proposed according to recent findings. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
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30
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Luong XG, Daldello EM, Rajkovic G, Yang CR, Conti M. Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption. Nucleic Acids Res 2020; 48:3257-3276. [PMID: 31970406 PMCID: PMC7102970 DOI: 10.1093/nar/gkaa010] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/27/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022] Open
Abstract
During oocyte maturation, changes in gene expression depend exclusively on translation and degradation of maternal mRNAs rather than transcription. Execution of this translation program is essential for assembling the molecular machinery required for meiotic progression, fertilization, and embryo development. With the present study, we used a RiboTag/RNA-Seq approach to explore the timing of maternal mRNA translation in quiescent oocytes as well as in oocytes progressing through the first meiotic division. This genome-wide analysis reveals a global switch in maternal mRNA translation coinciding with oocyte re-entry into the meiotic cell cycle. Messenger RNAs whose translation is highly active in quiescent oocytes invariably become repressed during meiotic re-entry, whereas transcripts repressed in quiescent oocytes become activated. Experimentally, we have defined the exact timing of the switch and the repressive function of CPE elements, and identified a novel role for CPEB1 in maintaining constitutive translation of a large group of maternal mRNAs during maturation.
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Affiliation(s)
- Xuan G Luong
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Enrico Maria Daldello
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Gabriel Rajkovic
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Cai-Rong Yang
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Marco Conti
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
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31
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Ganesh S, Horvat F, Drutovic D, Efenberkova M, Pinkas D, Jindrova A, Pasulka J, Iyyappan R, Malik R, Susor A, Vlahovicek K, Solc P, Svoboda P. The most abundant maternal lncRNA Sirena1 acts post-transcriptionally and impacts mitochondrial distribution. Nucleic Acids Res 2020; 48:3211-3227. [PMID: 31956907 PMCID: PMC7102984 DOI: 10.1093/nar/gkz1239] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/10/2019] [Accepted: 01/02/2020] [Indexed: 12/13/2022] Open
Abstract
Tens of thousands of rapidly evolving long non-coding RNA (lncRNA) genes have been identified, but functions were assigned to relatively few of them. The lncRNA contribution to the mouse oocyte physiology remains unknown. We report the evolutionary history and functional analysis of Sirena1, the most expressed lncRNA and the 10th most abundant poly(A) transcript in mouse oocytes. Sirena1 appeared in the common ancestor of mouse and rat and became engaged in two different post-transcriptional regulations. First, antisense oriented Elob pseudogene insertion into Sirena1 exon 1 is a source of small RNAs targeting Elob mRNA via RNA interference. Second, Sirena1 evolved functional cytoplasmic polyadenylation elements, an unexpected feature borrowed from translation control of specific maternal mRNAs. Sirena1 knock-out does not affect fertility, but causes minor dysregulation of the maternal transcriptome. This includes increased levels of Elob and mitochondrial mRNAs. Mitochondria in Sirena1−/− oocytes disperse from the perinuclear compartment, but do not change in number or ultrastructure. Taken together, Sirena1 contributes to RNA interference and mitochondrial aggregation in mouse oocytes. Sirena1 exemplifies how lncRNAs stochastically engage or even repurpose molecular mechanisms during evolution. Simultaneously, Sirena1 expression levels and unique functional features contrast with the lack of functional importance assessed under laboratory conditions.
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Affiliation(s)
- Sravya Ganesh
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Filip Horvat
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia
| | - David Drutovic
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Michaela Efenberkova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dominik Pinkas
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Anna Jindrova
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Josef Pasulka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Rajan Iyyappan
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Andrej Susor
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia
| | - Petr Solc
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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32
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Nousch M, Yeroslaviz A, Eckmann CR. Stage-specific combinations of opposing poly(A) modifying enzymes guide gene expression during early oogenesis. Nucleic Acids Res 2020; 47:10881-10893. [PMID: 31511882 PMCID: PMC6845980 DOI: 10.1093/nar/gkz787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 11/14/2022] Open
Abstract
RNA-modifying enzymes targeting mRNA poly(A) tails are universal regulators of post-transcriptional gene expression programs. Current data suggest that an RNA-binding protein (RBP) directed tug-of-war between tail shortening and re-elongating enzymes operates in the cytoplasm to repress or activate specific mRNA targets. While this concept is widely accepted, it was primarily described in the final meiotic stages of frog oogenesis and relies molecularly on a single class of RBPs, i.e. CPEBs, the deadenylase PARN and cytoplasmic poly(A) polymerase GLD-2. Using the spatial and temporal resolution of female gametogenesis in the nematode C. elegans, we determined the distinct roles of known deadenylases throughout germ cell development and discovered that the Ccr4-Not complex is the main antagonist to GLD-2-mediated mRNA regulation. We find that the Ccr4-Not/GLD-2 balance is critical for essentially all steps of oocyte production and reiteratively employed by various classes of RBPs. Interestingly, its two deadenylase subunits appear to affect mRNAs stage specifically: while a Caf1/GLD-2 antagonism regulates mRNA abundance during all stages of oocyte production, a Ccr4/GLD-2 antagonism regulates oogenesis in an mRNA abundance independent manner. Our combined data suggests that the Ccr4-Not complex represents the evolutionarily conserved molecular opponent to GLD-2 providing an antagonistic framework of gene-specific poly(A)-tail regulation.
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Affiliation(s)
- Marco Nousch
- Developmental Genetics, Institute of Biology, Martin Luther University Halle-Wittenberg (MLU), Weinbergweg 10, Halle (Saale) 06120, Germany
| | - Assa Yeroslaviz
- Max Planck Institute of Biochemistry (MPIB), Am Klopferspitz 18, Martinsried 82152, Germany
| | - Christian R Eckmann
- Developmental Genetics, Institute of Biology, Martin Luther University Halle-Wittenberg (MLU), Weinbergweg 10, Halle (Saale) 06120, Germany
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Waltero C, Martins R, Calixto C, da Fonseca RN, Abreu LAD, da Silva Vaz I, Logullo C. The hallmarks of GSK-3 in morphogenesis and embryonic development metabolism in arthropods. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 118:103307. [PMID: 31857215 DOI: 10.1016/j.ibmb.2019.103307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 11/26/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Several research groups around the world have studied diverse aspects of energy metabolism in arthropod disease vectors, with the aim of discovering potential control targets. As in all oviparous organisms, arthropod embryonic development is characterized by the mobilization of maternally-derived metabolites for the formation of new tissues and organs. Glycogen synthase kinase-3 (GSK-3) is a serine-threonine kinase described as an important regulator of metabolism and development in a wide range of organisms. GSK-3 was first identified based on its action upon glycogen synthase, a central enzyme in glycogen biosynthesis. Currently, it is recognized as a key component of multiple cellular processes such as glucose metabolism, apoptosis, cell proliferation, transcription, cell migration, and immune response. The present review will describe the current knowledge on GSK-3 activation and its role in morphogenesis and embryonic metabolism in arthropods. Altogether, the information discussed here can spark new approaches and strategies for further studies, enhancing our understanding of these important arthropod vectors and strengthening the resources in the search for novel control methods.
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Affiliation(s)
- Camila Waltero
- Instituto de Biodiversidade e Sustentabilidade NUPEM, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil
| | - Renato Martins
- Instituto de Biodiversidade e Sustentabilidade NUPEM, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil
| | - Christiano Calixto
- Instituto de Biodiversidade e Sustentabilidade NUPEM, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil
| | - Rodrigo Nunes da Fonseca
- Instituto de Biodiversidade e Sustentabilidade NUPEM, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Brazil
| | - Leonardo Araujo de Abreu
- Instituto de Biodiversidade e Sustentabilidade NUPEM, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Brazil
| | - Itabajara da Silva Vaz
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Brazil; Centro de Biotecnologia and Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Brazil
| | - Carlos Logullo
- Instituto de Biodiversidade e Sustentabilidade NUPEM, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Brazil.
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Yang F, Wang W, Cetinbas M, Sadreyev RI, Blower MD. Genome-wide analysis identifies cis-acting elements regulating mRNA polyadenylation and translation during vertebrate oocyte maturation. RNA (NEW YORK, N.Y.) 2020; 26:324-344. [PMID: 31896558 PMCID: PMC7025505 DOI: 10.1261/rna.073247.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/30/2019] [Indexed: 05/10/2023]
Abstract
Most cells change patterns of gene expression through transcriptional regulation. In contrast, oocytes are transcriptionally silent and regulate mRNA poly(A) tail length to control protein production. However, the genome-wide relationship of poly(A) tail changes to mRNA translation during vertebrate oocyte maturation is not known. We used Tail-seq and polyribosome analysis to measure poly(A) tail and translational changes during oocyte maturation in Xenopus laevis We identified large-scale poly(A) and translational changes during oocyte maturation, with poly(A) tail length changes preceding translational changes. Proteins important for completion of the meiotic divisions and early development exhibited increased polyadenylation and translation during oocyte maturation. A family of U-rich sequence elements was enriched near the polyadenylation signal of polyadenylated and translationally activated mRNAs. We propose that changes in mRNA polyadenylation are a conserved mechanism regulating protein expression during vertebrate oocyte maturation and that these changes are controlled by a spatial code of cis-acting sequence elements.
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Affiliation(s)
- Fei Yang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wei Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Zebrafish embryogenesis – A framework to study regulatory RNA elements in development and disease. Dev Biol 2020; 457:172-180. [DOI: 10.1016/j.ydbio.2019.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/26/2022]
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Flora P, Wong-Deyrup SW, Martin ET, Palumbo RJ, Nasrallah M, Oligney A, Blatt P, Patel D, Fuchs G, Rangan P. Sequential Regulation of Maternal mRNAs through a Conserved cis-Acting Element in Their 3' UTRs. Cell Rep 2019; 25:3828-3843.e9. [PMID: 30590052 PMCID: PMC6328254 DOI: 10.1016/j.celrep.2018.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/28/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022] Open
Abstract
Maternal mRNAs synthesized during oogenesis initiate the development of future generations. Some maternal mRNAs are either somatic or germline determinants and must be translationally repressed until embryogenesis. However, the translational repressors themselves are temporally regulated. We used polar granule component (pgc), a Drosophila maternal mRNA, to ask how maternal transcripts are repressed while the regulatory landscape is shifting. pgc, a germline determinant, is translationally regulated throughout oogenesis. We find that different conserved RNA-binding proteins bind a 10-nt sequence in the 3′ UTR of pgc mRNA to continuously repress translation at different stages of oogenesis. Pumilio binds to this sequence in undifferentiated and early-differentiating oocytes to block Pgc translation. After differentiation, Bruno levels increase, allowing Bruno to bind the same sequence and take over translational repression of pgc mRNA. We have identified a class of maternal mRNAs that are regulated similarly, including zelda, the activator of the zygotic genome. Flora et al. show that pgc, a germline determinant, is translationally regulated throughout oogenesis. Different conserved RBPs bind a 10-nt sequence in the 3′ UTR to continuously repress translation throughout oogenesis. This mode of regulation applies to a class of maternal mRNAs, including zelda, the activator of the zygotic genome.
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Affiliation(s)
- Pooja Flora
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Siu Wah Wong-Deyrup
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Elliot Todd Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Ryan J Palumbo
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Mohamad Nasrallah
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Andrew Oligney
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Dhruv Patel
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Gabriele Fuchs
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA.
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Blatt P, Martin ET, Breznak SM, Rangan P. Post-transcriptional gene regulation regulates germline stem cell to oocyte transition during Drosophila oogenesis. Curr Top Dev Biol 2019; 140:3-34. [PMID: 32591078 DOI: 10.1016/bs.ctdb.2019.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
During oogenesis, several developmental processes must be traversed to ensure effective completion of gametogenesis including, stem cell maintenance and asymmetric division, differentiation, mitosis and meiosis, and production of maternally contributed mRNAs, making the germline a salient model for understanding how cell fate transitions are mediated. Due to silencing of the genome during meiotic divisions, there is little instructive transcription, barring a few examples, to mediate these critical transitions. In Drosophila, several layers of post-transcriptional regulation ensure that the mRNAs required for these processes are expressed in a timely manner and as needed during germline differentiation. These layers of regulation include alternative splicing, RNA modification, ribosome production, and translational repression. Many of the molecules and pathways involved in these regulatory activities are conserved from Drosophila to humans making the Drosophila germline an elegant model for studying the role of post-transcriptional regulation during stem cell differentiation and meiosis.
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Affiliation(s)
- Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States
| | - Elliot T Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States
| | - Shane M Breznak
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY, United States; University at Albany SUNY, Albany, NY, United States.
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Zeng SL, Sudlow LC, Berezin MY. Using Xenopus oocytes in neurological disease drug discovery. Expert Opin Drug Discov 2019; 15:39-52. [PMID: 31674217 DOI: 10.1080/17460441.2020.1682993] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Introduction: Neurological diseases present a difficult challenge in drug discovery. Many of the current treatments have limited efficiency or result in a variety of debilitating side effects. The search of new therapies is of a paramount importance, since the number of patients that require a better treatment is growing rapidly. As an in vitro model, Xenopus oocytes provide the drug developer with many distinct advantages, including size, durability, and efficiency in exogenous protein expression. However, there is an increasing need to refine the recent breakthroughs.Areas covered: This review covers the usage and recent advancements of Xenopus oocytes for drug discovery in neurological diseases from expression and functional measurement techniques to current applications in Alzheimer's disease, painful neuropathies, and amyotrophic lateral sclerosis (ALS). The existing limitations of Xenopus oocytes in drug discovery are also discussed.Expert opinion: With the rise of aging population and neurological disorders, Xenopus oocytes, will continue to play an important role in understanding the mechanism of the disease, identification and validation of novel molecular targets, and drug screening, providing high-quality data despite the technical limitations. With further advances in oocytes-related techniques toward an accurate modeling of the disease, the diagnostics and treatment of neuropathologies will be becoming increasing personalized.
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Affiliation(s)
- Steven L Zeng
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Leland C Sudlow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mikhail Y Berezin
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
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Bezerra FTG, Lima FEO, Paulino LRFM, Silva BR, Silva AWB, Souza ALP, van den Hurk R, Silva JRV. In vitro culture of secondary follicles and prematuration of cumulus-oocyte complexes from antral follicles increase the levels of maturation-related transcripts in bovine oocytes. Mol Reprod Dev 2019; 86:1874-1886. [PMID: 31621988 DOI: 10.1002/mrd.23284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/02/2019] [Indexed: 11/11/2022]
Abstract
This study evaluates the levels of messenger RNA (mRNA) for eIF4E, PARN, H1FOO, cMOS, GDF9, and CCNB1 in oocytes from secondary and antral follicles at different stages of development. The effects of in vitro culture, in vitro prematuration, and in vitro maturation on the expression of these genes on oocytes were also analyzed. The results showed that mRNA levels for H1FOO, GDF9, and PARN were higher in oocytes from small, medium, and large antral follicles, respectively, than those seen in secondary follicles. Oocytes from small, medium, and large antral follicles had higher levels of CCNB1 than oocytes from secondary follicles. Oocytes from cultured secondary follicles had higher levels of GDF9, CMOS, PARN, eIF4E, CCNB1, and H1FOO than before culture. Prematured oocytes from small antral follicles had higher levels of mRNA for GDF9, PARN, and eIF4E than before culture. In addition, higher levels of cMOS and H1FOO were identified in prematured oocytes from medium antral follicles. In conclusion, follicular growth is associated with an increase in the expression of H1FOO, GDF9, CCNB1, and PARN. The culture of secondary follicles, prematuration, and maturation of oocytes from antral follicles increase the expression of eIF4E, PARN, H1FOO, cMOS, GDF9, and CCNB1.
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Affiliation(s)
- Francisco Taiã G Bezerra
- Laboratory of Biotechnology and Physiology of Reproduction (LABIREP), Federal University of Ceara, Sobral-CE, Brazil
| | - Francisco Edilcarlos O Lima
- Laboratory of Biotechnology and Physiology of Reproduction (LABIREP), Federal University of Ceara, Sobral-CE, Brazil
| | - Laís Rayani F M Paulino
- Laboratory of Biotechnology and Physiology of Reproduction (LABIREP), Federal University of Ceara, Sobral-CE, Brazil
| | - Bianca R Silva
- Laboratory of Biotechnology and Physiology of Reproduction (LABIREP), Federal University of Ceara, Sobral-CE, Brazil
| | - Anderson W B Silva
- Laboratory of Biotechnology and Physiology of Reproduction (LABIREP), Federal University of Ceara, Sobral-CE, Brazil
| | - Ana Liza P Souza
- Laboratory of Biotechnology and Physiology of Reproduction (LABIREP), Federal University of Ceara, Sobral-CE, Brazil
| | - Robert van den Hurk
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - José Roberto V Silva
- Laboratory of Biotechnology and Physiology of Reproduction (LABIREP), Federal University of Ceara, Sobral-CE, Brazil
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Anda S, Grallert B. Cell-Cycle-Dependent Regulation of Translation: New Interpretations of Old Observations in Light of New Approaches. Bioessays 2019; 41:e1900022. [PMID: 31210378 DOI: 10.1002/bies.201900022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/29/2019] [Indexed: 12/22/2022]
Abstract
It is a long-standing view that global translation varies during the cell cycle and is much lower in mitosis than in other cell-cycle phases. However, the central papers in the literature are not in agreement about the extent of downregulation in mitosis, ranging from a dramatic decrease to only a marginal reduction. Herein, it is argued that the discrepancy derives from technical challenges. Cell-cycle-dependent variations are most conveniently studied in synchronized cells, but the synchronization methods by themselves often evoke stress responses that, in turn, affect translation rates. Further, it is argued that previously reported cell-cycle-dependent changes in the global translation rate to a large extent reflect responses to the synchronization methods. Recent findings strongly suggest that the global translation rate is not regulated in a cell-cycle-dependent manner. Novel techniques allowing a genome-wide analysis of translational profiles suggest that the extent and importance of selective translational regulation associated with cell-cycle transitions have been underestimated. Therefore, the main question is which messenger RNAs (mRNAs) are translated, rather than whether the global translation rate is decreased.
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Affiliation(s)
- Silje Anda
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
| | - Beáta Grallert
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
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41
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Nelms B, Walbot V. Defining the developmental program leading to meiosis in maize. Science 2019; 364:52-56. [DOI: 10.1126/science.aav6428] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 03/01/2019] [Indexed: 01/22/2023]
Abstract
In multicellular organisms, the entry into meiosis is a complex process characterized by increasing meiotic specialization. Using single-cell RNA sequencing, we reconstructed the developmental program into maize male meiosis. A smooth continuum of expression stages before meiosis was followed by a two-step transcriptome reorganization in leptotene, during which 26.7% of transcripts changed in abundance by twofold or more. Analysis of cell-cycle gene expression indicated that nearly all pregerminal cells proliferate, eliminating a stem-cell model to generate meiotic cells. Mutants defective in somatic differentiation or meiotic commitment expressed transcripts normally present in early meiosis after a delay; thus, the germinal transcriptional program is cell autonomous and can proceed despite meiotic failure.
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42
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Karlic R, Ganesh S, Franke V, Svobodova E, Urbanova J, Suzuki Y, Aoki F, Vlahovicek K, Svoboda P. Long non-coding RNA exchange during the oocyte-to-embryo transition in mice. DNA Res 2018; 24:129-141. [PMID: 28087610 PMCID: PMC5397607 DOI: 10.1093/dnares/dsw058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/28/2016] [Indexed: 01/02/2023] Open
Abstract
The oocyte-to-embryo transition (OET) transforms a differentiated gamete into pluripotent blastomeres. The accompanying maternal-zygotic RNA exchange involves remodeling of the long non-coding RNA (lncRNA) pool. Here, we used next generation sequencing and de novo transcript assembly to define the core population of 1,600 lncRNAs expressed during the OET (lncRNAs). Relative to mRNAs, OET lncRNAs were less expressed and had shorter transcripts, mainly due to fewer exons and shorter 5′ terminal exons. Approximately half of OET lncRNA promoters originated in retrotransposons suggesting their recent emergence. Except for a small group of ubiquitous lncRNAs, maternal and zygotic lncRNAs formed two distinct populations. The bulk of maternal lncRNAs was degraded before the zygotic genome activation. Interestingly, maternal lncRNAs seemed to undergo cytoplasmic polyadenylation observed for dormant mRNAs. We also identified lncRNAs giving rise to trans-acting short interfering RNAs, which represent a novel lncRNA category. Altogether, we defined the core OET lncRNA transcriptome and characterized its remodeling during early development. Our results are consistent with the notion that rapidly evolving lncRNAs constitute signatures of cells-of-origin while a minority plays an active role in control of gene expression across OET. Our data presented here provide an excellent source for further OET lncRNA studies.
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Affiliation(s)
- Rosa Karlic
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Sravya Ganesh
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Vedran Franke
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Eliska Svobodova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Jana Urbanova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
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43
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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Kalous J, Tetkova A, Kubelka M, Susor A. Importance of ERK1/2 in Regulation of Protein Translation during Oocyte Meiosis. Int J Mol Sci 2018; 19:ijms19030698. [PMID: 29494492 PMCID: PMC5877559 DOI: 10.3390/ijms19030698] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 02/07/2023] Open
Abstract
Although the involvement of the extracellular signal-regulated kinases 1 and 2 (ERK1/2) pathway in the regulation of cytostatic factor (CSF) activity; as well as in microtubules organization during meiotic maturation of oocytes; has already been described in detail; rather less attention has been paid to the role of ERK1/2 in the regulation of mRNA translation. However; important data on the role of ERK1/2 in translation during oocyte meiosis have been documented. This review focuses on recent findings regarding the regulation of translation and the role of ERK1/2 in this process in the meiotic cycle of mammalian oocytes. The specific role of ERK1/2 in the regulation of mammalian target of rapamycin (mTOR); eukaryotic translation initiation factor 4E (eIF4E) and cytoplasmic polyadenylation element binding protein 1 (CPEB1) activity is addressed along with additional focus on the other key players involved in protein translation.
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Affiliation(s)
- Jaroslav Kalous
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburska 89, 27721 Libechov, Czech Republic.
| | - Anna Tetkova
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburska 89, 27721 Libechov, Czech Republic.
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Albertov 6, 12843 Prague 2, Czech Republic.
| | - Michal Kubelka
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburska 89, 27721 Libechov, Czech Republic.
| | - Andrej Susor
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburska 89, 27721 Libechov, Czech Republic.
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Vimal D, Kumar S, Pandey A, Sharma D, Saini S, Gupta S, Ravi Ram K, Chowdhuri DK. Mlh1 is required for female fertility in Drosophila melanogaster: An outcome of effects on meiotic crossing over, ovarian follicles and egg activation. Eur J Cell Biol 2018; 97:75-89. [DOI: 10.1016/j.ejcb.2017.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/29/2017] [Accepted: 12/15/2017] [Indexed: 10/18/2022] Open
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MAPK signaling couples SCF-mediated degradation of translational regulators to oocyte meiotic progression. Proc Natl Acad Sci U S A 2018; 115:E2772-E2781. [PMID: 29496961 DOI: 10.1073/pnas.1715439115] [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] [Indexed: 12/17/2022] Open
Abstract
RNA-binding proteins (RBPs) are important regulators of gene expression programs, especially during gametogenesis. How the abundance of particular RBPs is restricted to defined stages of meiosis remains largely elusive. Here, we report a molecular pathway that subjects two nonrelated but broadly evolutionarily conserved translational regulators (CPB-3/CPEB and GLD-1/STAR) to proteosomal degradation in Caenorhabditis elegans germ cells at the transition from pachytene to diplotene of meiotic prophase. Both RBPs are recognized by the same ubiquitin ligase complex, containing the molecular scaffold Cullin-1 and the tumor suppressor SEL-10/FBXW7 as its substrate recognition subunit. Destabilization of either RBP through this Skp, Cullin, F-box-containing complex (SCF) ubiquitin ligase appears to loosen its negative control over established target mRNAs, and presumably depends on a prior phosphorylation of CPB-3 and GLD-1 by MAPK (MPK-1), whose activity increases in mid- to late pachytene to promote meiotic progression and oocyte differentiation. Thus, we propose that the orchestrated degradation of RBPs via MAPK-signaling cascades during germ cell development may act to synchronize meiotic with sexual differentiation gene expression changes.
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Skeparnias I, Αnastasakis D, Shaukat AN, Grafanaki K, Stathopoulos C. Expanding the repertoire of deadenylases. RNA Biol 2017; 14:1320-1325. [PMID: 28267419 PMCID: PMC5711463 DOI: 10.1080/15476286.2017.1300222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/13/2017] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Deadenylases belong to an expanding family of exoribonucleases involved mainly in mRNA stability and turnover, with the exception of PARN which has additional roles in the biogenesis of several important non-coding RNAs, including miRNAs and piRNAs. Recently, PARN in C. elegans and its homolog PNLDC1 in B. mori were reported as the elusive trimmers mediating piRNA biogenesis. In addition, characterization of mammalian PNLDC1 in comparison to PARN, showed that is specifically expressed in embryonic stem and germ cells, as well as during early embryo development. Moreover, its expression is correlated with epigenetic events mediated by the de novo DNMT3b methyltransferase and knockdown in stem cells upregulates important genes that regulate multipotency. The recent data suggest that at least some new deadenylases may have expanded roles in cell metabolism as regulators of gene expression, through mRNA deadenylation, ncRNAs biogenesis and ncRNA-mediated mRNA targeting, linking essential mechanisms that regulate epigenetic control and transition events during differentiation. The possible roles of mammalian PNLDC1 along those dynamic networks are discussed in the light of new extremely important findings.
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Affiliation(s)
- Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, Greece
| | | | | | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, Greece
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Long and small noncoding RNAs during oocyte-to-embryo transition in mammals. Biochem Soc Trans 2017; 45:1117-1124. [PMID: 28939692 DOI: 10.1042/bst20170033] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 02/07/2023]
Abstract
Oocyte-to-embryo transition is a process during which an oocyte ovulates, is fertilized, and becomes a developing embryo. It involves the first major genome reprogramming event in life of an organism where gene expression, which gave rise to a differentiated oocyte, is remodeled in order to establish totipotency in blastomeres of an early embryo. This remodeling involves replacement of maternal RNAs with zygotic RNAs through maternal RNA degradation and zygotic genome activation. This review is focused on expression and function of long noncoding RNAs (lncRNAs) and small RNAs during oocyte-to-embryo transition in mammals. LncRNAs are an assorted rapidly evolving collection of RNAs, which have no apparent protein-coding capacity. Their biogenesis is similar to mRNAs including transcriptional control and post-transcriptional processing. Diverse molecular and biological roles were assigned to lncRNAs although most of them probably did not acquire a detectable biological role. Since some lncRNAs serve as precursors for small noncoding regulatory RNAs in RNA silencing pathways, both types of noncoding RNA are reviewed together.
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49
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Aguero T, Jin Z, Chorghade S, Kalsotra A, King ML, Yang J. Maternal Dead-end 1 promotes translation of nanos1 by binding the eIF3 complex. Development 2017; 144:3755-3765. [PMID: 28870987 DOI: 10.1242/dev.152611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/22/2017] [Indexed: 12/30/2022]
Abstract
In the developing embryo, primordial germ cells (PGCs) represent the exclusive progenitors of the gametes, and their loss results in adult infertility. During early development, PGCs are exposed to numerous signals that specify somatic cell fates. To prevent somatic differentiation, PGCs must transiently silence their genome, an early developmental process that requires Nanos activity. However, it is unclear how Nanos translation is regulated in developing embryos. We report here that translation of nanos1 after fertilization requires Dead-end 1 (Dnd1), a vertebrate-specific germline RNA-binding protein. We provide evidence that Dnd1 protein, expression of which is low in oocytes, but increases dramatically after fertilization, directly interacts with, and relieves the inhibitory function of eukaryotic initiation factor 3f, a repressive component in the 43S preinitiation complex. This work uncovers a novel translational regulatory mechanism that is fundamentally important for germline development.
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Affiliation(s)
- Tristan Aguero
- Department of Cell Biology, University of Miami, Miami, FL 33136, USA
| | - Zhigang Jin
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
| | - Sandip Chorghade
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mary Lou King
- Department of Cell Biology, University of Miami, Miami, FL 33136, USA
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, IL 61802, USA
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Boateng R, Nguyen KCQ, Hall DH, Golden A, Allen AK. Novel functions for the RNA-binding protein ETR-1 in Caenorhabditis elegans reproduction and engulfment of germline apoptotic cell corpses. Dev Biol 2017; 429:306-320. [PMID: 28648844 PMCID: PMC5603194 DOI: 10.1016/j.ydbio.2017.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 01/31/2023]
Abstract
RNA-binding proteins (RBPs) are essential regulators of gene expression that act through a variety of mechanisms to ensure the proper post-transcriptional regulation of their target RNAs. RBPs in multiple species have been identified as playing crucial roles during development and as having important functions in various adult organ systems, including the heart, nervous, muscle, and reproductive systems. ETR-1, a highly conserved ELAV-Type RNA-binding protein belonging to the CELF/Bruno protein family, has been previously reported to be involved in C. elegans muscle development. Animals depleted of ETR-1 have been previously characterized as arresting at the two-fold stage of embryogenesis. In this study, we show that ETR-1 is expressed in the hermaphrodite somatic gonad and germ line, and that reduction of ETR-1 via RNA interference (RNAi) results in reduced hermaphrodite fecundity. Detailed characterization of this fertility defect indicates that ETR-1 is required in both the somatic tissue and the germ line to ensure wild-type reproductive levels. Additionally, the ability of ETR-1 depletion to suppress the published WEE-1.3-depletion infertility phenotype is dependent on ETR-1 being reduced in the soma. Within the germline of etr-1(RNAi) hermaphrodite animals, we observe a decrease in average oocyte size and an increase in the number of germline apoptotic cell corpses as evident by an increased number of CED-1::GFP and acridine orange positive apoptotic germ cells. Transmission Electron Microscopy (TEM) studies confirm the significant increase in apoptotic cells in ETR-1-depleted animals, and reveal a failure of the somatic gonadal sheath cells to properly engulf dying germ cells in etr-1(RNAi) animals. Through investigation of an established engulfment pathway in C. elegans, we demonstrate that co-depletion of CED-1 and ETR-1 suppresses both the reduced fecundity and the increase in the number of apoptotic cell corpses observed in etr-1(RNAi) animals. Combined, this data identifies a novel role for ETR-1 in hermaphrodite gametogenesis and in the process of engulfment of germline apoptotic cell corpses.
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Affiliation(s)
- Ruby Boateng
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Ken C Q Nguyen
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - David H Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Andy Golden
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna K Allen
- Department of Biology, Howard University, Washington, DC 20059, USA
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