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Castro Colabianchi AM, González Pérez NG, Franchini LF, López SL. A maternal dorsoventral prepattern revealed by an asymmetric distribution of ventralizing molecules before fertilization in Xenopus laevis. Front Cell Dev Biol 2024; 12:1365705. [PMID: 38572484 PMCID: PMC10987785 DOI: 10.3389/fcell.2024.1365705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
The establishment of the embryonic dorsoventral axis in Xenopus occurs when the radial symmetry around the egg's animal-vegetal axis is broken to give rise to the typical symmetry of Bilaterians. We have previously shown that the Notch1 protein is ventrally enriched during early embryogenesis in Xenopus laevis and zebrafish and exerts ventralizing activity through β-Catenin destabilization and the positive regulation of ventral center genes in X. laevis. These findings led us to further investigate when these asymmetries arise. In this work, we show that the asymmetrical distribution of Notch1 protein and mRNA precedes cortical rotation and even fertilization in X. laevis. Moreover, we found that in unfertilized eggs transcripts encoded by the ventralizing gene bmp4 are also asymmetrically distributed in the animal hemisphere and notch1 transcripts accumulate consistently on the same side of the eccentric maturation point. Strikingly, a Notch1 asymmetry orthogonal to the animal-vegetal axis appears during X. laevis oogenesis. Thus, we show for the first time a maternal bias in the distribution of molecules that are later involved in ventral patterning during embryonic axialization, strongly supporting the hypothesis of a dorsoventral prepattern or intrinsic bilaterality of Xenopus eggs before fertilization.
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Affiliation(s)
- Aitana M. Castro Colabianchi
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Biología Celular e Histología / 1° U.A. Departamento de Histología, Embriología, Biología Celular y Genética, Laboratorio de Embriología Molecular “Prof. Dr. Andrés E. Carrasco”, Buenos Aires, Argentina
- CONICET–Universidad de Buenos Aires, Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), Buenos Aires, Argentina
| | - Nicolás G. González Pérez
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Biología Celular e Histología / 1° U.A. Departamento de Histología, Embriología, Biología Celular y Genética, Laboratorio de Embriología Molecular “Prof. Dr. Andrés E. Carrasco”, Buenos Aires, Argentina
- CONICET–Universidad de Buenos Aires, Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), Buenos Aires, Argentina
| | - Lucía F. Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Silvia L. López
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Biología Celular e Histología / 1° U.A. Departamento de Histología, Embriología, Biología Celular y Genética, Laboratorio de Embriología Molecular “Prof. Dr. Andrés E. Carrasco”, Buenos Aires, Argentina
- CONICET–Universidad de Buenos Aires, Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), Buenos Aires, Argentina
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2
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Šimková K, Naraine R, Vintr J, Soukup V, Šindelka R. RNA localization during early development of the axolotl. Front Cell Dev Biol 2023; 11:1260795. [PMID: 37928901 PMCID: PMC10620976 DOI: 10.3389/fcell.2023.1260795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
The asymmetric localization of biomolecules is critical for body plan development. One of the most popular model organisms for early embryogenesis studies is Xenopus laevis but there is a lack of information in other animal species. Here, we compared the early development of two amphibian species-the frog X. laevis and the axolotl Ambystoma mexicanum. This study aimed to identify asymmetrically localized RNAs along the animal-vegetal axis during the early development of A. mexicanum. For that purpose, we performed spatial transcriptome-wide analysis at low resolution, which revealed dynamic changes along the animal-vegetal axis classified into the following categories: profile alteration, de novo synthesis and degradation. Surprisingly, our results showed that many of the vegetally localized genes, which are important for germ cell development, are degraded during early development. Furthermore, we assessed the motif presence in UTRs of degraded mRNAs and revealed the enrichment of several motifs in RNAs of germ cell markers. Our results suggest novel reorganization of the transcriptome during embryogenesis of A. mexicanum to converge to the similar developmental pattern as the X. laevis.
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Affiliation(s)
- Kateřina Šimková
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Ravindra Naraine
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Jan Vintr
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Vladimír Soukup
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Radek Šindelka
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
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3
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Houston DW, Elliott KL, Coppenrath K, Wlizla M, Horb ME. Maternal Wnt11b regulates cortical rotation during Xenopus axis formation: analysis of maternal-effect wnt11b mutants. Development 2022; 149:dev200552. [PMID: 35946588 PMCID: PMC9515810 DOI: 10.1242/dev.200552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/01/2022] [Indexed: 12/13/2022]
Abstract
Asymmetric signalling centres in the early embryo are essential for axis formation in vertebrates. These regions (e.g. amphibian dorsal morula, mammalian anterior visceral endoderm) require stabilised nuclear β-catenin, but the role of localised Wnt ligand signalling activity in their establishment remains unclear. In Xenopus, dorsal β-catenin is initiated by vegetal microtubule-mediated symmetry breaking in the fertilised egg, known as 'cortical rotation'. Localised wnt11b mRNA and ligand-independent activators of β-catenin have been implicated in dorsal β-catenin activation, but the extent to which each contributes to axis formation in this paradigm remains unclear. Here, we describe a CRISPR-mediated maternal-effect mutation in Xenopus laevis wnt11b.L. We find that wnt11b is maternally required for robust dorsal axis formation and for timely gastrulation, and zygotically for left-right asymmetry. Importantly, we show that vegetal microtubule assembly and cortical rotation are reduced in wnt11b mutant eggs. In addition, we show that activated Wnt coreceptor Lrp6 and Dishevelled lack behaviour consistent with roles in early β-catenin stabilisation, and that neither is regulated by Wnt11b. This work thus implicates Wnt11b in the distribution of putative dorsal determinants rather than in comprising the determinants themselves. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Douglas W. Houston
- Department of Biology, The University of Iowa, 257 BB, Iowa City, IA 52242-1324, USA
| | - Karen L. Elliott
- Department of Biology, The University of Iowa, 257 BB, Iowa City, IA 52242-1324, USA
| | - Kelsey Coppenrath
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Marcin Wlizla
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Marko E. Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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4
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Zhang Z, Dubiak KM, Shishkova E, Huber PW, Coon JJ, Dovichi NJ. High-Throughput, Comprehensive Single-Cell Proteomic Analysis of Xenopus laevis Embryos at the 50-Cell Stage Using a Microplate-Based MICROFASP System. Anal Chem 2022; 94:3254-3259. [PMID: 35143156 PMCID: PMC8929430 DOI: 10.1021/acs.analchem.1c04987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report both the design of a high-throughput MICROFASP (a miniaturized filter aided sample preparation) system and its use for the comprehensive proteomic analysis of single blastomeres isolated from 50-cell stage Xenopus laevis embryos (∼200 ng of yolk-free protein/blastomere). A single run of the MICROFASP system was used to process 146 of these blastomeres in parallel. Three samples failed to generate signals presumably due to membrane clogging. Two cells were lost due to operator error. Of the surviving samples, 32 were analyzed using a Q Exactive HF mass spectrometer in survey experiments (data not included). The 109 remaining blastomeres were analyzed using a capillary LC-ESI-MS/MS system coupled to an Orbitrap Fusion Lumos mass spectrometer, which identified a total of 4189 protein groups and 40,998 unique peptides. On average, 3468 ± 229 protein groups and 14,525 ± 2437 unique peptides were identified from each blastomere, which is the highest throughput and deepest proteome coverage to date of single blastomeres at this stage of development. We also compared two dissociation buffers, Newport and calcium-magnesium-free (CMFM) buffers; the two buffers generated similar numbers of protein identifications (3615 total protein IDs from use of the Newport dissociation buffer and 3671 total protein IDs from use of the CMFM buffer).
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Affiliation(s)
- Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kyle M Dubiak
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Paul W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Joshua J Coon
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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5
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Dubail J, Cormier-Daire V. Chondrodysplasias With Multiple Dislocations Caused by Defects in Glycosaminoglycan Synthesis. Front Genet 2021; 12:642097. [PMID: 34220933 PMCID: PMC8242584 DOI: 10.3389/fgene.2021.642097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Chondrodysplasias with multiple dislocations form a group of severe disorders characterized by joint laxity and multiple dislocations, severe short stature of pre- and post-natal onset, hand anomalies, and/or vertebral anomalies. The majority of chondrodysplasias with multiple dislocations have been associated with mutations in genes encoding glycosyltransferases, sulfotransferases, and transporters implicated in the synthesis or sulfation of glycosaminoglycans, long and unbranched polysaccharides composed of repeated disaccharide bond to protein core of proteoglycan. Glycosaminoglycan biosynthesis is a tightly regulated process that occurs mainly in the Golgi and that requires the coordinated action of numerous enzymes and transporters as well as an adequate Golgi environment. Any disturbances of this chain of reactions will lead to the incapacity of a cell to construct correct glycanic chains. This review focuses on genetic and glycobiological studies of chondrodysplasias with multiple dislocations associated with glycosaminoglycan biosynthesis defects and related animal models. Strong comprehension of the molecular mechanisms leading to those disorders, mostly through extensive phenotypic analyses of in vitro and/or in vivo models, is essential for the development of novel biomarkers for clinical screenings and innovative therapeutics for these diseases.
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Affiliation(s)
- Johanne Dubail
- Université de Paris, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Valérie Cormier-Daire
- Université de Paris, INSERM UMR 1163, Institut Imagine, Paris, France.,Service de Génétique Clinique, Centre de Référence Pour Les Maladies Osseuses Constitutionnelles, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
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6
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Lombard-Banek C, Li J, Portero EP, Onjiko RM, Singer CD, Plotnick DO, Al Shabeeb RQ, Nemes P. In Vivo Subcellular Mass Spectrometry Enables Proteo-Metabolomic Single-Cell Systems Biology in a Chordate Embryo Developing to a Normally Behaving Tadpole (X. laevis)*. Angew Chem Int Ed Engl 2021; 60:12852-12858. [PMID: 33682213 PMCID: PMC8176382 DOI: 10.1002/anie.202100923] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 01/05/2023]
Abstract
We report the development of in vivo subcellular high-resolution mass spectrometry (HRMS) for proteo-metabolomic molecular systems biology in complex tissues. With light microscopy, we identified the left-dorsal and left-ventral animal cells in cleavage-stage non-sentient Xenopus laevis embryos. Using precision-translated fabricated microcapillaries, the subcellular content of each cell was double-probed, each time swiftly (<5 s/event) aspirating <5 % of cell volume (≈10 nL). The proteins and metabolites were analyzed by home-built ultrasensitive capillary electrophoresis electrospray ionization employing orbitrap or time-of-flight HRMS. Label-free detection of ≈150 metabolites (57 identified) and 738 proteins found proteo-metabolomic networks with differential quantitative activities between the cell types. With spatially and temporally scalable sampling, the technology preserved the integrity of the analyzed cells, the neighboring cells, and the embryo. 95 % of the analyzed embryos developed into sentient tadpoles that were indistinguishable from their wild-type siblings based on anatomy and visual function in a background color preference assay.
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Affiliation(s)
- Camille Lombard-Banek
- Department of Chemistry & Biochemistry, University of Maryland, 0107 Chemistry Building, 8051 Regents Drive, College Park, MD 20742 (USA)
| | - Jie Li
- Department of Chemistry & Biochemistry, University of Maryland, 0107 Chemistry Building, 8051 Regents Drive, College Park, MD 20742 (USA)
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 0107 Chemistry Building, 8051 Regents Drive, College Park, MD 20742 (USA)
| | - Rosemary M. Onjiko
- Department of Chemistry, The George Washington University, 800 22nd St NW, Washington, DC 20052 (USA)
| | - Chase D. Singer
- Department of Chemistry & Biochemistry, University of Maryland, 0107 Chemistry Building, 8051 Regents Drive, College Park, MD 20742 (USA)
| | - David O. Plotnick
- Department of Chemistry, The George Washington University, 800 22nd St NW, Washington, DC 20052 (USA)
| | - Reem Q. Al Shabeeb
- Department of Chemistry, The George Washington University, 800 22nd St NW, Washington, DC 20052 (USA)
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 0107 Chemistry Building, 8051 Regents Drive, College Park, MD 20742 (USA)
- Department of Chemistry, The George Washington University, 800 22nd St NW, Washington, DC 20052 (USA)
- Department of Anatomy & Cell Biology, School of Medicine and Health Sciences, The George Washington University, 2300 I Street NW, Washington, DC 20037 (USA)
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7
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Lombard‐Banek C, Li J, Portero EP, Onjiko RM, Singer CD, Plotnick DO, Al Shabeeb RQ, Nemes P. In Vivo Subcellular Mass Spectrometry Enables Proteo‐Metabolomic Single‐Cell Systems Biology in a Chordate Embryo Developing to a Normally Behaving Tadpole (
X. laevis
)**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Camille Lombard‐Banek
- Department of Chemistry & Biochemistry University of Maryland 0107 Chemistry Building 8051 Regents Drive College Park MD 20742 USA
| | - Jie Li
- Department of Chemistry & Biochemistry University of Maryland 0107 Chemistry Building 8051 Regents Drive College Park MD 20742 USA
| | - Erika P. Portero
- Department of Chemistry & Biochemistry University of Maryland 0107 Chemistry Building 8051 Regents Drive College Park MD 20742 USA
| | - Rosemary M. Onjiko
- Department of Chemistry The George Washington University 800 22nd St NW Washington DC 20052 USA
| | - Chase D. Singer
- Department of Chemistry & Biochemistry University of Maryland 0107 Chemistry Building 8051 Regents Drive College Park MD 20742 USA
| | - David O. Plotnick
- Department of Chemistry The George Washington University 800 22nd St NW Washington DC 20052 USA
| | - Reem Q. Al Shabeeb
- Department of Chemistry The George Washington University 800 22nd St NW Washington DC 20052 USA
| | - Peter Nemes
- Department of Chemistry & Biochemistry University of Maryland 0107 Chemistry Building 8051 Regents Drive College Park MD 20742 USA
- Department of Chemistry The George Washington University 800 22nd St NW Washington DC 20052 USA
- Department of Anatomy & Cell Biology School of Medicine and Health Sciences The George Washington University 2300 I Street NW Washington DC 20037 USA
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8
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Onjiko RM, Nemes P, Moody SA. Altering metabolite distribution at Xenopus cleavage stages affects left-right gene expression asymmetries. Genesis 2021; 59:e23418. [PMID: 33826226 DOI: 10.1002/dvg.23418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
The left-right (L-R) axis of most bilateral animals is established during gastrulation when a transient ciliated structure creates a directional flow of signaling molecules that establish asymmetric gene expression in the lateral plate mesoderm. However, in some animals, an earlier differential distribution of molecules and cell division patterns initiate or at least influence L-R patterning. Using single-cell high-resolution mass spectrometry, we previously reported a limited number of small molecule (metabolite) concentration differences between left and right dorsal-animal blastomeres of the eight-cell Xenopus embryo. Herein, we examined whether altering the distribution of some of these molecules influenced early events in L-R patterning. Using lineage tracing, we found that injecting right-enriched metabolites into the left cell caused its descendant cells to disperse in patterns that varied from those in control gastrulae; this did not occur when left-enriched metabolites were injected into the right cell. At later stages, injecting left-enriched metabolites into the right cell perturbed the expression of genes known to: (a) be required for the formation of the gastrocoel roof plate (foxj1); (b) lead to the asymmetric expression of Nodal (dand5/coco); or (c) result from asymmetrical nodal expression (pitx2). Despite these perturbations in gene expression, we did not observe heterotaxy in heart or gut looping at tadpole stages. These studies indicate that altering metabolite distribution at cleavage stages at the concentrations tested in this study impacts the earliest steps of L-R gene expression that then can be compensated for during organogenesis.
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Affiliation(s)
- Rosemary M Onjiko
- Department of Chemistry, The George Washington University, Washington, District of Columbia
| | - Peter Nemes
- Department of Chemistry, The George Washington University, Washington, District of Columbia.,Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia.,Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland
| | - Sally A Moody
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia
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9
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Paraiso KD, Blitz IL, Coley M, Cheung J, Sudou N, Taira M, Cho KWY. Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation. Cell Rep 2020; 27:2962-2977.e5. [PMID: 31167141 PMCID: PMC6610736 DOI: 10.1016/j.celrep.2019.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/30/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023] Open
Abstract
Elucidation of the sequence of events underlying the dynamic interaction
between transcription factors and chromatin states is essential. Maternal
transcription factors function at the top of the regulatory hierarchy to specify
the primary germ layers at the onset of zygotic genome activation (ZGA). We
focus on the formation of endoderm progenitor cells and examine the interactions
between maternal transcription factors and chromatin state changes underlying
the cell specification process. Endoderm-specific factors Otx1 and Vegt together
with Foxh1 orchestrate endoderm formation by coordinated binding to select
regulatory regions. These interactions occur before the deposition of enhancer
histone marks around the regulatory regions, and these TFs recruit RNA
polymerase II, regulate enhancer activity, and establish super-enhancers
associated with important endodermal genes. Therefore, maternal transcription
factors Otx1, Vegt, and Foxh1 combinatorially regulate the activity of
super-enhancers, which in turn activate key lineage-specifying genes during
ZGA. How do maternal transcription factors interact with chromatin regions to
coordinate the endodermal gene regulatory program? Paraiso et al. demonstrate
that combinatorial binding of maternal Otx1, Vegt, and Foxh1 to select enhancers
and super-enhancers in the genome controls endodermal cell fate specification
during zygotic gene activation.
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Affiliation(s)
- Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Masani Coley
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jessica Cheung
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Norihiro Sudou
- Department of Anatomy, Tokyo Women's Medical University, Tokyo, Japan
| | - Masanori Taira
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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10
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Paraiso KD, Cho JS, Yong J, Cho KWY. Early Xenopus gene regulatory programs, chromatin states, and the role of maternal transcription factors. Curr Top Dev Biol 2020; 139:35-60. [PMID: 32450966 PMCID: PMC11344482 DOI: 10.1016/bs.ctdb.2020.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For decades, the early development of the Xenopus embryo has been an essential model system to study the gene regulatory mechanisms that govern cellular specification. At the top of the hierarchy of gene regulatory networks, maternally deposited transcription factors initiate this process and regulate the expression of zygotic genes that give rise to three distinctive germ layer cell types (ectoderm, mesoderm, and endoderm), and subsequent generation of organ precursors. The onset of germ layer specification is also closely coupled with changes associated with chromatin modifications. This review will examine the timing of maternal transcription factors initiating the zygotic genome activation, the epigenetic landscape of embryonic chromatin, and the network structure that governs the process.
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Affiliation(s)
- Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States; Center for Complex Biological Systems, University of California, Irvine, CA, United States
| | - Jin S Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States
| | - Junseok Yong
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States; Center for Complex Biological Systems, University of California, Irvine, CA, United States.
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11
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Gilchrist MJ, Veenstra GJC, Cho KWY. Transcriptomics and Proteomics Methods for Xenopus Embryos and Tissues. Cold Spring Harb Protoc 2020; 2020:098350. [PMID: 31772075 DOI: 10.1101/pdb.top098350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The general field of quantitative biology has advanced significantly on the back of recent improvements in both sequencing technology and proteomics methods. The development of high-throughput, short-read sequencing has revolutionized RNA-based expression studies, while improvements in proteomics methods have enabled quantitative studies to attain better resolution. Here we introduce methods to undertake global analyses of gene expression through RNA and protein quantification in Xenopus embryos and tissues.
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Affiliation(s)
- Michael J Gilchrist
- The Francis Crick Institute, London NW1 1AT, United Kingdom; .,Department of Molecular Developmental Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- The Francis Crick Institute, London NW1 1AT, United Kingdom; .,Department of Molecular Developmental Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, California 92697
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12
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Gentsch GE, Spruce T, Owens NDL, Smith JC. Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals. Nat Commun 2019; 10:4269. [PMID: 31537794 PMCID: PMC6753111 DOI: 10.1038/s41467-019-12263-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/30/2019] [Indexed: 12/14/2022] Open
Abstract
Embryonic development yields many different cell types in response to just a few families of inductive signals. The property of signal-receiving cells that determines how they respond to inductive signals is known as competence, and it differs in different cell types. Here, we explore the ways in which maternal factors modify chromatin to specify initial competence in the frog Xenopus tropicalis. We identify early-engaged regulatory DNA sequences, and infer from them critical activators of the zygotic genome. Of these, we show that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox3 determines competence for germ layer formation by extensively remodelling compacted chromatin before the onset of inductive signalling. This remodelling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work identifies significant developmental principles that inform our understanding of how pluripotent stem cells interpret inductive signals.
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Affiliation(s)
- George E Gentsch
- Developmental Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
| | - Thomas Spruce
- Centre for Genomic Regulation, Barcelona Institute for Science and Technology, 08003, Barcelona, Spain
| | - Nick D L Owens
- Department of Stem Cell and Developmental Biology, Pasteur Institute, 75015, Paris, France
| | - James C Smith
- Developmental Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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13
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Keiper BD. Cap-Independent mRNA Translation in Germ Cells. Int J Mol Sci 2019; 20:ijms20010173. [PMID: 30621249 PMCID: PMC6337596 DOI: 10.3390/ijms20010173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 02/07/2023] Open
Abstract
Cellular mRNAs in plants and animals have a 5'-cap structure that is accepted as the recognition point to initiate translation by ribosomes. Consequently, it was long assumed that the translation initiation apparatus was built solely for a cap-dependent (CD) mechanism. Exceptions that emerged invoke structural damage (proteolytic cleavage) to eukaryotic initiation factor 4 (eIF4) factors that disable cap recognition. The residual eIF4 complex is thought to be crippled, but capable of cap-independent (CI) translation to recruit viral or death-associated mRNAs begrudgingly when cells are in great distress. However, situations where CI translation coexists with CD translation are now known. In such cases, CI translation is still a minor mechanism in the major background of CD synthesis. In this review, I propose that germ cells do not fit this mold. Using observations from various animal models of oogenesis and spermatogenesis, I suggest that CI translation is a robust partner to CD translation to carry out the translational control that is so prevalent in germ cell development. Evidence suggests that CI translation provides surveillance of germ cell homeostasis, while CD translation governs the regulated protein synthesis that ushers these meiotic cells through the remarkable steps in sperm/oocyte differentiation.
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Affiliation(s)
- Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA.
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14
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Janesick A, Tang W, Shioda T, Blumberg B. RARγ is required for mesodermal gene expression prior to gastrulation in Xenopus. Development 2018; 145:dev147769. [PMID: 30111657 DOI: 10.1242/dev.147769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 07/31/2018] [Indexed: 12/12/2022]
Abstract
The developing vertebrate embryo is exquisitely sensitive to retinoic acid (RA) concentration, particularly during anteroposterior patterning. In contrast to Nodal and Wnt signaling, RA was not previously considered to be an instructive signal in mesoderm formation during gastrulation. Here, we show in Xenopus that RARγ is indispensable for the expression of early mesoderm markers and is, therefore, an obligatory factor in mesodermal competence and/or maintenance. We identified several novel targets upregulated by RA receptor signaling in the early gastrula that are expressed in the circumblastoporal ring and linked to mesodermal development. Despite overlapping expression patterns of the genes encoding the RA-synthesizing enzyme Aldh1a2 and the RA-degrading enzyme Cyp26a1, RARγ1 functions as a transcriptional activator in early mesoderm development, suggesting that RA ligand is available to the embryo earlier than previously appreciated. RARγ1 is required for cellular adhesion, as revealed by spontaneous dissociation and depletion of ncam1 mRNA in animal caps harvested from RARγ1 knockdown embryos. RARγ1 knockdown obliterates somite boundaries, and causes loss of Myod protein in the presomitic mesoderm, but ectopic, persistent expression of Myod protein in the trunk. Thus, RARγ1 is required for stabilizing the mesodermal fate, myogenic commitment, somite boundary formation, and terminal skeletal muscle differentiation.
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Affiliation(s)
- Amanda Janesick
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300, USA
| | - Weiyi Tang
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300, USA
| | - Toshi Shioda
- Center for Cancer Research, Massachusetts General Hospital, Building 149, 13th Street, Charlestown, MA 02129, USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-2300, USA
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15
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Monteiro RS, Gentsch GE, Smith JC. Transcriptomics of dorso-ventral axis determination in Xenopus tropicalis. Dev Biol 2018; 439:69-79. [PMID: 29709598 PMCID: PMC5971218 DOI: 10.1016/j.ydbio.2018.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/08/2018] [Accepted: 04/24/2018] [Indexed: 11/26/2022]
Abstract
Amphibian embryos provide a powerful system to study early cell fate determination because their eggs are externally fertilised, large, and easy to manipulate. Ultraviolet (UV) or lithium chloride (LiCl) treatment are classic embryonic manipulations frequently used to perturb specification of the dorso-ventral (DV) axis by affecting the stability of the maternal Wnt mediator β-catenin. Such treatments result in the formation of so-called ventralised or dorsalised embryos. Although these phenotypes have been well described with respect to their morphology and some aspects of gene expression, their whole transcriptomes have never been systematically characterised and compared. Here we show that at the early gastrula stage UV-treated embryos are transcriptionally more closely related to untreated embryos than to LiCl-treated embryos. Transcriptional comparisons with dissected ventral and dorsal regions of unperturbed gastrula embryos indicate that UV and LiCl treatments indeed enrich for ventral and dorsal cells, respectively. However, these treatments also affect the balance of neural induction in the ectodermal germ layer, with LiCl stimulating pro-neural BMP inhibition and UV preferentially generating epidermis because of elevated BMP levels. Thus the transcriptomes of UV- and LiCl-treated embryos can best be described as ventro-epidermalised and dorso-neuralised. These descriptions notwithstanding, our profiling reveals several hitherto uncharacterized genes with differential expression along the DV axis. At least one of these genes, a RNF220-like ubiquitin ligase, is activated dorsally by β-catenin. Our analysis of UV/LiCl-mediated axis perturbation will enhance the mechanistic understanding of DV axis determination in vertebrates.
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Affiliation(s)
- Rita S Monteiro
- The Francis Crick Institute, Developmental Biology Laboratory, 1 Midland Road, London NW1 1AT, United Kingdom.
| | - George E Gentsch
- The Francis Crick Institute, Developmental Biology Laboratory, 1 Midland Road, London NW1 1AT, United Kingdom
| | - James C Smith
- The Francis Crick Institute, Developmental Biology Laboratory, 1 Midland Road, London NW1 1AT, United Kingdom.
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16
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Sindelka R, Abaffy P, Qu Y, Tomankova S, Sidova M, Naraine R, Kolar M, Peuchen E, Sun L, Dovichi N, Kubista M. Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan. Sci Rep 2018; 8:8315. [PMID: 29844480 PMCID: PMC5974320 DOI: 10.1038/s41598-018-26592-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/08/2018] [Indexed: 12/24/2022] Open
Abstract
Asymmetric cell division is a ubiquitous feature during the development of higher organisms. Asymmetry is achieved by differential localization or activities of biological molecules such as proteins, and coding and non-coding RNAs. Here, we present subcellular transcriptomic and proteomic analyses along the animal-vegetal axis of Xenopus laevis eggs. More than 98% of the maternal mRNAs could be categorized into four localization profile groups: animal, vegetal, extremely vegetal, and a newly described group of mRNAs that we call extremely animal, which are mRNAs enriched in the animal cortex region. 3′UTRs of localized mRNAs were analyzed for localization motifs. Several putative motifs were discovered for vegetal and extremely vegetal mRNAs, while no distinct conserved motifs for the extremely animal mRNAs were identified, suggesting different localization mechanisms. Asymmetric profiles were also found for proteins, with correlation to those of corresponding mRNAs. Based on unexpected observation of the profiles of the homoeologous genes exd2 we propose a possible mechanism of genetic evolution.
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Affiliation(s)
- Radek Sindelka
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic.
| | - Pavel Abaffy
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Yanyan Qu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Silvie Tomankova
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Monika Sidova
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Ravindra Naraine
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic
| | - Michal Kolar
- Institute of Molecular Genetics, Videnska 1083, 142 20, Prague 4, Czech Republic
| | - Elizabeth Peuchen
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Norman Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Mikael Kubista
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Prumyslova 595, Vestec, 252 50, Czech Republic.,TATAA Biocenter, Odinsgatan 28, Göteborg, 411 03, Sweden
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17
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Owens DA, Butler AM, Aguero TH, Newman KM, Van Booven D, King ML. High-throughput analysis reveals novel maternal germline RNAs crucial for primordial germ cell preservation and proper migration. Development 2017; 144:292-304. [PMID: 28096217 DOI: 10.1242/dev.139220] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 11/25/2016] [Indexed: 01/10/2023]
Abstract
During oogenesis, hundreds of maternal RNAs are selectively localized to the animal or vegetal pole, including determinants of somatic and germline fates. Although microarray analysis has identified localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high-throughput RNA-sequencing analysis to comprehensively interrogate animal and vegetal pole RNAs in the fully grown Xenopus laevis oocyte. We identified 411 (198 annotated) and 27 (15 annotated) enriched mRNAs at the vegetal and animal pole, respectively. Ninety were novel mRNAs over 4-fold enriched at the vegetal pole and six were over 10-fold enriched at the animal pole. Unlike mRNAs, microRNAs were not asymmetrically distributed. Whole-mount in situ hybridization confirmed that all 17 selected mRNAs were localized. Biological function and network analysis of vegetally enriched transcripts identified protein-modifying enzymes, receptors, ligands, RNA-binding proteins, transcription factors and co-factors with five defining hubs linking 47 genes in a network. Initial functional studies of maternal vegetally localized mRNAs show that sox7 plays a novel and important role in primordial germ cell (PGC) development and that ephrinB1 (efnb1) is required for proper PGC migration. We propose potential pathways operating at the vegetal pole that highlight where future investigations might be most fruitful.
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Affiliation(s)
- Dawn A Owens
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Amanda M Butler
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Tristan H Aguero
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Karen M Newman
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Derek Van Booven
- The Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
| | - Mary Lou King
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
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18
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Onjiko RM, Plotnick DO, Moody SA, Nemes P. Metabolic Comparison of Dorsal versus Ventral Cells Directly in the Live 8-cell Frog Embryo by Microprobe Single-cell CE-ESI-MS. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2017; 9:4964-4970. [PMID: 29062391 PMCID: PMC5650250 DOI: 10.1039/c7ay00834a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single-cell mass spectrometry (MS) empowers the characterization of metabolomic changes as cells differentiate to different tissues during early embryogenesis. Using whole-cell dissection and capillary electrophoresis electrospray ionization (CE-ESI) MS, we recently uncovered metabolic cell-to-cell differences in the 8- and 16-cell embryo of the South African clawed frog (Xenopus laevis), raising the question whether metabolic cell heterogeneity is also detectable across the dorsal-ventral axis of the 8-cell embryo. Here, we tested this hypothesis directly in the live embryo by quantifying single-cell metabolism between the left dorsal-animal (D1L) and left ventral-animal (V1L) cell pairs in the same embryo using microprobe single-cell CE-ESI-MS in the positive ion mode. After quantifying ~70 molecular features, including 52 identified metabolites, that were reproducibly detected in both cells among n = 5 different embryos, we employed supervised multivariate data analysis based on partial least squares discriminant analysis (PLSDA) to compare metabolism between the cell types. Statistical analysis revealed that asparagine, glycine betaine, and a yet-unidentified molecule were statistically significantly enriched in the D1L cell compared to V1L (p < 0.05 and fold change ≥ 1.5). These results demonstrate that cells derived from the same hemisphere (animal pole) harbor different metabolic activity along the dorsal-ventral axis as early as the 8-cell stage. Apart from providing new evidence of metabolic cell heterogeneity during early embryogenesis, this study demonstrates that microprobe single-cell CE-ESI-MS enables the analysis of multiple single cells in the same live vertebrate embryo.
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Affiliation(s)
- Rosemary M. Onjiko
- Department of Chemistry, The George Washington University, Washington DC, 20052
| | - David O. Plotnick
- Department of Chemistry, The George Washington University, Washington DC, 20052
| | - Sally A. Moody
- Department of Anatomy and Regenerative Biology, The George Washington University, Washington DC, 20052
| | - Peter Nemes
- Department of Chemistry, The George Washington University, Washington DC, 20052
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19
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Spemann organizer transcriptome induction by early beta-catenin, Wnt, Nodal, and Siamois signals in Xenopus laevis. Proc Natl Acad Sci U S A 2017; 114:E3081-E3090. [PMID: 28348214 DOI: 10.1073/pnas.1700766114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The earliest event in Xenopus development is the dorsal accumulation of nuclear β-catenin under the influence of cytoplasmic determinants displaced by fertilization. In this study, a genome-wide approach was used to examine transcription of the 43,673 genes annotated in the Xenopus laevis genome under a variety of conditions that inhibit or promote formation of the Spemann organizer signaling center. Loss of function of β-catenin with antisense morpholinos reproducibly reduced the expression of 247 mRNAs at gastrula stage. Interestingly, only 123 β-catenin targets were enriched on the dorsal side and defined an early dorsal β-catenin gene signature. These genes included several previously unrecognized Spemann organizer components. Surprisingly, only 3 of these 123 genes overlapped with the late Wnt signature recently defined by two other groups using inhibition by Dkk1 mRNA or Wnt8 morpholinos, which indicates that the effects of β-catenin/Wnt signaling in early development are exquisitely regulated by stage-dependent mechanisms. We analyzed transcriptome responses to a number of treatments in a total of 46 RNA-seq libraries. These treatments included, in addition to β-catenin depletion, regenerating dorsal and ventral half-embryos, lithium chloride treatment, and the overexpression of Wnt8, Siamois, and Cerberus mRNAs. Only some of the early dorsal β-catenin signature genes were activated at blastula whereas others required the induction of endomesoderm, as indicated by their inhibition by Cerberus overexpression. These comprehensive data provide a rich resource for analyzing how the dorsal and ventral regions of the embryo communicate with each other in a self-organizing vertebrate model embryo.
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20
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Charney RM, Paraiso KD, Blitz IL, Cho KWY. A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs. Semin Cell Dev Biol 2017; 66:12-24. [PMID: 28341363 DOI: 10.1016/j.semcdb.2017.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/12/2017] [Accepted: 03/20/2017] [Indexed: 02/08/2023]
Abstract
Germ layer formation is among the earliest differentiation events in metazoan embryos. In triploblasts, three germ layers are formed, among which the endoderm gives rise to the epithelial lining of the gut tube and associated organs including the liver, pancreas and lungs. In frogs (Xenopus), where early germ layer formation has been studied extensively, the process of endoderm specification involves the interplay of dozens of transcription factors. Here, we review the interactions between these factors, summarized in a transcriptional gene regulatory network (GRN). We highlight regulatory connections conserved between frog, fish, mouse, and human endodermal lineages. Especially prominent is the conserved role and regulatory targets of the Nodal signaling pathway and the T-box transcription factors, Vegt and Eomes. Additionally, we highlight network topologies and motifs, and speculate on their possible roles in development.
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Affiliation(s)
- Rebekah M Charney
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA.
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21
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Sindelka R, Sidova M, Abaffy P, Kubista M. Asymmetric Localization and Distribution of Factors Determining Cell Fate During Early Development of Xenopus laevis. Results Probl Cell Differ 2017; 61:229-241. [PMID: 28409307 DOI: 10.1007/978-3-319-53150-2_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Asymmetric division is a property of eukaryotic cells that is fundamental to the formation of higher life forms. Despite its importance, the mechanism behind it remains elusive. Asymmetry in the cell is induced by polarization of cell fate determinants that become unevenly distributed among progeny cells. So far dozens of determinants have been identified. Xenopus laevis is an ideal system to study asymmetric cell division during early development, because of the huge size of its oocytes and early-stage blastomeres. Here, we present the current knowledge about localization and distribution of cell fate determinants along the three body axes: animal-vegetal, dorsal-ventral, and left-right. Uneven distribution of cell fate determinants during early development specifies the formation of the embryonic body plan.
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Affiliation(s)
- Radek Sindelka
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic-Biocev, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Monika Sidova
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic-Biocev, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Pavel Abaffy
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic-Biocev, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic-Biocev, Prumyslova 595, 252 50, Vestec, Czech Republic.
- TATAA Biocenter AB, Odinsgatan 28, 411 03, Göteborg, Sweden.
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22
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Tassan JP, Wühr M, Hatte G, Kubiak J. Asymmetries in Cell Division, Cell Size, and Furrowing in the Xenopus laevis Embryo. Results Probl Cell Differ 2017; 61:243-260. [PMID: 28409308 DOI: 10.1007/978-3-319-53150-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Asymmetric cell divisions produce two daughter cells with distinct fate. During embryogenesis, this mechanism is fundamental to build tissues and organs because it generates cell diversity. In adults, it remains crucial to maintain stem cells. The enthusiasm for asymmetric cell division is not only motivated by the beauty of the mechanism and the fundamental questions it raises, but has also very pragmatic reasons. Indeed, misregulation of asymmetric cell divisions is believed to have dramatic consequences potentially leading to pathogenesis such as cancers. In diverse model organisms, asymmetric cell divisions result in two daughter cells, which differ not only by their fate but also in size. This is the case for the early Xenopus laevis embryo, in which the two first embryonic divisions are perpendicular to each other and generate two pairs of blastomeres, which usually differ in size: one pair of blastomeres is smaller than the other. Small blastomeres will produce embryonic dorsal structures, whereas the larger pair will evolve into ventral structures. Here, we present a speculative model on the origin of the asymmetry of this cell division in the Xenopus embryo. We also discuss the apparently coincident asymmetric distribution of cell fate determinants and cell-size asymmetry of the 4-cell stage embryo. Finally, we discuss the asymmetric furrowing during epithelial cell cytokinesis occurring later during Xenopus laevis embryo development.
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Affiliation(s)
- Jean-Pierre Tassan
- , CNRS UMR 6290, Rennes, France. .,Université de Rennes 1, Institut de Génétique et Développement de Rennes, Rennes, France.
| | - Martin Wühr
- Department of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Guillaume Hatte
- , CNRS UMR 6290, Rennes, France.,Université de Rennes 1, Institut de Génétique et Développement de Rennes, Rennes, France
| | - Jacek Kubiak
- , CNRS UMR 6290, Rennes, France.,Université de Rennes 1, Institut de Génétique et Développement de Rennes, Rennes, France
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23
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King ML. Maternal messages to live by: a personal historical perspective. Genesis 2017; 55:10.1002/dvg.23007. [PMID: 28095642 PMCID: PMC5276792 DOI: 10.1002/dvg.23007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 12/17/2022]
Abstract
In the 1980s, the study of localized maternal mRNAs was just emerging as a new research area. Classic embryological studies had linked the inheritance of cytoplasmic domains with specific cell lineages, but the underlying molecular nature of these putative determinants remained a mystery. The model system Xenopus would play a pivotal role in the progress of this new field. In fact, the first localized maternal mRNA to be identified and cloned from any organism was Xenopus vg1, a TGF-beta family member. This seminal finding opened the door to many subsequent studies focused on how RNAs are localized and what functions they had in development. As the field moves into the future, Xenopus remains the system of choice for studies identifying RNA/protein transport particles and maternal RNAs through RNA-sequencing.
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Affiliation(s)
- Mary Lou King
- Department of Cell Biology, University of Miami Miller School of Medicine, 1011 NW 15th St, Miami, FL 33136, USA
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24
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Lombard-Banek C, Moody SA, Nemes P. High-Sensitivity Mass Spectrometry for Probing Gene Translation in Single Embryonic Cells in the Early Frog ( Xenopus) Embryo. Front Cell Dev Biol 2016; 4:100. [PMID: 27761436 PMCID: PMC5050209 DOI: 10.3389/fcell.2016.00100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/29/2016] [Indexed: 01/01/2023] Open
Abstract
Direct measurement of protein expression with single-cell resolution promises to deepen the understanding of the basic molecular processes during normal and impaired development. High-resolution mass spectrometry provides detailed coverage of the proteomic composition of large numbers of cells. Here we discuss recent mass spectrometry developments based on single-cell capillary electrophoresis that extend discovery proteomics to sufficient sensitivity to enable the measurement of proteins in single cells. The single-cell mass spectrometry system is used to detect a large number of proteins in single embryonic cells in the 16-cell embryo of the South African clawed frog (Xenopus laevis) that give rise to distinct tissue types. Single-cell measurements of protein expression provide complementary information on gene transcription during early development of the vertebrate embryo, raising a potential to understand how differential gene expression coordinates normal cell heterogeneity during development.
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Affiliation(s)
| | - Sally A Moody
- Department of Anatomy and Regenerative Biology, The George Washington University Washington, DC, USA
| | - Peter Nemes
- Department of Chemistry, The George Washington University Washington, DC, USA
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25
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Lombard-Banek C, Reddy S, Moody SA, Nemes P. Label-free Quantification of Proteins in Single Embryonic Cells with Neural Fate in the Cleavage-Stage Frog (Xenopus laevis) Embryo using Capillary Electrophoresis Electrospray Ionization High-Resolution Mass Spectrometry (CE-ESI-HRMS). Mol Cell Proteomics 2016; 15:2756-68. [PMID: 27317400 PMCID: PMC4974349 DOI: 10.1074/mcp.m115.057760] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/16/2016] [Indexed: 12/12/2022] Open
Abstract
Quantification of protein expression in single cells promises to advance a systems-level understanding of normal development. Using a bottom-up proteomic workflow and multiplexing quantification by tandem mass tags, we recently demonstrated relative quantification between single embryonic cells (blastomeres) in the frog (Xenopus laevis) embryo. In this study, we minimize derivatization steps to enhance analytical sensitivity and use label-free quantification (LFQ) for single Xenopus cells. The technology builds on a custom-designed capillary electrophoresis microflow-electrospray ionization high-resolution mass spectrometry platform and LFQ by MaxLFQ (MaxQuant). By judiciously tailoring performance to peptide separation, ionization, and data-dependent acquisition, we demonstrate an ∼75-amol (∼11 nm) lower limit of detection and quantification for proteins in complex cell digests. The platform enabled the identification of 438 nonredundant protein groups by measuring 16 ng of protein digest, or <0.2% of the total protein contained in a blastomere in the 16-cell embryo. LFQ intensity was validated as a quantitative proxy for protein abundance. Correlation analysis was performed to compare protein quantities between the embryo and n = 3 different single D11 blastomeres, which are fated to develop into the nervous system. A total of 335 nonredundant protein groups were quantified in union between the single D11 cells spanning a 4 log-order concentration range. LFQ and correlation analysis detected expected proteomic differences between the whole embryo and blastomeres, and also found translational differences between individual D11 cells. LFQ on single cells raises exciting possibilities to study gene expression in other cells and models to help better understand cell processes on a systems biology level.
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Affiliation(s)
| | - Sushma Reddy
- From the ‡Department of Chemistry and ¶Thomas Jefferson High School for Science and Technology, Alexandria, Virginia
| | - Sally A Moody
- §Department of Anatomy and Regenerative Biology, The George Washington University, Washington, DC
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26
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Onjiko RM, Morris SE, Moody SA, Nemes P. Single-cell mass spectrometry with multi-solvent extraction identifies metabolic differences between left and right blastomeres in the 8-cell frog (Xenopus) embryo. Analyst 2016; 141:3648-56. [PMID: 27004603 PMCID: PMC4899105 DOI: 10.1039/c6an00200e] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Single-cell metabolic mass spectrometry enables the discovery (untargeted) analysis of small molecules in individual cells. Using single-cell capillary electrophoresis high-resolution mass spectrometry (CE-HRMS), we recently uncovered small-molecule differences between embryonic cells located along the animal-vegetal and dorsal-ventral axes of the 16-cell frog (Xenopus laevis) embryo, raising the question whether metabolic cell heterogeneity also exists along the left-right body axis. To address this question, we here advance single-cell CE-HRMS for identifying and quantifying metabolites in higher analytical sensitivity, and then use the methodology to compare metabolite production between left and right cells. Our strategy utilizes multiple solvents with complementary physicochemical properties to extract small molecules from single cells and improve electrophoretic separation, increasing metabolite ion signals for quantification and tandem HRMS. As a result, we were able to identify 55 different small molecules in D1 cells that were isolated from 8-cell embryos. To quantify metabolite production between left and right cells, we analyzed n = 24 different D1 cells in technical duplicate-triplicate measurements. Statistical and multivariate analysis based on 80 of the most repeatedly quantified compounds revealed 10 distinct metabolites that were significantly differentially accumulated in the left or right cells (p < 0.05 and fold change ≥1.5). These metabolites were enriched in the arginine-proline metabolic pathway in the right, but not the left D1 cells. Besides providing analytical benefits for single-cell HRMS, this work provides new metabolic data on the establishment of normal body asymmetry in the early developing embryo.
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Affiliation(s)
- Rosemary M Onjiko
- Department of Chemistry, The George Washington University, Washington, DC 20052, USA.
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Gaur S, Mandelbaum M, Herold M, Majumdar HD, Neilson KM, Maynard TM, Mood K, Daar IO, Moody SA. Neural transcription factors bias cleavage stage blastomeres to give rise to neural ectoderm. Genesis 2016; 54:334-49. [PMID: 27092474 PMCID: PMC4912902 DOI: 10.1002/dvg.22943] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 01/23/2023]
Abstract
The decision by embryonic ectoderm to give rise to epidermal versus neural derivatives is the result of signaling events during blastula and gastrula stages. However, there also is evidence in Xenopus that cleavage stage blastomeres contain maternally derived molecules that bias them toward a neural fate. We used a blastomere explant culture assay to test whether maternally deposited transcription factors bias 16-cell blastomere precursors of epidermal or neural ectoderm to express early zygotic neural genes in the absence of gastrulation interactions or exogenously supplied signaling factors. We found that Foxd4l1, Zic2, Gmnn, and Sox11 each induced explants made from ventral, epidermis-producing blastomeres to express early neural genes, and that at least some of the Foxd4l1 and Zic2 activities are required at cleavage stages. Similarly, providing extra Foxd4l1 or Zic2 to explants made from dorsal, neural plate-producing blastomeres significantly increased the expression of early neural genes, whereas knocking down either significantly reduced them. These results show that maternally delivered transcription factors bias cleavage stage blastomeres to a neural fate. We demonstrate that mouse and human homologs of Foxd4l1 have similar functional domains compared to the frog protein, as well as conserved transcriptional activities when expressed in Xenopus embryos and blastomere explants. genesis 54:334-349, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Shailly Gaur
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | - Max Mandelbaum
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | - Mona Herold
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | - Himani Datta Majumdar
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | - Karen M. Neilson
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
| | | | - Kathy Mood
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Ira O. Daar
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Sally A. Moody
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, 2300 I Street, NW, Washington DC, USA
- George Washington University Institute for Neuroscience
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Lombard-Banek C, Moody SA, Nemes P. Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog (Xenopus) Embryo. Angew Chem Int Ed Engl 2016; 55:2454-8. [PMID: 26756663 PMCID: PMC4755155 DOI: 10.1002/anie.201510411] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/21/2015] [Indexed: 01/05/2023]
Abstract
We advance mass spectrometry from a cell population‐averaging tool to one capable of quantifying the expression of diverse proteins in single embryonic cells. Our instrument combines capillary electrophoresis (CE), electrospray ionization, and a tribrid ultrahigh‐resolution mass spectrometer (HRMS) to enable untargeted (discovery) proteomics with ca. 25 amol lower limit of detection. CE‐μESI‐HRMS enabled the identification of 500–800 nonredundant protein groups by measuring 20 ng, or <0.2% of the total protein content in single blastomeres that were isolated from the 16‐cell frog (Xenopus laevis) embryo, amounting to a total of 1709 protein groups identified between n=3 biological replicates. By quantifying ≈150 nonredundant protein groups between all blastomeres and replicate measurements, we found significant translational cell heterogeneity along multiple axes of the embryo at this very early stage of development when the transcriptional program of the embryo has yet to begin.
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Affiliation(s)
- Camille Lombard-Banek
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, 800 22ndStreet, NW, Suite 4000, Washington, DC, 20052, USA
| | - Sally A Moody
- Department of Anatomy and Regenerative Biology, The George Washington University, Washington, DC, 20052, USA
| | - Peter Nemes
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, 800 22ndStreet, NW, Suite 4000, Washington, DC, 20052, USA.
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Lombard‐Banek C, Moody SA, Nemes P. Single‐Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16‐Cell Frog (
Xenopus
) Embryo. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510411] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Camille Lombard‐Banek
- Department of Chemistry W. M. Keck Institute for Proteomics Technology and Applications The George Washington University 800 22ndStreet, NW, Suite 4000 Washington DC 20052 USA
| | - Sally A. Moody
- Department of Anatomy and Regenerative Biology The George Washington University Washington DC 20052 USA
| | - Peter Nemes
- Department of Chemistry W. M. Keck Institute for Proteomics Technology and Applications The George Washington University 800 22ndStreet, NW, Suite 4000 Washington DC 20052 USA
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Claußen M, Lingner T, Pommerenke C, Opitz L, Salinas G, Pieler T. Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species. Mol Biol Cell 2015; 26:3777-87. [PMID: 26337391 PMCID: PMC4626063 DOI: 10.1091/mbc.e15-02-0115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/28/2015] [Indexed: 12/27/2022] Open
Abstract
Subcellular localization of mRNAs contributes to the generation of cellular asymmetries and cell fate determination. A comparative global analysis is given of animally and vegetally enriched RNAs in oocytes from two closely related Xenopus species. RNAs that localize to the vegetal cortex during Xenopus laevis oogenesis have been reported to function in germ layer patterning, axis determination, and development of the primordial germ cells. Here we report on the genome-wide, comparative analysis of differentially localizing RNAs in Xenopus laevis and Xenopus tropicalis oocytes, revealing a surprisingly weak degree of conservation in respect to the identity of animally as well as vegetally enriched transcripts in these closely related species. Heterologous RNA injections and protein binding studies indicate that the different RNA localization patterns in these two species are due to gain/loss of cis-acting localization signals rather than to differences in the RNA-localizing machinery.
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Affiliation(s)
- Maike Claußen
- Institute of Developmental Biochemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Thomas Lingner
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Claudia Pommerenke
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Lennart Opitz
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Gabriela Salinas
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Tomas Pieler
- Institute of Developmental Biochemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
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