51
|
Induced androgenetic development in rainbow trout and transcriptome analysis of irradiated eggs. Sci Rep 2019; 9:8084. [PMID: 31147623 PMCID: PMC6542805 DOI: 10.1038/s41598-019-44568-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Ionizing radiation is administered to damage nuclear genome in fish eggs during induced androgenesis. In this study, we examined whether 350 Gy of X-ray applied to damage chromosomes in the rainbow trout eggs affects maternal RNA. Shortly after irradiation, we did not find any symptoms of RNA degradation in the treated eggs. Significant (p < 0.01) differences between non-irradiated and irradiated eggs concerned only a few transcripts including increased expression of immediate early response 2 (IER2) and early growth response 1 (EGR1) genes observed in the irradiated eggs. Both genes belong to the group of “immediate early genes” that respond quickly to the diverse extracellular stimuli. Elevated expression of these genes was accompanied by decreased level of ssa-miR-10b-5p and ssa-miR-21b-5p (p < 0.05), for which IER2 and EGR1 are target genes. The level of RNA in the fertilized irradiated eggs was highly significantly lower than in the non-irradiated eggs (p < 0.001) and in the unfertilized irradiated eggs (p < 0.0001). However, transcriptome profiles of fertilized non-irradiated eggs and fertilized irradiated eggs did not differ significantly. Thus, we assume that reduced abundance of mRNA in the fertilized irradiated eggs was associated with post-translational degradation and clearance of the maternal transcripts rather than from the irradiation of eggs.
Collapse
|
52
|
Maternal DCAF13 Regulates Chromatin Tightness to Contribute to Embryonic Development. Sci Rep 2019; 9:6278. [PMID: 31000741 PMCID: PMC6472424 DOI: 10.1038/s41598-019-42179-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 03/13/2019] [Indexed: 12/23/2022] Open
Abstract
Maternal-zygotic transition (MZT) is critical for the developmental control handed from maternal products to newly synthesized zygotic genome in the earliest stage of embryogenesis. However, the spatiotemporal dynamic regulation of MZT by maternal factors is largely unknown. Here, we reported a novel maternal factor, DCAF13, which was highly expressed in growing oocyte nucleolus and had key maternal effects on oocyte and zygotic chromatin tightness during maternal to zygotic transition. DCAF13 specifically deleted in oocytes resulted in loose chromatin structure in fully grown germinal vesicle oocytes. Despite normal nuclear maturation in maternal DCAF13-deleted oocytes, the chromosomes at MII stage were not properly condensed. Consequently, the nuclear and nucleolar structure reorganized abnormally, and transcription was inactive in zygotic embryos. RNA-seq analysis of MII oocytes and 2-cell embryos demonstrated that the transcriptomes between knockout and control oocyte were similar, but the maternal DCAF13 deleted two-cell embryos showed a significant decrease in transcription. In addition, the maternal DCAF13-deleted embryos displayed arrest at the two-cell stage, which could not be rescued by injecting flag-Dcaf13 mRNA in the zygote. This revealed that DCAF13 was a unique maternal effect factor regulating the nucleolus.
Collapse
|
53
|
Chang H, Yeo J, Kim JG, Kim H, Lim J, Lee M, Kim HH, Ohk J, Jeon HY, Lee H, Jung H, Kim KW, Kim VN. Terminal Uridylyltransferases Execute Programmed Clearance of Maternal Transcriptome in Vertebrate Embryos. Mol Cell 2019; 70:72-82.e7. [PMID: 29625039 DOI: 10.1016/j.molcel.2018.03.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/07/2018] [Accepted: 03/01/2018] [Indexed: 12/26/2022]
Abstract
During the maternal-to-zygotic transition (MZT), maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However, it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here, through genome-wide profiling of RNA abundance and 3' modification, we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 (TUT4/7) are depleted in zebrafish and Xenopus, maternal mRNA clearance is significantly delayed, leading to developmental defects during gastrulation. Short-tailed mRNAs are selectively uridylated by TUT4/7, with the highly uridylated transcripts degraded faster during the MZT than those with unmodified poly(A) tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation, thereby allowing the progression of early development.
Collapse
Affiliation(s)
- Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Jinah Yeo
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Jeong-Gyun Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Seoul National University, Seoul 08826, Korea
| | - Hyunjoon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Hyun Ho Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Seoul National University, Seoul 08826, Korea
| | - Jiyeon Ohk
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hee-Yeon Jeon
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyunsook Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hosung Jung
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Kyu-Won Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
| |
Collapse
|
54
|
Larose H, Shami AN, Abbott H, Manske G, Lei L, Hammoud SS. Gametogenesis: A journey from inception to conception. Curr Top Dev Biol 2019; 132:257-310. [PMID: 30797511 PMCID: PMC7133493 DOI: 10.1016/bs.ctdb.2018.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gametogenesis, the process of forming mature germ cells, is an integral part of both an individual's and a species' health and well-being. This chapter focuses on critical male and female genetic and epigenetic processes underlying normal gamete formation through their differentiation to fertilization. Finally, we explore how knowledge gained from this field has contributed to progress in areas with great clinical promise, such as in vitro gametogenesis.
Collapse
Affiliation(s)
- Hailey Larose
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | | | - Haley Abbott
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Gabriel Manske
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Lei Lei
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI, United States.
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, United States.
| |
Collapse
|
55
|
Sun J, Yan L, Shen W, Meng A. Maternal Ybx1 safeguards zebrafish oocyte maturation and maternal-to-zygotic transition by repressing global translation. Development 2018; 145:dev.166587. [PMID: 30135188 DOI: 10.1242/dev.166587] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/23/2018] [Indexed: 12/22/2022]
Abstract
Maternal mRNAs and proteins dictate early embryonic development before zygotic genome activation. In the absence of transcription, elaborate control of maternal mRNA translation is of particular importance for oocyte maturation and early embryogenesis. By analyzing zebrafish ybx1 mutants with a null allele, we demonstrate an essential role of maternal ybx1 in repressing global translation in oocytes and embryos. Loss of maternal Ybx1 leads to impaired oocyte maturation and egg activation. Maternal ybx1 (Mybx1) mutant embryos fail to undergo normal cleavage and the maternal-to-zygotic transition (MZT). Morpholino knockdown of ybx1 also results in MZT loss and epiboly failure, suggesting the postfertilization requirement of Ybx1. In addition, elevated global translation level and the unfolded protein response were found in Ybx1-depleted embryos. Supplementing translational repression by eIF4E inhibition markedly rescues the Mybx1 phenotype. Mechanistically, Ybx1 in embryos may associate with processing body components and repress translation when tethered to target mRNAs. Collectively, our results identify maternal Ybx1 as a global translational repressor required for oocyte maturation and early embryogenesis.
Collapse
Affiliation(s)
- Jiawei Sun
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lu Yan
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| |
Collapse
|
56
|
Kami D, Kitani T, Nakamura A, Wakui N, Mizutani R, Ohue M, Kametani F, Akimitsu N, Gojo S. The DEAD-box RNA-binding protein DDX6 regulates parental RNA decay for cellular reprogramming to pluripotency. PLoS One 2018; 13:e0203708. [PMID: 30273347 PMCID: PMC6166933 DOI: 10.1371/journal.pone.0203708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/24/2018] [Indexed: 12/30/2022] Open
Abstract
Cellular transitions and differentiation processes require mRNAs supporting the new phenotype but also the clearance of existing mRNAs for the parental phenotype. Cellular reprogramming from fibroblasts to induced pluripotent stem cells (iPSCs) occurs at the early stage of mesenchymal epithelial transition (MET) and involves drastic morphological changes. We examined the molecular mechanism for MET, focusing on RNA metabolism. DDX6, an RNA helicase, was indispensable for iPSC formation, in addition to RO60 and RNY1, a non-coding RNA, which form complexes involved in intracellular nucleotide sensing. RO60/RNY1/DDX6 complexes formed prior to processing body formation, which is central to RNA metabolism. The abrogation of DDX6 expression inhibited iPSC generation, which was mediated by RNA decay targeting parental mRNAs supporting mesenchymal phenotypes, along with microRNAs, such as miR-302b-3p. These results show that parental mRNA clearance is a prerequisite for cellular reprogramming and that DDX6 plays a central role in this process.
Collapse
Affiliation(s)
- Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomoya Kitani
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akihiro Nakamura
- Department of Pediatric Cardiology and Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naoki Wakui
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo, Japan
| | - Rena Mizutani
- Radioisotope Center, The University of Tokyo, Tokyo, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo, Japan
| | - Fuyuki Kametani
- Department of Dementia and Higher Brain Function, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | | | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- * E-mail:
| |
Collapse
|
57
|
Beaudoin JD, Novoa EM, Vejnar CE, Yartseva V, Takacs CM, Kellis M, Giraldez AJ. Analyses of mRNA structure dynamics identify embryonic gene regulatory programs. Nat Struct Mol Biol 2018; 25:677-686. [PMID: 30061596 PMCID: PMC6690192 DOI: 10.1038/s41594-018-0091-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/20/2018] [Indexed: 01/22/2023]
Abstract
RNA folding plays a crucial role in RNA function. However, knowledge of the global structure of the transcriptome is limited to cellular systems at steady state, thus hindering the understanding of RNA structure dynamics during biological transitions and how it influences gene function. Here, we characterized mRNA structure dynamics during zebrafish development. We observed that on a global level, translation guides structure rather than structure guiding translation. We detected a decrease in structure in translated regions and identified the ribosome as a major remodeler of RNA structure in vivo. In contrast, we found that 3' untranslated regions (UTRs) form highly folded structures in vivo, which can affect gene expression by modulating microRNA activity. Furthermore, dynamic 3'-UTR structures contain RNA-decay elements, such as the regulatory elements in nanog and ccna1, two genes encoding key maternal factors orchestrating the maternal-to-zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs.
Collapse
Affiliation(s)
- Jean-Denis Beaudoin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Eva Maria Novoa
- Computer Science and Electrical Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neuroscience, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- School of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- College of Arts and Sciences, University of New Haven, West Haven, CT, USA
| | - Manolis Kellis
- Computer Science and Electrical Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
58
|
Effect of Larval Nutrition on Maternal mRNA Contribution to the Drosophila Egg. G3-GENES GENOMES GENETICS 2018; 8:1933-1941. [PMID: 29666195 PMCID: PMC5982822 DOI: 10.1534/g3.118.200283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Embryonic development begins under the control of maternal gene products, mRNAs and proteins that the mother deposits into the egg; the zygotic genome is activated some time later. Maternal control of early development is conserved across metazoans. Gene products contributed by mothers are critical to many early developmental processes, and set up trajectories for the rest of development. Maternal deposition of these factors is an often-overlooked aspect of parental investment. If the mother experiences challenging environmental conditions, such as poor nutrition, previous studies in Drosophila melanogaster have demonstrated a plastic response wherein these mothers may produce larger eggs to buffer the offspring against the same difficult environment. This additional investment can produce offspring that are more fit in the challenging environment. With this study, we ask whether D. melanogaster mothers who experience poor nutrition during their own development change their gene product contribution to the egg. We perform mRNA-Seq on eggs at a stage where all mRNAs are maternally derived, from mothers with different degrees of nutritional limitation. We find that nutritional limitation produces similar transcript changes at all degrees of limitation tested. Genes that have lower transcript abundance in nutritionally limited mothers are those involved in translation, which is likely one of the most energetically costly processes occurring in the early embryo. We find an increase in transcripts for transport and localization of macromolecules, and for the electron transport chain. The eggs produced by nutrition-limited mothers show a plastic response in mRNA deposition, which may better prepare the future embryo for development in a nutrition-limited environment.
Collapse
|
59
|
Masala L, Ariu F, Bogliolo L, Bellu E, Ledda S, Bebbere D. Delay in maternal transcript degradation in ovine embryos derived from low competence oocytes. Mol Reprod Dev 2018; 85:427-439. [PMID: 29542856 DOI: 10.1002/mrd.22977] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 02/14/2018] [Accepted: 02/18/2018] [Indexed: 01/06/2023]
Abstract
Oocytes from prepubertal animals have a reduced ability to undergo embryo development and produce viable offspring. The present work used an ovine model consisting of oocytes derived from adult and prepubertal donors to assess the molecular status of oocytes and preimplantation embryos with different developmental competence. The lower potential of oocytes of young donors was confirmed in terms of in vitro developmental capabilities and kinetics. A panel of genes including maternal effect (DPPA3, GDF9, NMP2, ZAR1) and housekeeping genes (ACTB, RPL19, SDHA, YWHAZ, ATP1A1), genes involved in DNA methylation (DNMT1, DNMT3A, DNMT3B), genomic imprinting (IGF2R), pluripotency (NANOG, POU5F1) and cell cycle regulation (CCNB1, CDK1, MELK) was relatively quantified. Temporal analysis during oocyte maturation and preimplantation embryo development evidenced patterns associated with donor age. With a few gene-specific exceptions, the differential model showed a reduced transcript abundance in immature prepubertal oocytes that completely reversed trend after fertilization, when higher mRNA levels were consistently observed in early embryos, indicating a delay in maternal transcript degradation. We propose that the molecular shortage in the prepubertal oocyte may affect its developmental potential and impair the early pathways of maternal mRNA clearance in the embryo. While confirming the different potential of oocytes derived from adult and prepubertal donors, our work showed for the first time a consistent delay in maternal transcript degradation in embryos derived from low competence oocytes that interestingly recalls the delayed developmental kinetics. Such abnormal transcript persistence may hinder further development and represents a novel perspective on the complexity of developmental competence.
Collapse
Affiliation(s)
- Laura Masala
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Federica Ariu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Luisa Bogliolo
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Emanuela Bellu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Sergio Ledda
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daniela Bebbere
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| |
Collapse
|
60
|
Liu C, Ma Y, Shang Y, Huo R, Li W. Post-translational regulation of the maternal-to-zygotic transition. Cell Mol Life Sci 2018; 75:1707-1722. [PMID: 29427077 PMCID: PMC11105290 DOI: 10.1007/s00018-018-2750-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/24/2017] [Accepted: 01/08/2018] [Indexed: 02/07/2023]
Abstract
The maternal-to-zygotic transition (MZT) is essential for the developmental control handed from maternal products to newly synthesized zygotic genome in the earliest stages of embryogenesis, including maternal component (mRNAs and proteins) degradation and zygotic genome activation (ZGA). Various protein post-translational modifications have been identified during the MZT, such as phosphorylation, methylation and ubiquitination. Precise post-translational regulation mechanisms are essential for the timely transition of early embryonic development. In this review, we summarize recent progress regarding the molecular mechanisms underlying post-translational regulation of maternal component degradation and ZGA during the MZT and discuss some important issues in the field.
Collapse
Affiliation(s)
- Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanjie Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- Department of Animal Science and Technology, Northeast Agricultural University, Haerbin, 150030, People's Republic of China
| | - Yongliang Shang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 210029, People's Republic of China.
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, 211166, People's Republic of China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| |
Collapse
|
61
|
Conti M, Franciosi F. Acquisition of oocyte competence to develop as an embryo: integrated nuclear and cytoplasmic events. Hum Reprod Update 2018; 24:245-266. [PMID: 29432538 PMCID: PMC5907346 DOI: 10.1093/humupd/dmx040] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/01/2017] [Accepted: 12/15/2017] [Indexed: 12/12/2022] Open
Abstract
Infertility affects ~7% of couples of reproductive age with little change in incidence in the last two decades. ART, as well as other interventions, have made major strides in correcting this condition. However, and in spite of advancements in the field, the age of the female partner remains a main factor for a successful outcome. A better understanding of the final stages of gamete maturation yielding an egg that can sustain embryo development and a pregnancy to term remains a major area for improvement in the field. This review will summarize the major cellular and molecular events unfolding at the oocyte-to-embryo transition. We will provide an update on the most important processes/pathways currently understood as the basis of developmental competence, including the molecular processes involved in mRNA storage, its recruitment to the translational machinery, and its degradation. We will discuss the hypothesis that the translational programme of maternal mRNAs plays a key role in establishing developmental competence. These regulations are essential to assemble the machinery that is used to establish a totipotent zygote. This hypothesis further supports the view that embryogenesis begins during oogenesis. A better understanding of the events required for developmental competence will guide the development of novel strategies to monitor and improve the success rate of IVF. Using this information, it will be possible to develop new biomarkers that may be used to better predict oocyte quality and in selection of the best egg for IVF.
Collapse
Affiliation(s)
- Marco Conti
- Department of OBGYN-RS, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143-0556, USA
| | - Federica Franciosi
- Department of OBGYN-RS, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143-0556, USA
| |
Collapse
|
62
|
Winata CL, Łapiński M, Pryszcz L, Vaz C, Bin Ismail MH, Nama S, Hajan HS, Lee SGP, Korzh V, Sampath P, Tanavde V, Mathavan S. Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal-to-zygotic transition. Development 2018; 145:dev.159566. [PMID: 29229769 DOI: 10.1242/dev.159566] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/20/2017] [Indexed: 10/18/2022]
Abstract
In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to the point of zygotic genome activation (ZGA). These maternal mRNAs undergo cytoplasmic polyadenylation (CPA), suggesting translational control of their activation. To elucidate the biological role of CPA during embryogenesis, we performed genome-wide polysome profiling at several stages of zebrafish development. Our analysis revealed a correlation between CPA and polysome-association dynamics, demonstrating a coupling of translation to the CPA of maternal mRNAs. Pan-embryonic CPA inhibition disrupted the maternal-to-zygotic transition (MZT), causing a failure of developmental progression beyond the mid-blastula transition and changes in global gene expression that indicated a failure of ZGA and maternal mRNA clearance. Among the genes that were differentially expressed were those encoding chromatin modifiers and key transcription factors involved in ZGA, including nanog, pou5f3 and sox19b, which have distinct CPA dynamics. Our results establish the necessity of CPA for ensuring progression of the MZT. The RNA-seq data generated in this study represent a valuable zebrafish resource for the discovery of novel elements of the early embryonic transcriptome.
Collapse
Affiliation(s)
- Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland .,Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Leszek Pryszcz
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Candida Vaz
- Bioinformatics Institute, Agency for Science Technology and Research, 138671 Singapore
| | | | - Srikanth Nama
- Institute of Medical Biology, Agency of Science Technology and Research, 138648 Singapore
| | - Hajira Shreen Hajan
- Genome Institute of Singapore, Agency of Science Technology and Research, 138672 Singapore
| | - Serene Gek Ping Lee
- Genome Institute of Singapore, Agency of Science Technology and Research, 138672 Singapore
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.,Institute of Molecular and Cell Biology, Agency of Science Technology and Research, 138673 Singapore
| | - Prabha Sampath
- Institute of Medical Biology, Agency of Science Technology and Research, 138648 Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, 117596 Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857 Singapore
| | - Vivek Tanavde
- Bioinformatics Institute, Agency for Science Technology and Research, 138671 Singapore.,Institute of Medical Biology, Agency of Science Technology and Research, 138648 Singapore
| | - Sinnakaruppan Mathavan
- Genome Institute of Singapore, Agency of Science Technology and Research, 138672 Singapore .,Vision Research Foundation, Sankara Nethralaya, 600 006 Chennai, India
| |
Collapse
|
63
|
Hwang YS, Seo M, Bang S, Kim H, Han JY. Transcriptional and translational dynamics during maternal‐to‐zygotic transition in early chicken development. FASEB J 2018; 32:2004-2011. [DOI: 10.1096/fj.201700955r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Young Sun Hwang
- Department of Agricultural BiotechnologyResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Minseok Seo
- C& K Genomics, SNU Research ParkSeoul National UniversitySeoulKorea
- Channing Division of Network MedicineHarvard Medical School and Brigham and Women's HospitalBostonMassachusettsUSA
| | - Sohyun Bang
- C& K Genomics, SNU Research ParkSeoul National UniversitySeoulKorea
| | - Heebal Kim
- Department of Agricultural BiotechnologyResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- C& K Genomics, SNU Research ParkSeoul National UniversitySeoulKorea
- Institute for Biomedical SciencesShinshu UniversityMinamiminowaJapan
| | - Jae Yong Han
- Department of Agricultural BiotechnologyResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Institute for Biomedical SciencesShinshu UniversityMinamiminowaJapan
| |
Collapse
|
64
|
A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster. PLoS Genet 2017; 13:e1007120. [PMID: 29261646 PMCID: PMC5752043 DOI: 10.1371/journal.pgen.1007120] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/03/2018] [Accepted: 11/20/2017] [Indexed: 12/13/2022] Open
Abstract
In nearly all metazoans, the earliest stages of development are controlled by maternally deposited mRNAs and proteins. The zygotic genome becomes transcriptionally active hours after fertilization. Transcriptional activation during this maternal-to-zygotic transition (MZT) is tightly coordinated with the degradation of maternally provided mRNAs. In Drosophila melanogaster, the transcription factor Zelda plays an essential role in widespread activation of the zygotic genome. While Zelda expression is required both maternally and zygotically, the mechanisms by which it functions to remodel the embryonic genome and prepare the embryo for development remain unclear. Using Cas9-mediated genome editing to generate targeted mutations in the endogenous zelda locus, we determined the functional relevance of protein domains conserved amongst Zelda orthologs. We showed that neither a conserved N-terminal zinc finger nor an acidic patch were required for activity. Similarly, a previously identified splice isoform of zelda is dispensable for viability. By contrast, we identified a highly conserved zinc-finger domain that is essential for the maternal, but not zygotic functions of Zelda. Animals homozygous for mutations in this domain survived to adulthood, but embryos inheriting these loss-of-function alleles from their mothers died late in embryogenesis. These mutations did not interfere with the capacity of Zelda to activate transcription in cell culture. Unexpectedly, these mutations generated a hyperactive form of the protein and enhanced Zelda-dependent gene expression. These data have defined a protein domain critical for controlling Zelda activity during the MZT, but dispensable for its roles later in development, for the first time separating the maternal and zygotic requirements for Zelda. This demonstrates that highly regulated levels of Zelda activity are required for establishing the developmental program during the MZT. We propose that tightly regulated gene expression is essential to navigate the MZT and that failure to precisely execute this developmental program leads to embryonic lethality. Following fertilization, the one-celled zygote must be rapidly reprogrammed to enable the development of a new, unique organism. During these initial stages of development there is little or no transcription of the zygotic genome, and maternally deposited products control this process. Among the essential maternal products are mRNAs that encode transcription factors required for preparing the zygotic genome for transcriptional activation. This ensures that there is a precisely coordinated hand-off from maternal to zygotic control. In Drosophila melanogaster, the transcription factor Zelda is essential for activating the zygotic genome and coupling this activation to the degradation of the maternally deposited products. Nonetheless, the mechanism by which Zelda functions remains unclear. Here we used Cas9-mediated genome engineering to determine the functional requirements for highly conserved domains within Zelda. We identified a domain required specifically for Zelda’s role in reprogramming the early embryonic genome, but not essential for its functions later in development. Surprisingly, this domain restricts the ability of Zelda to activate transcription. These data demonstrate that Zelda activity is tightly regulated, and we propose that precise regulation of both the timing and levels of genome activation is required for the embryo to successfully transition from maternal to zygotic control.
Collapse
|
65
|
Jukam D, Shariati SAM, Skotheim JM. Zygotic Genome Activation in Vertebrates. Dev Cell 2017; 42:316-332. [PMID: 28829942 PMCID: PMC5714289 DOI: 10.1016/j.devcel.2017.07.026] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/25/2017] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
Abstract
The first major developmental transition in vertebrate embryos is the maternal-to-zygotic transition (MZT) when maternal mRNAs are degraded and zygotic transcription begins. During the MZT, the embryo takes charge of gene expression to control cell differentiation and further development. This spectacular organismal transition requires nuclear reprogramming and the initiation of RNAPII at thousands of promoters. Zygotic genome activation (ZGA) is mechanistically coordinated with other embryonic events, including changes in the cell cycle, chromatin state, and nuclear-to-cytoplasmic component ratios. Here, we review progress in understanding vertebrate ZGA dynamics in frogs, fish, mice, and humans to explore differences and emphasize common features.
Collapse
Affiliation(s)
- David Jukam
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - S Ali M Shariati
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
66
|
Abstract
During the maternal-to-zygotic transition, maternal mRNAs are cleared by multiple distinct but interrelated pathways. A recent study in Nature by Zhao et al. (2017) finds that YTHDF2, a reader of N6- methylation, facilitates maternal mRNA decay, introducing an additional facet of control over transcript fate and developmental reprogramming.
Collapse
Affiliation(s)
- Cassandra Kontur
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Antonio Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
67
|
Joseph SR, Pálfy M, Hilbert L, Kumar M, Karschau J, Zaburdaev V, Shevchenko A, Vastenhouw NL. Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos. eLife 2017; 6. [PMID: 28425915 PMCID: PMC5451213 DOI: 10.7554/elife.23326] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/19/2017] [Indexed: 01/09/2023] Open
Abstract
Upon fertilization, the genome of animal embryos remains transcriptionally inactive until the maternal-to-zygotic transition. At this time, the embryo takes control of its development and transcription begins. How the onset of zygotic transcription is regulated remains unclear. Here, we show that a dynamic competition for DNA binding between nucleosome-forming histones and transcription factors regulates zebrafish genome activation. Taking a quantitative approach, we found that the concentration of non-DNA-bound core histones sets the time for the onset of transcription. The reduction in nuclear histone concentration that coincides with genome activation does not affect nucleosome density on DNA, but allows transcription factors to compete successfully for DNA binding. In agreement with this, transcription factor binding is sensitive to histone levels and the concentration of transcription factors also affects the time of transcription. Our results demonstrate that the relative levels of histones and transcription factors regulate the onset of transcription in the embryo. DOI:http://dx.doi.org/10.7554/eLife.23326.001 The DNA in a fertilized egg contains all the information required to form an animal’s body. In order for the animal to develop properly, particular genes encoded in the DNA are only active at specific times. The DNA is wrapped around proteins called histones, which allows the DNA to be tightly packed inside the cell. However, histones can block other proteins called transcription factors from binding to the DNA to activate the genes. Young embryos initially develop with all of their genes switched off, relying on the nutrients and other molecules provided by their mother. After some time, the embryo starts to switch on its own genes to take control of its own development, but it was not clear how this happens. Joseph et al. investigated how genes are activated in zebrafish embryos, which are often used as models to study how animals develop. The experiments show that competition between histones and transcription factors for binding to DNA controls when genes are switched on. In young fish embryos, there are so many histones present that transcription factors have no opportunity to bind to DNA. Over time, however, the numbers of histones decrease, allowing transcription factors to bind to DNA and switch on genes. Histones and transcription factors regulate the activity of genes throughout the life of the animal. Therefore, competition between these two types of protein may also control gene activity in other situations. A better understanding of how gene activity is controlled could allow researchers to more easily grow different types of cell in the laboratory or to reprogram specific cells in the body. As such, these new findings may aid the development of therapies to regenerate organs or tissues that have been damaged by injury or disease. DOI:http://dx.doi.org/10.7554/eLife.23326.002
Collapse
Affiliation(s)
- Shai R Joseph
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Máté Pálfy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lennart Hilbert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Mukesh Kumar
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jens Karschau
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Vasily Zaburdaev
- Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| |
Collapse
|
68
|
Pálfy M, Joseph SR, Vastenhouw NL. The timing of zygotic genome activation. Curr Opin Genet Dev 2017; 43:53-60. [PMID: 28088031 DOI: 10.1016/j.gde.2016.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 12/20/2022]
Abstract
After fertilization, the embryonic genome is inactive until transcription is initiated during the maternal-to-zygotic transition. How the onset of transcription is regulated in a precisely timed manner, however, is a long standing question in biology. Several mechanisms have been shown to contribute to the temporal regulation of genome activation but none of them can fully explain the general absence of transcription as well the gene specific onset that follows. Here we review the work that has been done toward elucidating the mechanisms underlying the temporal regulation of transcription in embryos.
Collapse
Affiliation(s)
- Máté Pálfy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Shai R Joseph
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
69
|
Rosa A, Brivanlou AH. Role of MicroRNAs in Zygotic Genome Activation: Modulation of mRNA During Embryogenesis. Methods Mol Biol 2017; 1605:31-43. [PMID: 28456956 DOI: 10.1007/978-1-4939-6988-3_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A fundamental process occurring during early development is the zygotic genome activation, i.e., the initiation of transcription from the embryonic genome. Before that step, cellular processes in the developing embryo are dictated by transcripts produced by the maternal genome and accumulated in the egg during oogenesis. The maternal-to-zygotic transition (MZT) involves both the clearance of maternal RNAs and the initiation of transcription of the embryonic genome and is a tightly regulated process. In some species, decay of maternal transcripts may be facilitated by the activity of microRNAs. These small RNAs can act pleiotropically, blocking translation and inducing destabilization of hundreds of different maternal targets. In this review, we will discuss the role of microRNAs during MZT, focusing on Drosophila melanogaster and vertebrate models, Xenopus laevis, Zebrafish and mouse, in which such a mechanism has been more extensively studied.
Collapse
Affiliation(s)
- Alessandro Rosa
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, 00185, Italy
- Laboratory of Molecular Vertebrate Embryology, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA
| | - Ali H Brivanlou
- Laboratory of Molecular Vertebrate Embryology, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA.
| |
Collapse
|
70
|
Yartseva V, Takacs CM, Vejnar CE, Lee MT, Giraldez AJ. RESA identifies mRNA-regulatory sequences at high resolution. Nat Methods 2016; 14:201-207. [PMID: 28024160 PMCID: PMC5423094 DOI: 10.1038/nmeth.4121] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/02/2016] [Indexed: 11/22/2022]
Abstract
Gene expression is regulated extensively at the level of mRNA stability, localization, and translation. However, decoding functional RNA regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. Here, we developed RNA Element Selection Assay (RESA), a method that selects RNA elements based on their activity in vivo and uses high-throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements, we developed a bisulfite-mediated nucleotide conversion strategy for large-scale mutational analysis (RESA-bisulfite). Finally, we used the versatile RESA platform to map candidate protein-RNA interactions in vivo (RESA-CLIP). The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.
Collapse
Affiliation(s)
- Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Carter M Takacs
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
71
|
Coulombel L. [Mitotic reprogramming of sperm injected into haploid parthenogenotes embryos]. Med Sci (Paris) 2016; 32:903-910. [PMID: 27758757 DOI: 10.1051/medsci/20163210026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Laure Coulombel
- Directrice de recherche émérite, Inserm U1130, conseillère scientifique de médecine/sciences, Paris, France
| |
Collapse
|
72
|
Chen YH, Coller J. A Universal Code for mRNA Stability? Trends Genet 2016; 32:687-688. [PMID: 27594172 DOI: 10.1016/j.tig.2016.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/16/2016] [Indexed: 01/27/2023]
Abstract
Precise elimination of maternal mRNAs plays a critical role during the maternal-to-zygotic transition (MZT) to promote developmental processing. Two new studies demonstrate that, in eukaryotes, codon-mediated decay is a conserved mechanism to shape maternal mRNA stability by affecting deadenylation rate in a translation-dependent manner. These studies add to a growing body of literature suggesting that translational elongation rates are a major determinant of mRNA stability.
Collapse
Affiliation(s)
- Ying-Hsin Chen
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Jeff Coller
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH, USA.
| |
Collapse
|
73
|
Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J 2016; 35:2087-2103. [PMID: 27436874 DOI: 10.15252/embj.201694699] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/16/2016] [Indexed: 12/26/2022] Open
Abstract
Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal-to-zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by post-transcriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs, this pathway does not fully explain mRNA clearance. We investigated how codon identity and translation affect mRNA stability during development and homeostasis. We show that the codon triplet contains translation-dependent regulatory information that influences transcript decay. Codon composition shapes maternal mRNA clearance during the maternal-to-zygotic transition in zebrafish, Xenopus, mouse, and Drosophila, and gene expression during homeostasis across human tissues. Some synonymous codons show consistent stabilizing or destabilizing effects, suggesting that amino acid composition influences mRNA stability. Codon composition affects both polyadenylation status and translation efficiency. Thus, the ribosome interprets two codes within the mRNA: the genetic code which specifies the amino acid sequence and a conserved "codon optimality code" that shapes mRNA stability and translation efficiency across vertebrates.
Collapse
Affiliation(s)
- Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Florencia Del Viso
- Departments of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Timothy G Johnstone
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Yidan Qin
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Mustafa K Khokha
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Departments of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
74
|
Bryant SA, Herdy JR, Amemiya CT, Smith JJ. Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus). Mol Biol Evol 2016; 33:2337-44. [PMID: 27288344 DOI: 10.1093/molbev/msw104] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The sea lamprey (Petromyzon marinus) is a basal vertebrate that undergoes developmentally programmed genome rearrangements (PGRs) during early development. These events facilitate the elimination of ∼20% of the genome from the somatic cell lineage, resulting in distinct somatic and germline genomes. Thus far only a handful of germline-specific genes have been definitively identified within the estimated 500 Mb of DNA that is deleted during PGR, although a few thousand germline-specific genes are thought to exist. To improve our understanding of the evolutionary/developmental logic of PGR, we generated computational predictions to identify candidate germline-specific genes within a new transcriptomic dataset derived from adult germline and the early embryonic stages during which PGR occurs. Follow-up validation studies identified 44 germline-specific genes and further characterized patterns of transcription and DNA loss during early embryogenesis. Expression analyses reveal that many of these genes are differentially expressed during early embryogenesis and presumably function in the early development of the germline. Ontology analyses indicate that many of these germline-specific genes play known roles in germline development, pluripotency, and oncogenesis (when misexpressed). These studies provide support for the theory that PGR serves to segregate molecular functions related to germline development/pluripotency in order to prevent their potential misexpression in somatic cells. This larger set of eliminated genes also allows us to extend the evolutionary/developmental breadth of this theory, as some deleted genes (or their gnathostome homologs) appear to be associated with the early development of somatic lineages, perhaps through the evolution of novel functions within gnathostome lineages.
Collapse
Affiliation(s)
| | | | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle Department of Biology, University of Washington, Seattle
| | | |
Collapse
|
75
|
Dallaire A, Simard MJ. The implication of microRNAs and endo-siRNAs in animal germline and early development. Dev Biol 2016; 416:18-25. [PMID: 27287880 DOI: 10.1016/j.ydbio.2016.06.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/31/2016] [Accepted: 06/06/2016] [Indexed: 01/13/2023]
Abstract
Germ cells provide maternal mRNAs that are stored in the oocyte, and later translated at a specific time of development. In this context, gene regulation depends mainly on post-transcriptional mechanisms that contribute to keep maternal transcripts in a stable and translationally silent state. In recent years, small non-coding RNAs, such as microRNAs have emerged as key post-transcriptional regulators of gene expression. microRNAs control the translation efficiency and/or stability of targeted mRNAs. microRNAs are present in animal germ cells and maternally inherited microRNAs are abundant in early embryos. However, it is not known how microRNAs control the stability and translation of maternal transcripts. In this review, we will discuss the implication of germline microRNAs in regulating animal oogenesis and early embryogenesis as well as compare their roles with endo-siRNAs, small RNA species that share key molecular components with the microRNA pathway.
Collapse
Affiliation(s)
- Alexandra Dallaire
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Centre (Hôtel-Dieu de Québec), Quebec City, Québec, Canada G1R 2J6; Laval University Cancer Research Centre, Quebec City, Québec, Canada G1R 2J6
| | - Martin J Simard
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Centre (Hôtel-Dieu de Québec), Quebec City, Québec, Canada G1R 2J6; Laval University Cancer Research Centre, Quebec City, Québec, Canada G1R 2J6.
| |
Collapse
|
76
|
The Drosophila prage Gene, Required for Maternal Transcript Destabilization in Embryos, Encodes a Predicted RNA Exonuclease. G3-GENES GENOMES GENETICS 2016; 6:1687-93. [PMID: 27172196 PMCID: PMC4889664 DOI: 10.1534/g3.116.028415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Egg activation, the transition of mature oocytes into developing embryos, is critical for the initiation of embryogenesis. This process is characterized by resumption of meiosis, changes in the egg's coverings and by alterations in the transcriptome and proteome of the egg; all of these occur in the absence of new transcription. Activation of the egg is prompted by ionic changes in the cytoplasm (usually a rise in cytosolic calcium levels) that are triggered by fertilization in some animals and by mechanosensitive cues in others. The egg's transcriptome is dramatically altered during the process, including by the removal of many maternal mRNAs that are not needed for embryogenesis. However, the mechanisms and regulators of this selective RNA degradation are not yet fully known. Forward genetic approaches in Drosophila have identified maternal-effect genes whose mutations prevent the transcriptome changes. One of these genes, prage (prg), was identified by Tadros et al. in a screen for mutants that fail to destabilize maternal transcripts. We identified the molecular nature of the prg gene through a combination of deficiency mapping, complementation analysis, and DNA sequencing of both extant prg mutant alleles. We find that prg encodes a ubiquitously expressed predicted exonuclease, consistent with its role in maternal mRNA destabilization during egg activation.
Collapse
|
77
|
Liu Y, Lu X, Shi J, Yu X, Zhang X, Zhu K, Yi Z, Duan E, Li L. BTG4 is a key regulator for maternal mRNA clearance during mouse early embryogenesis. J Mol Cell Biol 2016; 8:366-8. [PMID: 27190313 DOI: 10.1093/jmcb/mjw023] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yusheng Liu
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junchao Shi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingjiang Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoxin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kai Zhu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaohong Yi
- College of Biological Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Enkui Duan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
78
|
Evolution and functions of Oct4 homologs in non-mammalian vertebrates. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:770-9. [PMID: 27058398 DOI: 10.1016/j.bbagrm.2016.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/13/2022]
Abstract
PouV class transcription factor Oct4/Pou5f1 is a central regulator of indefinite pluripotency in mammalian embryonic stem cells (ESCs) but also participates in cell lineage specification in mouse embryos and in differentiating cell cultures. The molecular basis for this versatility, which is shared between Oct4 and its non-mammalian homologs Pou5f1 and Pou5f3, is not yet completely understood. Here, I review the current understanding of the evolution of PouV class transcription factors and discuss equivalent and diverse roles of Oct4 homologs in pluripotency, differentiation, and cell behavior in different vertebrate embryos. This article is part of a Special Issue entitled: The Oct Transcription Factor Family, edited by Dr. Dean Tantin.
Collapse
|
79
|
Johnstone TG, Bazzini AA, Giraldez AJ. Upstream ORFs are prevalent translational repressors in vertebrates. EMBO J 2016; 35:706-23. [PMID: 26896445 DOI: 10.15252/embj.201592759] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/08/2016] [Indexed: 12/20/2022] Open
Abstract
Regulation of gene expression is fundamental in establishing cellular diversity and a target of natural selection. Untranslated mRNA regions (UTRs) are key mediators of post-transcriptional regulation. Previous studies have predicted thousands of ORFs in 5'UTRs, the vast majority of which have unknown function. Here, we present a systematic analysis of the translation and function of upstream open reading frames (uORFs) across vertebrates. Using high-resolution ribosome footprinting, we find that (i)uORFs are prevalent within vertebrate transcriptomes, (ii) the majority show signatures of active translation, and (iii)uORFs act as potent regulators of translation and RNA levels, with a similar magnitude to miRNAs. Reporter experiments reveal clear repression of downstream translation by uORFs/oORFs. uORF number, intercistronic distance, overlap with the CDS, and initiation context most strongly influence translation. Evolution has targeted these features to favor uORFs amenable to regulation over constitutively repressive uORFs/oORFs. Finally, we observe that the regulatory potential of uORFs on individual genes is conserved across species. These results provide insight into the regulatory code within mRNA leader sequences and their capacity to modulate translation across vertebrates.
Collapse
Affiliation(s)
- Timothy G Johnstone
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ariel A Bazzini
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
80
|
Onichtchouk D, Driever W. Zygotic Genome Activators, Developmental Timing, and Pluripotency. Curr Top Dev Biol 2016; 116:273-97. [PMID: 26970624 DOI: 10.1016/bs.ctdb.2015.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The transcription factors Pou5f1, Sox2, and Nanog are central regulators of pluripotency in mammalian ES and iPS cells. In vertebrate embryos, Pou5f1/3, SoxB1, and Nanog control zygotic genome activation and participate in lineage decisions. We review the current knowledge of the roles of these genes in developing vertebrate embryos from fish to mammals and suggest a model for pluripotency gene regulatory network functions in early development.
Collapse
Affiliation(s)
- Daria Onichtchouk
- Developmental Biology Unit, Institute Biology I, Faculty of Biology, and Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-University, Freiburg, Germany.
| | - Wolfgang Driever
- Developmental Biology Unit, Institute Biology I, Faculty of Biology, and Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-University, Freiburg, Germany.
| |
Collapse
|
81
|
Rauwerda H, Wackers P, Pagano JFB, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink HP, Jonker M, Breit TM. Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs. PLoS One 2016; 11:e0147151. [PMID: 26799215 PMCID: PMC4723340 DOI: 10.1371/journal.pone.0147151] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/28/2015] [Indexed: 12/19/2022] Open
Abstract
Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize technical interference, we used mature, unfertilized eggs from siblings. About half of the number of analyzed genes was found to be expressed as maternal RNA. The expressed and non-expressed genes showed that maternal mRNA accumulation is a non-random process, as it is related to specific biological pathways and processes relevant in early embryogenesis. Moreover, it turned out that overall the composition of the maternal transcriptome is tightly regulated as about half of the expressed genes display a less than twofold expression range between the observed minimum and maximum expression values of a gene in the experiment. Even more, the maximum gene-expression difference within clutches is for 88% of the expressed genes lower than twofold. This means that expression differences observed in maternally expressed genes are primarily caused by differences between mothers, with only limited variability between eggs from the same mother. This was underlined by the fact that 99% of the expressed genes were found to be differentially expressed between any of the mothers in an ANOVA test. Furthermore, linking chromosome location, transcription factor binding sites, and miRNA target sites of the genes in clusters of distinct and unique mother-specific gene-expression, suggest biological relevance of the mother-specific signatures in the maternal transcriptome composition. Altogether, the maternal transcriptome composition of mature zebrafish oocytes seems to be tightly regulated with a distinct mother-specific signature.
Collapse
Affiliation(s)
- Han Rauwerda
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Paul Wackers
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Johanna F. B. Pagano
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Mark de Jong
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Wim Ensink
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Rob Dekker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Ulrike Nehrdich
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Herman P. Spaink
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Martijs Jonker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Timo M. Breit
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|