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Ermakova GV, Kucheryavyy AV, Zaraisky AG, Bayramov AV. The Molecular Mechanism of Body Axis Induction in Lampreys May Differ from That in Amphibians. Int J Mol Sci 2024; 25:2412. [PMID: 38397089 PMCID: PMC10889193 DOI: 10.3390/ijms25042412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/12/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Lamprey homologues of the classic embryonic inducer Noggin are similar in expression pattern and functional properties to Noggin homologues of jawed vertebrates. All noggin genes of vertebrates apparently originated from a single ancestral gene as a result of genome duplications. nogginA, nogginB and nogginC of lampreys, like noggin1 and noggin2 of gnathostomes, demonstrate the ability to induce complete secondary axes with forebrain and eye structures when overexpressed in Xenopus laevis embryos. According to current views, this finding indicates the ability of lamprey Noggin proteins to suppress the activity of the BMP, Nodal/Activin and Wnt/beta-catenin signaling pathways, as shown for Noggin proteins of gnathostomes. In this work, by analogy with experiments in Xenopus embryos, we attempted to induce secondary axes in the European river lamprey Lampetra fluviatilis by injecting noggin mRNAs into lamprey eggs in vivo. Surprisingly, unlike what occurs in amphibians, secondary axis induction in the lampreys either by noggin mRNAs or by chordin and cerberus mRNAs, the inductive properties of which have been described, was not observed. Only wnt8a mRNA demonstrated the ability to induce secondary axes in the lampreys. Such results may indicate that the mechanism of axial specification in lampreys, which represent jawless vertebrates, may differ in detail from that in the jawed clade.
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Affiliation(s)
- Galina V. Ermakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Aleksandr V. Kucheryavyy
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 119071, Russia;
| | - Andrey G. Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
- Department of Regenerative Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Andrey V. Bayramov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
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2
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Kocere A, Lalonde RL, Mosimann C, Burger A. Lateral thinking in syndromic congenital cardiovascular disease. Dis Model Mech 2023; 16:dmm049735. [PMID: 37125615 PMCID: PMC10184679 DOI: 10.1242/dmm.049735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Syndromic birth defects are rare diseases that can present with seemingly pleiotropic comorbidities. Prime examples are rare congenital heart and cardiovascular anomalies that can be accompanied by forelimb defects, kidney disorders and more. Whether such multi-organ defects share a developmental link remains a key question with relevance to the diagnosis, therapeutic intervention and long-term care of affected patients. The heart, endothelial and blood lineages develop together from the lateral plate mesoderm (LPM), which also harbors the progenitor cells for limb connective tissue, kidneys, mesothelia and smooth muscle. This developmental plasticity of the LPM, which founds on multi-lineage progenitor cells and shared transcription factor expression across different descendant lineages, has the potential to explain the seemingly disparate syndromic defects in rare congenital diseases. Combining patient genome-sequencing data with model organism studies has already provided a wealth of insights into complex LPM-associated birth defects, such as heart-hand syndromes. Here, we summarize developmental and known disease-causing mechanisms in early LPM patterning, address how defects in these processes drive multi-organ comorbidities, and outline how several cardiovascular and hematopoietic birth defects with complex comorbidities may be LPM-associated diseases. We also discuss strategies to integrate patient sequencing, data-aggregating resources and model organism studies to mechanistically decode congenital defects, including potentially LPM-associated orphan diseases. Eventually, linking complex congenital phenotypes to a common LPM origin provides a framework to discover developmental mechanisms and to anticipate comorbidities in congenital diseases affecting the cardiovascular system and beyond.
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Affiliation(s)
- Agnese Kocere
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
- Department of Molecular Life Science, University of Zurich, 8057 Zurich, Switzerland
| | - Robert L. Lalonde
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
| | - Christian Mosimann
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
| | - Alexa Burger
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
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3
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Shen W, Gong B, Xing C, Zhang L, Sun J, Chen Y, Yang C, Yan L, Chen L, Yao L, Li G, Deng H, Wu X, Meng A. Comprehensive maturity of nuclear pore complexes regulates zygotic genome activation. Cell 2022; 185:4954-4970.e20. [PMID: 36493774 DOI: 10.1016/j.cell.2022.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/23/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Nuclear pore complexes (NPCs) are channels for nucleocytoplasmic transport of proteins and RNAs. However, it remains unclear whether composition, structure, and permeability of NPCs dynamically change during the cleavage period of vertebrate embryos and affect embryonic development. Here, we report that the comprehensive NPC maturity (CNM) controls the onset of zygotic genome activation (ZGA) during zebrafish early embryogenesis. We show that more nucleoporin proteins are recruited to and assembled into NPCs with development, resulting in progressive increase of NPCs in size and complexity. Maternal transcription factors (TFs) transport into nuclei more efficiently with increasing CNM. Deficiency or dysfunction of Nup133 or Ahctf1/Elys impairs NPC assembly, maternal TFs nuclear transport, and ZGA onset, while nup133 overexpression promotes these processes. Therefore, CNM may act as a molecular timer for ZGA by controlling nuclear transport of maternal TFs that reach nuclear concentration thresholds at a given time to initiate ZGA.
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Affiliation(s)
- 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
| | - Bo Gong
- 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
| | - Cencan Xing
- 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
| | - Lin Zhang
- 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
| | - 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
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Changmei Yang
- MOE Key Laboratory of Bioinformatics, 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
| | - Luxi Chen
- 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
| | - Likun Yao
- 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
| | - Guangyuan Li
- 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
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaotong Wu
- 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; Developmental Diseases and Cancer Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Laboratory of Stem Cell Regulation, Guangzhou Laboratory, Guangzhou 510320, China.
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4
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Talbot CD, Walsh MD, Cutty SJ, Elsayed R, Vlachaki E, Bruce AEE, Wardle FC, Nelson AC. Eomes function is conserved between zebrafish and mouse and controls left-right organiser progenitor gene expression via interlocking feedforward loops. Front Cell Dev Biol 2022; 10:982477. [PMID: 36133924 PMCID: PMC9483813 DOI: 10.3389/fcell.2022.982477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
The T-box family transcription factor Eomesodermin (Eomes) is present in all vertebrates, with many key roles in the developing mammalian embryo and immune system. Homozygous Eomes mutant mouse embryos exhibit early lethality due to defects in both the embryonic mesendoderm and the extraembryonic trophoblast cell lineage. In contrast, zebrafish lacking the predominant Eomes homologue A (Eomesa) do not suffer complete lethality and can be maintained. This suggests fundamental differences in either the molecular function of Eomes orthologues or the molecular configuration of processes in which they participate. To explore these hypotheses we initially analysed the expression of distinct Eomes isoforms in various mouse cell types. Next we compared the functional capabilities of these murine isoforms to zebrafish Eomesa. These experiments provided no evidence for functional divergence. Next we examined the functions of zebrafish Eomesa and other T-box family members expressed in early development, as well as its paralogue Eomesb. Though Eomes is a member of the Tbr1 subfamily we found evidence for functional redundancy with the Tbx6 subfamily member Tbx16, known to be absent from eutherians. However, Tbx16 does not appear to synergise with Eomesa cofactors Mixl1 and Gata5. Finally, we analysed the ability of Eomesa and other T-box factors to induce zebrafish left-right organiser progenitors (known as dorsal forerunner cells) known to be positively regulated by vgll4l, a gene we had previously shown to be repressed by Eomesa. Here we demonstrate that Eomesa indirectly upregulates vgll4l expression via interlocking feedforward loops, suggesting a role in establishment of left-right asymmetry. Conversely, other T-box factors could not similarly induce left-right organiser progenitors. Overall these findings demonstrate conservation of Eomes molecular function and participation in similar processes, but differential requirements across evolution due to additional co-expressed T-box factors in teleosts, albeit with markedly different molecular capabilities. Our analyses also provide insights into the role of Eomesa in left-right organiser formation in zebrafish.
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Affiliation(s)
- Conor D. Talbot
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Mark D. Walsh
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Stephen J. Cutty
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, King’s College London, London, United Kingdom
| | - Randa Elsayed
- Warwick Medical School, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Eirini Vlachaki
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Ashley E. E. Bruce
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Fiona C. Wardle
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, King’s College London, London, United Kingdom
| | - Andrew C. Nelson
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
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5
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Stutt N, Song M, Wilson MD, Scott IC. Cardiac specification during gastrulation - The Yellow Brick Road leading to Tinman. Semin Cell Dev Biol 2021; 127:46-58. [PMID: 34865988 DOI: 10.1016/j.semcdb.2021.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023]
Abstract
The question of how the heart develops, and the genetic networks governing this process have become intense areas of research over the past several decades. This research is propelled by classical developmental studies and potential clinical applications to understand and treat congenital conditions in which cardiac development is disrupted. Discovery of the tinman gene in Drosophila, and examination of its vertebrate homolog Nkx2.5, along with other core cardiac transcription factors has revealed how cardiac progenitor differentiation and maturation drives heart development. Careful observation of cardiac morphogenesis along with lineage tracing approaches indicated that cardiac progenitors can be divided into two broad classes of cells, namely the first and second heart fields, that contribute to the heart in two distinct waves of differentiation. Ample evidence suggests that the fate of individual cardiac progenitors is restricted to distinct cardiac structures quite early in development, well before the expression of canonical cardiac progenitor markers like Nkx2.5. Here we review the initial specification of cardiac progenitors, discuss evidence for the early patterning of cardiac progenitors during gastrulation, and consider how early gene expression programs and epigenetic patterns can direct their development. A complete understanding of when and how the developmental potential of cardiac progenitors is determined, and their potential plasticity, is of great interest developmentally and also has important implications for both the study of congenital heart disease and therapeutic approaches based on cardiac stem cell programming.
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Affiliation(s)
- Nathan Stutt
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Mengyi Song
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Michael D Wilson
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Ian C Scott
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada.
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6
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González-Stegmaier R, Peña A, Villarroel-Espíndola F, Aguila P, Oliver C, MacLeod-Carey D, Rozas-Serri M, Enriquez R, Figueroa J. Full recombinant flagellin B from Vibrio anguillarum (rFLA) and its recombinant D1 domain (rND1) promote a pro-inflammatory state and improve vaccination against P. salmonis in Atlantic salmon (S. salar). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 117:103988. [PMID: 33359361 DOI: 10.1016/j.dci.2020.103988] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/20/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Flagellin is the major component of the flagellum, and a ligand for Toll-like receptor 5. As reported, recombinant flagellin (rFLA) from Vibrio anguillarum and its D1 domain (rND1) are able to promote in vitro an upregulation of pro-inflammatory genes in gilthead seabream (Sparus aurata) and rainbow trout (Oncorhynchus mykiss) macrophages. This study evaluated the in vitro and in vivo stimulatory/adjuvant effect for rFLA and rND1 during P. salmonis vaccination in Atlantic salmon (Salmo salar). We demonstrated that rFLA and rND1 are molecules able to generate an acute upregulation of pro-inflammatory cytokines (IL-1β, IL-8, IL-12β), allowing the expression of genes associated with T-cell activation (IL-2, CD4, CD8β), and differentiation (IFNγ, IL-4/13, T-bet, Eomes, GATA3), in a differential manner, tissue/time dependent way. Altogether, our results suggest that rFLA and rND1 are valid candidates to be used as an immuno-stimulant or adjuvants with existing vaccines in farmed salmon.
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Affiliation(s)
- Roxana González-Stegmaier
- Laboratorio de Biología Molecular de Peces, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile; Laboratorio Medicina Traslacional. Instituto Clínico Oncológico. Fundación Arturo López Pérez, Santiago, Chile.
| | - Andrea Peña
- Laboratorio Pathovet Ltda, Puerto Montt, Chile
| | - Franz Villarroel-Espíndola
- Laboratorio Medicina Traslacional. Instituto Clínico Oncológico. Fundación Arturo López Pérez, Santiago, Chile
| | - Patricia Aguila
- Escuela de Tecnología Médica, Universidad Austral de Chile, Sede Puerto Montt, Chile
| | - Cristian Oliver
- Laboratorio de Inmunología y estrés de Organismos Acuáticos, Departamento de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Desmond MacLeod-Carey
- Universidad Autónoma de Chile, Facultad de Ingeniería, Instituto de Ciencias Químicas Aplicadas, Polymers and Macromolecules Center, El Llano Subercaseaux, 2801, Santiago, Chile
| | | | - Ricardo Enriquez
- Laboratorio de Biotecnología y Patología Acuática, Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
| | - Jaime Figueroa
- Laboratorio de Biología Molecular de Peces, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
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7
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Figiel DM, Elsayed R, Nelson AC. Investigating the molecular guts of endoderm formation using zebrafish. Brief Funct Genomics 2021:elab013. [PMID: 33754635 DOI: 10.1093/bfgp/elab013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
The vertebrate endoderm makes major contributions to the respiratory and gastrointestinal tracts and all associated organs. Zebrafish and humans share a high degree of genetic homology and strikingly similar endodermal organ systems. Combined with a multitude of experimental advantages, zebrafish are an attractive model organism to study endoderm development and disease. Recent functional genomics studies have shed considerable light on the gene regulatory programs governing early zebrafish endoderm development, while advances in biological and technological approaches stand to further revolutionize our ability to investigate endoderm formation, function and disease. Here, we discuss the present understanding of endoderm specification in zebrafish compared to other vertebrates, how current and emerging methods will allow refined and enhanced analysis of endoderm formation, and how integration with human data will allow modeling of the link between non-coding sequence variants and human disease.
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Affiliation(s)
- Daniela M Figiel
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
| | - Randa Elsayed
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
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8
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Axis Specification in Zebrafish Is Robust to Cell Mixing and Reveals a Regulation of Pattern Formation by Morphogenesis. Curr Biol 2020; 30:2984-2994.e3. [PMID: 32559447 PMCID: PMC7416079 DOI: 10.1016/j.cub.2020.05.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/01/2020] [Accepted: 05/14/2020] [Indexed: 12/21/2022]
Abstract
A fundamental question in developmental biology is how the early embryo establishes the spatial coordinate system that is later important for the organization of the embryonic body plan. Although we know a lot about the signaling and gene-regulatory networks required for this process, much less is understood about how these can operate to pattern tissues in the context of the extensive cell movements that drive gastrulation. In zebrafish, germ layer specification depends on the inheritance of maternal mRNAs [1, 2, 3], cortical rotation to generate a dorsal pole of β-catenin activity [4, 5, 6, 7, 8], and the release of Nodal signals from the yolk syncytial layer (YSL) [9, 10, 11, 12]. To determine whether germ layer specification is robust to altered cell-to-cell positioning, we separated embryonic cells from the yolk and allowed them to develop as spherical aggregates. These aggregates break symmetry autonomously to form elongated structures with an anterior-posterior pattern. Both forced reaggregation and endogenous cell mixing reveals how robust early axis specification is to spatial disruption of maternal pre-patterning. During these movements, a pole of Nodal signaling emerges that is required for explant elongation via the planar cell polarity (PCP) pathway. Blocking of PCP-dependent elongation disrupts the shaping of opposing poles of BMP and Wnt/TCF activity and the anterior-posterior patterning of neural tissue. These results lead us to suggest that embryo elongation plays a causal role in timing the exposure of cells to changes in BMP and Wnt signal activity during zebrafish gastrulation. Video Abstract
Whole-zebrafish 256-cell stage embryo explants elongate Patterned germ layers are established Mesoderm formation is robust to extensive cell mixing Inhibition of morphogenesis blocks formation of signaling gradients
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9
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Fuentes R, Tajer B, Kobayashi M, Pelliccia JL, Langdon Y, Abrams EW, Mullins MC. The maternal coordinate system: Molecular-genetics of embryonic axis formation and patterning in the zebrafish. Curr Top Dev Biol 2020; 140:341-389. [PMID: 32591080 DOI: 10.1016/bs.ctdb.2020.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Axis specification of the zebrafish embryo begins during oogenesis and relies on proper formation of well-defined cytoplasmic domains within the oocyte. Upon fertilization, maternally-regulated cytoplasmic flow and repositioning of dorsal determinants establish the coordinate system that will build the structure and developmental body plan of the embryo. Failure of specific genes that regulate the embryonic coordinate system leads to catastrophic loss of body structures. Here, we review the genetic principles of axis formation and discuss how maternal factors orchestrate axis patterning during zebrafish early embryogenesis. We focus on the molecular identity and functional contribution of genes controlling critical aspects of oogenesis, egg activation, blastula, and gastrula stages. We examine how polarized cytoplasmic domains form in the oocyte, which set off downstream events such as animal-vegetal polarity and germ line development. After gametes interact and form the zygote, cytoplasmic segregation drives the animal-directed reorganization of maternal determinants through calcium- and cell cycle-dependent signals. We also summarize how maternal genes control dorsoventral, anterior-posterior, mesendodermal, and left-right cell fate specification and how signaling pathways pattern these axes and tissues during early development to instruct the three-dimensional body plan. Advances in reverse genetics and phenotyping approaches in the zebrafish model are revealing positional patterning signatures at the single-cell level, thus enhancing our understanding of genotype-phenotype interactions in axis formation. Our emphasis is on the genetic interrogation of novel and specific maternal regulatory mechanisms of axis specification in the zebrafish.
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Affiliation(s)
- Ricardo Fuentes
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - Benjamin Tajer
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - Manami Kobayashi
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - Jose L Pelliccia
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | | | - Elliott W Abrams
- Department of Biology, Purchase College, State University of New York, Harrison, NY, United States
| | - Mary C Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States.
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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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Chi H, Sørmo KG, Diao J, Dalmo RA. T-box transcription factor eomesodermin/Tbr2 in Atlantic cod (Gadus morhua L.): Molecular characterization, promoter structure and function analysis. FISH & SHELLFISH IMMUNOLOGY 2019; 93:28-38. [PMID: 31302288 DOI: 10.1016/j.fsi.2019.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/01/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Eomesodermin (Eomes) is a member of T-box transcription factor family and plays an important role in the regulation of a wide variety of developmental processes and immune response in animals. Here we report cloning and characterization of the full-length cDNA of Atlantic cod Eomes (GmEomes), which possesses a TBOX_3 domain similar to its counterpart in mammals. The regulated expression was observed in head kidney and spleen in response to live Vibrio anguillarum infection in vivo, and spleen leukocytes in vitro after PMA and poly I:C stimulation. Furthermore, we determined a 694 bp sequence, upstream of the transcriptional start site (TSS), to contain a number of sequence motifs that matched known transcription factor-binding sites. Activities of the presumptive regulatory gene were assessed by transfecting different 5'-deletion constructs in CHSE-214 cells. The results showed that the basal promoters and positive transcriptional regulator activities of GmEomes were dependent by sequences located from -694 to -376 bp upstream of TSS. Furthermore, we found that some Eomes binding sites were present in the 5'-flanking regions of the cod IFNγ gene predicted by bioinformatics. However, Co-transfection of eomesodermin overexpression plasmids with INFγ reporter vector into CHSE-214 cells determined that Atlantic cod eomesodermin played a minor role in activation of the INFγ promoter.
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Affiliation(s)
- Heng Chi
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway; Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, 266104, Qingdao, China; Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Institute of Oceanology, 266071, Qingdao, China.
| | - Kristian Gillebo Sørmo
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway
| | - Jing Diao
- Shandong Key Laboratory of Disease Control in Mariculture, Marine Biology Institute of Shandong Province, 266104, Qingdao, China
| | - Roy Ambli Dalmo
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway.
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12
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Tewary M, Dziedzicka D, Ostblom J, Prochazka L, Shakiba N, Heydari T, Aguilar-Hidalgo D, Woodford C, Piccinini E, Becerra-Alonso D, Vickers A, Louis B, Rahman N, Danovi D, Geens M, Watt FM, Zandstra PW. High-throughput micropatterning platform reveals Nodal-dependent bisection of peri-gastrulation-associated versus preneurulation-associated fate patterning. PLoS Biol 2019; 17:e3000081. [PMID: 31634368 PMCID: PMC6822778 DOI: 10.1371/journal.pbio.3000081] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/31/2019] [Accepted: 09/25/2019] [Indexed: 12/22/2022] Open
Abstract
In vitro models of postimplantation human development are valuable to the fields of regenerative medicine and developmental biology. Here, we report characterization of a robust in vitro platform that enabled high-content screening of multiple human pluripotent stem cell (hPSC) lines for their ability to undergo peri-gastrulation-like fate patterning upon bone morphogenetic protein 4 (BMP4) treatment of geometrically confined colonies and observed significant heterogeneity in their differentiation propensities along a gastrulation associable and neuralization associable axis. This cell line-associated heterogeneity was found to be attributable to endogenous Nodal expression, with up-regulation of Nodal correlated with expression of a gastrulation-associated gene profile, and Nodal down-regulation correlated with a preneurulation-associated gene profile expression. We harness this knowledge to establish a platform of preneurulation-like fate patterning in geometrically confined hPSC colonies in which fates arise because of a BMPs signalling gradient conveying positional information. Our work identifies a Nodal signalling-dependent switch in peri-gastrulation versus preneurulation-associated fate patterning in hPSC cells, provides a technology to robustly assay hPSC differentiation outcomes, and suggests conserved mechanisms of organized fate specification in differentiating epiblast and ectodermal tissues.
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Affiliation(s)
- Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Dominika Dziedzicka
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joel Ostblom
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura Prochazka
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Nika Shakiba
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Tiam Heydari
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Aguilar-Hidalgo
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis Woodford
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Elia Piccinini
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - David Becerra-Alonso
- Department of Quantitative Methods, Universidad Loyola Andalucia, Sevilla, Spain
| | - Alice Vickers
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Blaise Louis
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Nafees Rahman
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Davide Danovi
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Mieke Geens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Fiona M. Watt
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Peter W. Zandstra
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
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13
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Abstract
Soon after fertilization the zebrafish embryo generates the pool of cells that will give rise to the germline and the three somatic germ layers of the embryo (ectoderm, mesoderm and endoderm). As the basic body plan of the vertebrate embryo emerges, evolutionarily conserved developmental signaling pathways, including Bmp, Nodal, Wnt, and Fgf, direct the nearly totipotent cells of the early embryo to adopt gene expression profiles and patterns of cell behavior specific to their eventual fates. Several decades of molecular genetics research in zebrafish has yielded significant insight into the maternal and zygotic contributions and mechanisms that pattern this vertebrate embryo. This new understanding is the product of advances in genetic manipulations and imaging technologies that have allowed the field to probe the cellular, molecular and biophysical aspects underlying early patterning. The current state of the field indicates that patterning is governed by the integration of key signaling pathways and physical interactions between cells, rather than a patterning system in which distinct pathways are deployed to specify a particular cell fate. This chapter focuses on recent advances in our understanding of the genetic and molecular control of the events that impart cell identity and initiate the patterning of tissues that are prerequisites for or concurrent with movements of gastrulation.
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Affiliation(s)
- Florence L Marlow
- Icahn School of Medicine Mount Sinai Department of Cell, Developmental and Regenerative Biology, New York, NY, United States.
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14
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Prummel KD, Hess C, Nieuwenhuize S, Parker HJ, Rogers KW, Kozmikova I, Racioppi C, Brombacher EC, Czarkwiani A, Knapp D, Burger S, Chiavacci E, Shah G, Burger A, Huisken J, Yun MH, Christiaen L, Kozmik Z, Müller P, Bronner M, Krumlauf R, Mosimann C. A conserved regulatory program initiates lateral plate mesoderm emergence across chordates. Nat Commun 2019; 10:3857. [PMID: 31451684 PMCID: PMC6710290 DOI: 10.1038/s41467-019-11561-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/22/2019] [Indexed: 01/06/2023] Open
Abstract
Cardiovascular lineages develop together with kidney, smooth muscle, and limb connective tissue progenitors from the lateral plate mesoderm (LPM). How the LPM initially emerges and how its downstream fates are molecularly interconnected remain unknown. Here, we isolate a pan-LPM enhancer in the zebrafish-specific draculin (drl) gene that provides specific LPM reporter activity from early gastrulation. In toto live imaging and lineage tracing of drl-based reporters captures the dynamic LPM emergence as lineage-restricted mesendoderm field. The drl pan-LPM enhancer responds to the transcription factors EomesoderminA, FoxH1, and MixL1 that combined with Smad activity drive LPM emergence. We uncover specific activity of zebrafish-derived drl reporters in LPM-corresponding territories of several chordates including chicken, axolotl, lamprey, Ciona, and amphioxus, revealing a universal upstream LPM program. Altogether, our work provides a mechanistic framework for LPM emergence as defined progenitor field, possibly representing an ancient mesodermal cell state that predates the primordial vertebrate embryo. Numerous tissues are derived from the lateral plate mesoderm (LPM) but how this is specified is unclear. Here, the authors identify a pan-LPM reporter activity found in the zebrafish draculin (drl) gene that also shows transgenic activity in LPM-corresponding territories of several chordates, including chicken, axolotl, lamprey, Ciona, and amphioxus.
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Affiliation(s)
- Karin D Prummel
- Institute of Molecular Life Sciences, University of Zurich, Zürich, 8057, Switzerland
| | - Christopher Hess
- Institute of Molecular Life Sciences, University of Zurich, Zürich, 8057, Switzerland
| | - Susan Nieuwenhuize
- Institute of Molecular Life Sciences, University of Zurich, Zürich, 8057, Switzerland
| | - Hugo J Parker
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, 66160, USA.,Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Katherine W Rogers
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, 72076, Germany
| | - Iryna Kozmikova
- Institute of Molecular Genetics of the ASCR, Prague, 142 20, Czech Republic
| | - Claudia Racioppi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, 10003, USA
| | - Eline C Brombacher
- Institute of Molecular Life Sciences, University of Zurich, Zürich, 8057, Switzerland
| | - Anna Czarkwiani
- TUD-CRTD Center for Regenerative Therapies Dresden, Dresden, 01307, Germany
| | - Dunja Knapp
- TUD-CRTD Center for Regenerative Therapies Dresden, Dresden, 01307, Germany
| | - Sibylle Burger
- Institute of Molecular Life Sciences, University of Zurich, Zürich, 8057, Switzerland
| | - Elena Chiavacci
- Institute of Molecular Life Sciences, University of Zurich, Zürich, 8057, Switzerland
| | - Gopi Shah
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | - Alexa Burger
- Institute of Molecular Life Sciences, University of Zurich, Zürich, 8057, Switzerland
| | - Jan Huisken
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Maximina H Yun
- TUD-CRTD Center for Regenerative Therapies Dresden, Dresden, 01307, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, 10003, USA
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the ASCR, Prague, 142 20, Czech Republic
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, 72076, Germany
| | - Marianne Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, 66160, USA.,Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zurich, Zürich, 8057, Switzerland.
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15
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Casser E, Israel S, Schlatt S, Nordhoff V, Boiani M. Retrospective analysis: reproducibility of interblastomere differences of mRNA expression in 2-cell stage mouse embryos is remarkably poor due to combinatorial mechanisms of blastomere diversification. Mol Hum Reprod 2019; 24:388-400. [PMID: 29746690 DOI: 10.1093/molehr/gay021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/05/2018] [Indexed: 01/13/2023] Open
Abstract
STUDY QUESTION What is the prevalence, reproducibility and biological significance of transcriptomic differences between sister blastomeres of the mouse 2-cell embryo? SUMMARY ANSWER Sister 2-cell stage blastomeres are distinguishable from each other by mRNA analysis, attesting to the fact that differentiation starts mostly early in the mouse embryo; however, the interblastomere differences are poorly reproducible and invoke the combinatorial effects of known and new mechanisms of blastomere diversification. WHAT IS KNOWN ALREADY Transcriptomic datasets for single blastomeres in mice have been available for years but have never been systematically analysed together, although such an analysis may shed light onto some unclarified topics of early mammalian development. Two unknowns that remain are at which stage embryonic blastomeres start to diversify from each other and what is the molecular origin of that difference. At the earliest postzygotic stage, the 2-cell stage, opinions differ regarding the answer to these questions; one group claims that the first zygotic division yields two equal blastomeres capable of forming a full organism (totipotency) and another group claims evidence for interblastomere differences reminiscent of the prepatterning found in embryos of lower taxa. Regarding the molecular origin of interblastomere differences, there are four prevalent models which invoke (1) oocyte anisotropy, (2) sperm entry point, (3) partition errors of the transcript pool and (4) asynchronous embryonic genome activation in the two blastomeres. STUDY DESIGN, SIZE, DURATION Seven transcriptomic studies published between 2011 and 2017 were eligible for retrospective analysis, since both blastomeres of the mouse 2-cell embryo had been analysed individually regarding the original pair associations and since the datasets were made available in public repositories. Five of these studies, encompassing a total of 43 pairs of sister blastomeres, were selected for further analyses based on high interblastomere correlations of mRNA levels. A double cut-off was used to select mRNAs that had robust interblastomere differences both within and between embryos (hits). The hits of each study were compared and contrasted with the hits of the other studies using Venn diagrams. The hits shared by at least four of five studies were analysed further by bioinformatics. PARTICIPANTS/MATERIALS, SETTING, METHODS PubMed was systematically examined for mRNA expression profiles of single 2-cell stage blastomeres in addition to publicly available microarray datasets (GEO, ArrayExpress). Based on the original normalizations, data from seven studies were screened for pairwise sample correlation at the gene level (Spearman), and the top five datasets with the highest correlation were subjected to hierarchical cluster analysis. Interblastomere differences of gene expression were expressed as a ratio of the higher to the lower mRNA level for each pair of blastomeres. A double cut-off was used to make the call of interblastomere difference, accepting genes with mRNA ratios above 2 when observed in at least 50% of the pairs, and discarding the other genes. The proportion of interblastomere differences common to at least four of the five datasets was calculated. Finally, the corresponding gene, pathway and enrichment analyses were performed utilizing PANTHER and GORILLA platforms. MAIN RESULTS AND THE ROLE OF CHANCE An average of 17% of genes within the datasets are differently expressed between sister blastomeres, a proportion which falls to 1% when considering the differences that are common to at least four of the five studies. Housekeeping mRNAs were not included in the 17% and 1% gene lists, suggesting that the interblastomere differences do not occur simply by chance. The 1% of shared interblastomere differences comprise 100 genes, of which 35 are consistent with at least one of the four prevalent models of sister blastomere diversification. Bioinformatics analysis of the remaining 65 genes that are not consistent with the four models suggests that at least one more mechanism is at play, potentially related to the endomembrane system. Although there are many dimensions to the issue of reproducibility (biological, experimental, analytical), we consider that the sister blastomeres are poised to escape high interblastomere correlations of mRNA levels, because at least five sources of diversity superimpose on each other, accounting for at least 25 = 32 different states. As a result, interblastomere mRNA differences of a given 2-cell embryo are necessarily difficult to reproduce in another 2-cell embryo. LARGE SCALE DATA Data were as provided by the original studies (GSE21688, GSE22182, GSE27396, GSE45719, GSE57249, E-MTAB-3321, GSE94050). LIMITATIONS, REASONS FOR CAUTION The original studies present similarities (e.g. fertilization in vivo after ovarian stimulation) as well as differences (e.g. mouse strains, method and timing of blastomere separation). We identified robust mRNA differences between the sister blastomeres, but these differences are underestimated because our double cut-off method works with thresholds and affords more protection against false positives than false negatives. Regarding the false negatives, transcriptome analysis may have captured only part of the interblastomere differences due to: (1) the 2-fold cut-off not being sensitive enough to detect the remaining part of the interblastomere differences, (2) the detection limit of the transcriptomic methods not being sufficient, or (3) interblastomere differences being oblivious to transcriptomic identification because transcriptional changes are oscillatory or because differences are mediated non-transcriptionally or post-transcriptionally. Regarding the false positives, it seems unlikely that a difference was found just by chance for the same group of transcripts due to the same technical error, given that different laboratories produced the data. WIDER IMPLICATIONS OF THE FINDINGS It is clear that the sister blastomeres are distinguishable from each other by mRNA analysis even at the 2-cell stage; however, efforts to identify large stable patterns may be in vain. This elicits thoughts about the wisdom of adding new transcriptomic datasets to the ones that already exist; if all transcriptomic datasets produced so far show a reproducibility of 1%, then any future study would probably face the same issue again. Possibly, a solid identification of the 'large stable pattern that should be there but was not found' requires an even larger dataset than the sum of the seven datasets considered here. Conversely, small stable patterns may be easier to identify, but their biological relevance is less obvious. Alternatively, interblastomere differences may not be mediated by nucleic acids but by other cellular components. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by the Deutsche Forschungsgemeinschaft (grant DFG BO 2540-4-3 to M.B. and grant NO 413/3-3 to V.N.). The authors declare that they have no competing financial interests.
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Affiliation(s)
- E Casser
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, Muenster, Germany
| | - S Israel
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, Muenster, Germany
| | - S Schlatt
- University Hospital Muenster, Centre of Reproductive Medicine and Andrology (CeRA), Albert Schweitzer-Campus 1, Building D11, Muenster, Germany
| | - V Nordhoff
- University Hospital Muenster, Centre of Reproductive Medicine and Andrology (CeRA), Albert Schweitzer-Campus 1, Building D11, Muenster, Germany
| | - M Boiani
- Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, Muenster, Germany
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16
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Bayramov AV, Ermakova GV, Kucheryavyy AV, Zaraisky AG. Lampreys, “Living Fossils,” in Research on Early Development and Regeneration in Vertebrates. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360418080015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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George L, Indig FE, Abdelmohsen K, Gorospe M. Intracellular RNA-tracking methods. Open Biol 2018; 8:rsob.180104. [PMID: 30282659 PMCID: PMC6223214 DOI: 10.1098/rsob.180104] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/03/2018] [Indexed: 12/26/2022] Open
Abstract
RNA tracking allows researchers to visualize RNA molecules in cells and tissues, providing important spatio-temporal information regarding RNA dynamics and function. Methods such as fluorescent in situ hybridization (FISH) and molecular beacons rely on complementary oligonucleotides to label and view endogenous transcripts. Other methods create artificial chimeric transcripts coupled with bacteriophage-derived coat proteins (e.g. MS2, λN) to tag molecules in live cells. In other approaches, endogenous RNAs are recognized by complementary RNAs complexed with noncatalytic Cas proteins. Each technique has its own set of strengths and limitations that must be considered when planning an experiment. Here, we discuss the mechanisms, advantages, and weaknesses of in situ hybridization, molecular beacons, MS2 tagging and Cas-derived systems, as well as how RNA tracking can be employed to study various aspects of molecular biology.
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Affiliation(s)
- Logan George
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.,Confocal Core Facility, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Fred E Indig
- Confocal Core Facility, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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18
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Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. Genome Res 2018; 28:998-1007. [PMID: 29844026 PMCID: PMC6028135 DOI: 10.1101/gr.228833.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 05/23/2018] [Indexed: 12/22/2022]
Abstract
For animals, epigenetic modifications can be globally or partially inherited from gametes after fertilization, and such information is required for proper transcriptional regulation, especially during the process of zygotic genome activation (ZGA). However, the mechanism underlying how the inherited epigenetic signatures affect transcriptional regulation during ZGA remains poorly understood. Here, we performed genome-wide profiling of chromatin accessibility during zebrafish ZGA, which is closely related to zygotic transcriptional regulation. We observed a clear trend toward a gradual increase in accessible chromatin during ZGA. Furthermore, accessible chromatin at the promoters displayed a sequential priority of emergence, and the locations of the accessible chromatin were precisely primed by the enrichment of unmethylated CpGs that were fully inherited from gametes. On the other hand, distal regions with high methylation levels that were inherited from the sperm facilitated the binding of DNA methylation-preferred transcription factors, such as Pou5f3 and Nanog, which contributed to the establishment of accessible chromatin at these loci. Our results demonstrate a model whereby inherited DNA methylation signatures from gametes prime the establishment of accessible chromatin during zebrafish ZGA through two distinct mechanisms.
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19
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Nelson AC, Cutty SJ, Gasiunas SN, Deplae I, Stemple DL, Wardle FC. In Vivo Regulation of the Zebrafish Endoderm Progenitor Niche by T-Box Transcription Factors. Cell Rep 2018; 19:2782-2795. [PMID: 28658625 PMCID: PMC5494305 DOI: 10.1016/j.celrep.2017.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/28/2017] [Accepted: 05/31/2017] [Indexed: 01/15/2023] Open
Abstract
T-box transcription factors T/Brachyury homolog A (Ta) and Tbx16 are essential for correct mesoderm development in zebrafish. The downstream transcriptional networks guiding their functional activities are poorly understood. Additionally, important contributions elsewhere are likely masked due to redundancy. Here, we exploit functional genomic strategies to identify Ta and Tbx16 targets in early embryogenesis. Surprisingly, we discovered they not only activate mesodermal gene expression but also redundantly regulate key endodermal determinants, leading to substantial loss of endoderm in double mutants. To further explore the gene regulatory networks (GRNs) governing endoderm formation, we identified targets of Ta/Tbx16-regulated homeodomain transcription factor Mixl1, which is absolutely required in zebrafish for endoderm formation. Interestingly, we find many endodermal determinants coordinately regulated through common genomic occupancy by Mixl1, Eomesa, Smad2, Nanog, Mxtx2, and Pou5f3. Collectively, these findings augment the endoderm GRN and reveal a panel of target genes underlying the Ta, Tbx16, and Mixl1 mutant phenotypes.
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Affiliation(s)
- Andrew C Nelson
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK; Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Stephen J Cutty
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Saule N Gasiunas
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Isabella Deplae
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Fiona C Wardle
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.
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20
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Teegala S, Chauhan R, Lei E, Weinstein DC. Tbx2 is required for the suppression of mesendoderm during early Xenopus development. Dev Dyn 2018; 247:903-913. [PMID: 29633424 DOI: 10.1002/dvdy.24633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/14/2018] [Accepted: 03/31/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND T-box family proteins are DNA-binding transcriptional regulators that play crucial roles during germ layer formation in the early vertebrate embryo. Well-characterized members of this family, including the transcriptional activators Brachyury and VegT, are essential for the proper formation of mesoderm and endoderm, respectively. To date, T-box proteins have not been shown to play a role in the promotion of the third primary germ layer, ectoderm. RESULTS Here, we report that the T-box factor Tbx2 is both sufficient and necessary for ectodermal differentiation in the frog Xenopus laevis. Tbx2 is expressed zygotically in the presumptive ectoderm, during blastula and gastrula stages. Ectopic expression of Tbx2 represses mesoderm and endoderm, while loss of Tbx2 leads to inappropriate expression of mesoderm- and endoderm-specific genes in the region fated to give rise to ectoderm. Misexpression of Tbx2 also promotes neural tissue in animal cap explants, suggesting that Tbx2 plays a role in both the establishment of ectodermal fate and its dorsoventral patterning. CONCLUSIONS Our studies demonstrate that Tbx2 functions as a transcriptional repressor during germ layer formation, and suggest that this activity is mediated in part through repression of target genes that are stimulated, in the mesendoderm, by transactivating T-box proteins. Taken together, our results point to a critical role for Tbx2 in limiting the potency of blastula-stage progenitor cells during vertebrate germ layer differentiation. Developmental Dynamics 247:903-913, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Sushma Teegala
- Department of Biology, The Graduate Center, City University of New York, New York.,Department of Biology, Queens College, City University of New York, Flushing, New York
| | - Riddhi Chauhan
- Department of Biology, Queens College, City University of New York, Flushing, New York
| | - Emily Lei
- Department of Biology, Queens College, City University of New York, Flushing, New York
| | - Daniel C Weinstein
- Department of Biology, Queens College, City University of New York, Flushing, New York
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21
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van Boxtel AL, Economou AD, Heliot C, Hill CS. Long-Range Signaling Activation and Local Inhibition Separate the Mesoderm and Endoderm Lineages. Dev Cell 2018; 44:179-191.e5. [PMID: 29275993 PMCID: PMC5791662 DOI: 10.1016/j.devcel.2017.11.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/20/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022]
Abstract
Specification of the three germ layers by graded Nodal signaling has long been seen as a paradigm for patterning through a single morphogen gradient. However, by exploiting the unique properties of the zebrafish embryo to capture the dynamics of signaling and cell fate allocation, we now demonstrate that Nodal functions in an incoherent feedforward loop, together with Fgf, to determine the pattern of endoderm and mesoderm specification. We show that Nodal induces long-range Fgf signaling while simultaneously inducing the cell-autonomous Fgf signaling inhibitor Dusp4 within the first two cell tiers from the margin. The consequent attenuation of Fgf signaling in these cells allows specification of endoderm progenitors, while the cells further from the margin, which receive Nodal and/or Fgf signaling, are specified as mesoderm. This elegant model demonstrates the necessity of feedforward and feedback interactions between multiple signaling pathways for providing cells with temporal and positional information.
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Affiliation(s)
- Antonius L van Boxtel
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew D Economou
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Claire Heliot
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Liu JX, Xu QH, Li S, Yu X, Liu W, Ouyang G, Zhang T, Chen LL. Transcriptional factors Eaf1/2 inhibit endoderm and mesoderm formation via suppressing TGF-β signaling. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1103-1116. [DOI: 10.1016/j.bbagrm.2017.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 01/11/2023]
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Fisher JB, Pulakanti K, Rao S, Duncan SA. GATA6 is essential for endoderm formation from human pluripotent stem cells. Biol Open 2017; 6:1084-1095. [PMID: 28606935 PMCID: PMC5550920 DOI: 10.1242/bio.026120] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protocols have been established that direct differentiation of human pluripotent stem cells into a variety of cell types, including the endoderm and its derivatives. This model of differentiation has been useful for investigating the molecular mechanisms that guide human developmental processes. Using a directed differentiation protocol combined with shRNA depletion we sought to understand the role of GATA6 in regulating the earliest switch from pluripotency to definitive endoderm. We reveal that GATA6 depletion during endoderm formation results in apoptosis of nascent endoderm cells, concomitant with a loss of endoderm gene expression. We show by chromatin immunoprecipitation followed by DNA sequencing that GATA6 directly binds to several genes encoding transcription factors that are necessary for endoderm differentiation. Our data support the view that GATA6 is a central regulator of the formation of human definitive endoderm from pluripotent stem cells by directly controlling endoderm gene expression. Summary: Using the differentiation of huESCs as a model for endoderm formation, we reveal that the transcription factor GATA6 regulates the onset of endoderm gene expression and is required for its viability.
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Affiliation(s)
- J B Fisher
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Blood Center of Wisconsin, Milwaukee, WI 53226, USA
| | - K Pulakanti
- Blood Center of Wisconsin, Milwaukee, WI 53226, USA
| | - S Rao
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Blood Center of Wisconsin, Milwaukee, WI 53226, USA.,Division of Pediatric Hematology, Oncology, and Blood and Marrow Transplant, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - S A Duncan
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA .,Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
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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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Cooperation Between T-Box Factors Regulates the Continuous Segregation of Germ Layers During Vertebrate Embryogenesis. Curr Top Dev Biol 2017; 122:117-159. [DOI: 10.1016/bs.ctdb.2016.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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28
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Kiecker C, Bates T, Bell E. Molecular specification of germ layers in vertebrate embryos. Cell Mol Life Sci 2016; 73:923-47. [PMID: 26667903 PMCID: PMC4744249 DOI: 10.1007/s00018-015-2092-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 10/11/2015] [Accepted: 11/09/2015] [Indexed: 11/17/2022]
Abstract
In order to generate the tissues and organs of a multicellular organism, different cell types have to be generated during embryonic development. The first step in this process of cellular diversification is the formation of the three germ layers: ectoderm, endoderm and mesoderm. The ectoderm gives rise to the nervous system, epidermis and various neural crest-derived tissues, the endoderm goes on to form the gastrointestinal, respiratory and urinary systems as well as many endocrine glands, and the mesoderm will form the notochord, axial skeleton, cartilage, connective tissue, trunk muscles, kidneys and blood. Classic experiments in amphibian embryos revealed the tissue interactions involved in germ layer formation and provided the groundwork for the identification of secreted and intracellular factors involved in this process. We will begin this review by summarising the key findings of those studies. We will then evaluate them in the light of more recent genetic studies that helped clarify which of the previously identified factors are required for germ layer formation in vivo, and to what extent the mechanisms identified in amphibians are conserved across other vertebrate species. Collectively, these studies have started to reveal the gene regulatory network (GRN) underlying vertebrate germ layer specification and we will conclude our review by providing examples how our understanding of this GRN can be employed to differentiate stem cells in a targeted fashion for therapeutic purposes.
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Affiliation(s)
- Clemens Kiecker
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, UK
| | - Thomas Bates
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, UK
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Esther Bell
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London, UK.
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29
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Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AEE, Wardle FC. Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression. BMC Biol 2014; 12:81. [PMID: 25277163 PMCID: PMC4206766 DOI: 10.1186/s12915-014-0081-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 12/27/2022] Open
Abstract
Background Nodal signalling is an absolute requirement for normal mesoderm and endoderm formation in vertebrate embryos, yet the transcriptional networks acting directly downstream of Nodal and the extent to which they are conserved is largely unexplored, particularly in vivo. Eomesodermin also plays a role in patterning mesoderm and endoderm in vertebrates, but its mechanisms of action and how it interacts with the Nodal signalling pathway are still unclear. Results Using a combination of expression analysis and chromatin immunoprecipitation with deep sequencing (ChIP-seq) we identify direct targets of Smad2, the effector of Nodal signalling in blastula stage zebrafish embryos, including many novel target genes. Through comparison of these data with published ChIP-seq data in human, mouse and Xenopus we show that the transcriptional network driven by Smad2 in mesoderm and endoderm is conserved in these vertebrate species. We also show that Smad2 and zebrafish Eomesodermin a (Eomesa) bind common genomic regions proximal to genes involved in mesoderm and endoderm formation, suggesting Eomesa forms a general component of the Smad2 signalling complex in zebrafish. Combinatorial perturbation of Eomesa and Smad2-interacting factor Foxh1 results in loss of both mesoderm and endoderm markers, confirming the role of Eomesa in endoderm formation and its functional interaction with Foxh1 for correct Nodal signalling. Finally, we uncover a novel role for Eomesa in repressing ectodermal genes in the early blastula. Conclusions Our data demonstrate that evolutionarily conserved developmental functions of Nodal signalling occur through maintenance of the transcriptional network directed by Smad2. This network is modulated by Eomesa in zebrafish which acts to promote mesoderm and endoderm formation in combination with Nodal signalling, whilst Eomesa also opposes ectoderm gene expression. Eomesa, therefore, regulates the formation of all three germ layers in the early zebrafish embryo. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0081-5) contains supplementary material, which is available to authorized users.
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Xu P, Zhu G, Wang Y, Sun J, Liu X, Chen YG, Meng A. Maternal Eomesodermin regulates zygotic nodal gene expression for mesendoderm induction in zebrafish embryos. J Mol Cell Biol 2014; 6:272-85. [DOI: 10.1093/jmcb/mju028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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31
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Aronson BE, Stapleton KA, Krasinski SD. Role of GATA factors in development, differentiation, and homeostasis of the small intestinal epithelium. Am J Physiol Gastrointest Liver Physiol 2014; 306:G474-90. [PMID: 24436352 PMCID: PMC3949026 DOI: 10.1152/ajpgi.00119.2013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The small intestinal epithelium develops from embryonic endoderm into a highly specialized layer of cells perfectly suited for the digestion and absorption of nutrients. The development, differentiation, and regeneration of the small intestinal epithelium require complex gene regulatory networks involving multiple context-specific transcription factors. The evolutionarily conserved GATA family of transcription factors, well known for its role in hematopoiesis, is essential for the development of endoderm during embryogenesis and the renewal of the differentiated epithelium in the mature gut. We review the role of GATA factors in the evolution and development of endoderm and summarize our current understanding of the function of GATA factors in the mature small intestine. We offer perspective on the application of epigenetics approaches to define the mechanisms underlying context-specific GATA gene regulation during intestinal development.
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Affiliation(s)
- Boaz E. Aronson
- 1Division of Gastroenterology and Nutrition, Department of Medicine, Children's Hospital Boston, and Harvard Medical School, Boston, Massachusetts; ,2Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; and
| | - Kelly A. Stapleton
- 1Division of Gastroenterology and Nutrition, Department of Medicine, Children's Hospital Boston, and Harvard Medical School, Boston, Massachusetts;
| | - Stephen D. Krasinski
- 1Division of Gastroenterology and Nutrition, Department of Medicine, Children's Hospital Boston, and Harvard Medical School, Boston, Massachusetts; ,3Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts
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Takizawa F, Araki K, Ohtani M, Toda H, Saito Y, Lampe VS, Dijkstra JM, Ototake M, Moritomo T, Nakanishi T, Fischer U. Transcription analysis of two Eomesodermin genes in lymphocyte subsets of two teleost species. FISH & SHELLFISH IMMUNOLOGY 2014; 36:215-222. [PMID: 24239596 DOI: 10.1016/j.fsi.2013.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 10/30/2013] [Accepted: 11/04/2013] [Indexed: 06/02/2023]
Abstract
Eomesodermin (Eomes), a T-box transcription factor, is a key molecule associated with function and differentiation of CD8(+) T cells and NK cells. Previously, two teleost Eomes genes (Eomes-a and -b), which are located on different chromosomes, were identified and shown to be expressed in zebrafish lymphocytes. For the present study, we identified these genes in rainbow trout and ginbuna crucian carp. Deduced Eomes-a and -b amino acid sequences in both fish species contain a highly conserved T-box DNA binding domain. In RT-PCR, both Eomes transcripts were readily detectable in a variety of tissues in rainbow trout and ginbuna. The high expression of Eomes-a and -b in brain and ovary suggests involvement in neurogenesis and oogenesis, respectively, while their expression in lymphoid tissues presumably is associated with immune functions. Investigation of separated lymphocyte populations from pronephros indicated that both Eomes-a and -b transcripts were few or absent in IgM(+) lymphocytes, while relatively abundant in IgM(-)/CD8α(+) and IgM(-)/CD8α(-) populations. Moreover, we sorted trout CD8α(+) lymphocytes from mucosal and non-mucosal lymphoid tissues and compared the expression profiles of Eomes-a and -b with those of other T cell-related transcription factor genes (GATA-3, T-bet and Runx3), a Th1 cytokine gene (IFN-γ) and a Th2 cytokine gene (IL-4/13A). Interestingly, the tissue distribution of Eomes-a/b, T-bet, and Runx3 versus IFN-γ transcripts did not reveal simple correlations, suggesting tissue-specific properties of CD8α(+) lymphocytes and/or multiple modes that drive IFN-γ expressions.
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Affiliation(s)
- Fumio Takizawa
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Infectiology, Insel Riems, Germany; Laboratory of Fish Pathology, Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa, Japan
| | - Kyosuke Araki
- Faculty of Fisheries, Kagoshima University, Shimoarata, Kagoshima 890-0056, Japan
| | - Maki Ohtani
- Laboratory of Fish Pathology, Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa, Japan
| | - Hideaki Toda
- Laboratory of Fish Pathology, Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa, Japan
| | - Yasutaka Saito
- Laboratory of Fish Pathology, Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa, Japan
| | - Veronica Soto Lampe
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Infectiology, Insel Riems, Germany
| | | | - Mitsuru Ototake
- Aquatic Animal Health Division, National Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Minami-Ise, Mie 516-0193, Japan
| | - Tadaaki Moritomo
- Laboratory of Fish Pathology, Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa, Japan
| | - Teruyuki Nakanishi
- Laboratory of Fish Pathology, Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa, Japan
| | - Uwe Fischer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Infectiology, Insel Riems, Germany.
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Response to the dorsal anterior gradient of EGFR signaling in Drosophila oogenesis is prepatterned by earlier posterior EGFR activation. Cell Rep 2013; 4:791-802. [PMID: 23972992 DOI: 10.1016/j.celrep.2013.07.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/21/2013] [Accepted: 07/26/2013] [Indexed: 11/22/2022] Open
Abstract
Spatially restricted epidermal growth factor receptor (EGFR) activity plays a central role in patterning the follicular epithelium of the Drosophila ovary. In midoogenesis, localized EGFR activation is achieved by the graded dorsal anterior localization of its ligand, Gurken. Graded EGFR activity determines multiple dorsal anterior fates along the dorsal-ventral axis but cannot explain the sharp posterior limit of this domain. Here, we show that posterior follicle cells express the T-box transcription factors Midline and H15, which render cells unable to adopt a dorsal anterior fate in response to EGFR activation. The posterior expression of Midline and H15 is itself induced in early oogenesis by posteriorly localized EGFR signaling, defining a feedback loop in which early induction of Mid and H15 confers a molecular memory that fundamentally alters the outcome of later EGFR signaling. Spatial regulation of the EGFR pathway thus occurs both through localization of the ligand and through localized regulation of the cellular response.
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Cattell MV, Garnett AT, Klymkowsky MW, Medeiros DM. A maternally established SoxB1/SoxF axis is a conserved feature of chordate germ layer patterning. Evol Dev 2013; 14:104-15. [PMID: 23016978 DOI: 10.1111/j.1525-142x.2011.00525.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Despite deep evolutionary roots in the metazoa, the gene regulatory network driving germ layer specification is surprisingly labile both between and within phyla. In Xenopus laevis, SoxB1- and SoxF-type transcription factors are intimately involved in germ-layer specification, in part through their regulation of Nodal signaling. However, it is unclear if X. laevis is representative of the ancestral vertebrate condition, as the precise roles of SoxF and SoxB1 in germ-layer specification vary among vertebrates, and there is no evidence that SoxF mediates germ-layer specification in any invertebrate. To better understand the evolution of germ-layer specification in the vertebrate lineage, we analyzed the expression of soxB1 and soxF genes in embryos and larvae of the basal vertebrate lamprey, and the basal chordate amphioxus. We find that both species maternally deposit soxB1 mRNA in the animal pole, soxF mRNA in the vegetal hemisphere, and zygotically express soxB1 and soxF throughout nascent ectoderm and mesendoderm, respectively. We also find that soxF is excluded from the vegetalmost blastomeres in lamprey and that, in contrast to vertebrates, amphioxus does not express soxF in the oral epithelium. In the context of recent work, our results suggest that a maternally established animal/vegetal Sox axis is a deeply conserved feature of chordate development that predates the role of Nodal in vertebrate germ-layer specification. Furthermore, exclusion of this axis from the vegetal pole in lamprey is consistent with the presence of an extraembryonic yolk mass, as has been previously proposed. Finally, conserved expression of SoxF in the forming mouth across the vertebrates, but not in amphioxus, lends support to the idea that the larval amphioxus mouth is nonhomologous to the vertebrate mouth.
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Affiliation(s)
- Maria V Cattell
- Ecology and Evolutionary Biology, University of Colorado-Boulder, CO 80309-0334, USA
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Zhao J, Lambert G, Meijer AH, Rosa FM. The transcription factor Vox represses endoderm development by interacting with Casanova and Pou2. Development 2013; 140:1090-9. [DOI: 10.1242/dev.082008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Endoderm and mesoderm are both formed upon activation of Nodal signaling but how endoderm differentiates from mesoderm is still poorly explored. The sox-related gene casanova (sox32) acts downstream of the Nodal signal, is essential for endoderm development and requires the co-factor Pou2 (Pou5f1, Oct3, Oct4) in this process. Conversely, BMP signals have been shown to inhibit endoderm development by an as yet unexplained mechanism. In a search for Casanova regulators in zebrafish, we identified two of its binding partners as the transcription factors Pou2 and Vox, a member of the Vent group of proteins also involved in the patterning of the gastrula. In overexpression studies we show that vox and/or Vent group genes inhibit the capacity of Casanova to induce endoderm, even in the presence of its co-factor Pou2, and that Vox acts as a repressor in this process. We further show that vox, but not other members of the Vent group, is essential for defining the proper endodermal domain size at gastrulation. In this process, vox acts downstream of BMPs. Cell fate analysis further shows that Vox plays a key role downstream of BMP signals in regulating the capacity of Nodal to induce endoderm versus mesoderm by modulating the activity of the Casanova/Pou2 regulatory system.
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Affiliation(s)
- Jue Zhao
- INSERM U1024, F-75005 Paris, France
- CNRS UMR 8197, F-75005 Paris, France
- IBENS, Institut de Biologie de l’Ecole Normale Supérieure, F-75230 Paris, France
- College of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Guillaume Lambert
- INSERM U1024, F-75005 Paris, France
- CNRS UMR 8197, F-75005 Paris, France
- IBENS, Institut de Biologie de l’Ecole Normale Supérieure, F-75230 Paris, France
| | | | - Frederic M. Rosa
- INSERM U1024, F-75005 Paris, France
- CNRS UMR 8197, F-75005 Paris, France
- IBENS, Institut de Biologie de l’Ecole Normale Supérieure, F-75230 Paris, France
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Kumari J, Bøgwald J, Dalmo RA. Eomesodermin of atlantic salmon: an important regulator of cytolytic gene and interferon gamma expression in spleen lymphocytes. PLoS One 2013; 8:e55893. [PMID: 23409078 PMCID: PMC3567031 DOI: 10.1371/journal.pone.0055893] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/03/2013] [Indexed: 11/25/2022] Open
Abstract
Eomesodermin (Eomes), a T-bet homologue expressed in activated CD8+T cells was recently proposed to act as a master regulator of cytotoxic CD8+ T cell effector function and offers an exciting avenue for future exploration. Here, we have identified and characterized the full-length Atlantic salmon Eomes cDNA (2477 bp). Promoter analysis of the salmon Eomes showed the presence of important putative transcription binding sites like SP1, FOXO, Oct-1, SMAD, STAT, IRF, and Ets-1. The basal core region responsible for the promoter activity was located between base −199 and +59. Quantitative PCR analysis revealed that the Atlantic salmon Eomes was ubiquitously expressed in all the tissues studied but strongly expressed in the ovary, spleen, brain, and the head kidney. Moreover, the involvement of Eomes in Atlantic salmon immune response and its relation with the cytolytic activity was demonstrated by investigating the early time dependent expression profile of Eomes and CD8α followed by high interferon gamma (IFN-γ) and granzyme A expression during challenge with live Aeromonas salmonicida and Infectious Pancreatic Necrosis (IPN) virus. Therefore, we further analyzed the regulated expression and function of this transcription factor in spleen lymphocytes. Overexpression of Eomes induced IFN-γ, and granzyme A expression but not perforin expression, whereas small interfering RNA (siRNA) mediated suppression of Eomes expression led to significantly reduced IFN-γ production. Thus, Eomes may be critical in cytolytic gene expression and function in fish similar to mammals. Furthermore, IFN-α, and mitogens induced Eomes expression. Taken together, this is the first study on the promoter activity and regulatory role of Eomes in fish.
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Affiliation(s)
- Jaya Kumari
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics University of Tromsø, Tromsø, Norway
- * E-mail: (JK); (RD)
| | - Jarl Bøgwald
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics University of Tromsø, Tromsø, Norway
| | - Roy A. Dalmo
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics University of Tromsø, Tromsø, Norway
- * E-mail: (JK); (RD)
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Eomesodermin induces Mesp1 expression and cardiac differentiation from embryonic stem cells in the absence of Activin. EMBO Rep 2012; 13:355-62. [PMID: 22402664 DOI: 10.1038/embor.2012.23] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 02/03/2012] [Accepted: 02/06/2012] [Indexed: 01/18/2023] Open
Abstract
The transcription factor Eomesodermin (Eomes) is involved in early embryonic patterning, but the range of cell fates that it controls as well as its mechanisms of action remain unclear. Here we show that transient expression of Eomes promotes cardiovascular fate during embryonic stem cell differentiation. Eomes also rapidly induces the expression of Mesp1, a key regulator of cardiovascular differentiation, and directly binds to regulatory sequences of Mesp1. Eomes effects are strikingly modulated by Activin signalling: high levels of Activin inhibit the promotion of cardiac mesoderm by Eomes, while they enhance Eomes-dependent endodermal specification. These results place Eomes upstream of the Mesp1-dependent programme of cardiogenesis, and at the intersection of mesodermal and endodermal specification, depending on the levels of Activin/Nodal signalling.
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Du S, Draper BW, Mione M, Moens CB, Bruce AEE. Differential regulation of epiboly initiation and progression by zebrafish Eomesodermin A. Dev Biol 2012; 362:11-23. [PMID: 22142964 PMCID: PMC3259739 DOI: 10.1016/j.ydbio.2011.10.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/24/2011] [Accepted: 10/19/2011] [Indexed: 01/07/2023]
Abstract
The T-box transcription factor Eomesodermin (Eomes) has been implicated in patterning and morphogenesis in frog, fish and mouse. In zebrafish, one of the two Eomes homologs, Eomesa, has been implicated in dorsal-ventral patterning, epiboly and endoderm specification in experiments employing over-expression, dominant-negative constructs and antisense morpholino oligonucleotides. Here we report for the first time the identification and characterization of an Eomesa mutant generated by TILLING. We find that Eomesa has a strictly maternal role in the initiation of epiboly, which involves doming of the yolk cell up into the overlying blastoderm. By contrast, epiboly progression is normal, demonstrating for the first time that epiboly initiation is genetically separable from progression. The yolk cell microtubules, which are required for epiboly, are defective in maternal-zygotic eomesa mutant embryos. In addition, the deep cells of the blastoderm are more tightly packed and exhibit more bleb-like protrusions than cells in control embryos. We postulate that the doming delay may be the consequence both of overly stabilized yolk cell microtubules and defects in the adhesive properties or motility of deep cells. We also show that Eomesa is required for normal expression of the endoderm markers sox32, bon and og9x; however it is not essential for endoderm formation.
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Affiliation(s)
- Susan Du
- Department of Cell and Systems Biology University of Toronto 25 Harbord Street Toronto, ON M5S 3G5 Canada
| | - Bruce W. Draper
- Molecular and Cellular Biology University of California, Davis One Shields Avenue Davis, CA 95616 USA
| | - Marina Mione
- IFOM, Istituto FIRC di Oncologia Molecolare Via Adamello 16 Milan, I-20139 Italy
| | - Cecilia B. Moens
- Howard Hughes Medical Institute Division of Basic Science Fred Hutchinson Cancer Research Center P.O. Box 19024 1100 Fairview Avenue North Seattle, WA 98109-1024 USA
| | - Ashley E. E. Bruce
- Department of Cell and Systems Biology University of Toronto 25 Harbord Street Toronto, ON M5S 3G5 Canada
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Wolf XA, Klein T, Garcia R, Hyttel P, Serup P. Identification of a conserved cis-acting region driving expression of mouse Eomesodermin to the primitive streak, node, and definitive endoderm. Gene Expr Patterns 2012; 12:85-93. [DOI: 10.1016/j.gep.2011.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 06/20/2011] [Accepted: 06/24/2011] [Indexed: 12/12/2022]
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Muto A, Calof AL, Lander AD, Schilling TF. Multifactorial origins of heart and gut defects in nipbl-deficient zebrafish, a model of Cornelia de Lange Syndrome. PLoS Biol 2011; 9:e1001181. [PMID: 22039349 PMCID: PMC3201921 DOI: 10.1371/journal.pbio.1001181] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 09/13/2011] [Indexed: 12/31/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is the founding member of a class of multi-organ system birth defect syndromes termed cohesinopathies, named for the chromatin-associated protein complex cohesin, which mediates sister chromatid cohesion. Most cases of CdLS are caused by haploinsufficiency for Nipped-B-like (Nipbl), a highly conserved protein that facilitates cohesin loading. Consistent with recent evidence implicating cohesin and Nipbl in transcriptional regulation, both CdLS cell lines and tissues of Nipbl-deficient mice show changes in the expression of hundreds of genes. Nearly all such changes are modest, however--usually less than 1.5-fold--raising the intriguing possibility that, in CdLS, severe developmental defects result from the collective action of many otherwise innocuous perturbations. As a step toward testing this hypothesis, we developed a model of nipbl-deficiency in zebrafish, an organism in which we can quantitatively investigate the combinatorial effects of gene expression changes. After characterizing the structure and embryonic expression of the two zebrafish nipbl genes, we showed that morpholino knockdown of these genes produces a spectrum of specific heart and gut/visceral organ defects with similarities to those in CdLS. Analysis of nipbl morphants further revealed that, as early as gastrulation, expression of genes involved in endodermal differentiation (sox32, sox17, foxa2, and gata5) and left-right patterning (spaw, lefty2, and dnah9) is altered. Experimental manipulation of the levels of several such genes--using RNA injection or morpholino knockdown--implicated both additive and synergistic interactions in causing observed developmental defects. These findings support the view that birth defects in CdLS arise from collective effects of quantitative changes in gene expression. Interestingly, both the phenotypes and gene expression changes in nipbl morphants differed from those in mutants or morphants for genes encoding cohesin subunits, suggesting that the transcriptional functions of Nipbl cannot be ascribed simply to its role in cohesin loading.
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Affiliation(s)
- Akihiko Muto
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Anne L. Calof
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
- Department of Anatomy and Neurobiology, University of California, Irvine, California, United States of America
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Thomas F. Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
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41
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Takechi M, Takeuchi M, Ota KG, Nishimura O, Mochii M, Itomi K, Adachi N, Takahashi M, Fujimoto S, Tarui H, Okabe M, Aizawa S, Kuratani S. Overview of the transcriptome profiles identified in hagfish, shark, and bichir: current issues arising from some nonmodel vertebrate taxa. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 316:526-46. [PMID: 21809437 DOI: 10.1002/jez.b.21427] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 04/28/2011] [Accepted: 06/14/2011] [Indexed: 02/02/2023]
Abstract
Because of their crucial phylogenetic positions, hagfishes, sharks, and bichirs are recognized as key taxa in our understanding of vertebrate evolution. The expression patterns of the regulatory genes involved in developmental patterning have been analyzed in the context of evolutionary developmental studies. However, in a survey of public sequence databases, we found that the large-scale sequence data for these taxa are still limited. To address this deficit, we used conventional Sanger DNA sequencing and a next-generation sequencing technology based on 454 GS FLX sequencing to obtain expressed sequence tags (ESTs) of the Japanese inshore hagfish (Eptatretus burgeri; 161,482 ESTs), cloudy catshark (Scyliorhinus torazame; 165,819 ESTs), and gray bichir (Polypterus senegalus; 34,336 ESTs). We deposited the ESTs in a newly constructed database, designated the "Vertebrate TimeCapsule." The ESTs include sequences from genes that can be effectively used in evolutionary developmental studies; for instance, several encode cartilaginous extracellular matrix proteins, which are central to an understanding of the ways in which evolutionary processes affected the skeletal elements, whereas others encode regulatory genes involved in craniofacial development and early embryogenesis. Here, we discuss how hagfishes, sharks, and bichirs contribute to our understanding of vertebrate evolution, we review the current status of the publicly available sequence data for these three taxa, and we introduce our EST projects and newly developed database.
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Affiliation(s)
- Masaki Takechi
- Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, Kobe, Japan
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Abstract
Morphogens are long-range signaling molecules that pattern developing tissues in a concentration-dependent manner. The graded activity of morphogens within tissues exposes cells to different signal levels and leads to region-specific transcriptional responses and cell fates. In its simplest incarnation, a morphogen signal forms a gradient by diffusion from a local source and clearance in surrounding tissues. Responding cells often transduce morphogen levels in a linear fashion, which results in the graded activation of transcriptional effectors. The concentration-dependent expression of morphogen target genes is achieved by their different binding affinities for transcriptional effectors as well as inputs from other transcriptional regulators. Morphogen distribution and interpretation are the result of complex interactions between the morphogen and responding tissues. The response to a morphogen is dependent not simply on morphogen concentration but also on the duration of morphogen exposure and the state of the target cells. In this review, we describe the morphogen concept and discuss the mechanisms that underlie the generation, modulation, and interpretation of morphogen gradients.
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Affiliation(s)
- Katherine W Rogers
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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43
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Awonuga AO, Zhong W, Abdallah ME, Slater JA, Zhou SC, Xie YF, Puscheck EE, Rappolee DA. Eomesodermin, HAND1, and CSH1 proteins are induced by cellular stress in a stress-activated protein kinase-dependent manner. Mol Reprod Dev 2011; 78:519-28. [PMID: 21710638 DOI: 10.1002/mrd.21342] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 05/17/2011] [Indexed: 11/11/2022]
Abstract
Eomesodermin (Eomes) is a transcription factor essential for trophoblast development. Stress stimuli activate stress-activated protein kinase (MAPK8/9) and modulate transcription factors in trophoblast stem cells (TSC). In this study, we test the hypothesis that stress-induced Eomes upregulation and downstream trophoblast development are MAPK8/9-dependent. Immunocytochemical and immunoblot assays suggest that Eomes is induced by hyperosmolar stress in a dose- and time-dependent manner. Two MAPK8/9 inhibitors that work by different mechanisms, LJNKl1 and SP600125, block induction of Eomes protein by stress. During normal TSC differentiation, the transcription factor heart and neural crest derivatives expressed 1 (HAND1) is dependent on Eomes, and chorionic somatomammotropin hormone 1 (CSH1) expression is dependent on HAND1. Similar to Eomes, HAND1 and CSH1 induction by stress are MAPK8/9-dependent, and CSH1 is induced in nearly all stressed TSC. CSH1 induction normally requires downregulation of the transcription factor inhibitor of differentiation 2 (ID2) as well as HAND1 upregulation. It was shown previously that hyperosmolar stress induces AMP-activated protein kinase (PRKAA1/2)-dependent ID2 loss in a MAPK8/9-independent manner. Inhibition of PRKAA1/2 with compound C and LJNKl1, more than MAPK8/9 inhibitors alone, inhibits the induction of CSH1 by stress. Taken together these data suggest that stress-induced MAPK8/9 and PRKAA1/2 regulate transcription factors Eomes/HAND1 and ID2, respectively. Together this network mediates induction of CSH1 by stress. Therefore, stress triggers a proportional increase in a normal early TSC differentiation event that could be adaptive in inducing CSH1. But the flexibility of TSC to undergo stress-induced differentiation could lead to pathophysiological consequences if stress endured and TSC differentiation became unbalanced.
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Affiliation(s)
- A O Awonuga
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
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Nodal-dependent mesendoderm specification requires the combinatorial activities of FoxH1 and Eomesodermin. PLoS Genet 2011; 7:e1002072. [PMID: 21637786 PMCID: PMC3102743 DOI: 10.1371/journal.pgen.1002072] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 03/23/2011] [Indexed: 12/24/2022] Open
Abstract
Vertebrate mesendoderm specification requires the Nodal signaling pathway and its transcriptional effector FoxH1. However, loss of FoxH1 in several species does not reliably cause the full range of loss-of-Nodal phenotypes, indicating that Nodal signals through additional transcription factors during early development. We investigated the FoxH1-dependent and -independent roles of Nodal signaling during mesendoderm patterning using a novel recessive zebrafish FoxH1 mutation called midway, which produces a C-terminally truncated FoxH1 protein lacking the Smad-interaction domain but retaining DNA–binding capability. Using a combination of gel shift assays, Nodal overexpression experiments, and genetic epistasis analyses, we demonstrate that midway more accurately represents a complete loss of FoxH1-dependent Nodal signaling than the existing zebrafish FoxH1 mutant schmalspur. Maternal-zygotic midway mutants lack notochords, in agreement with FoxH1 loss in other organisms, but retain near wild-type expression of markers of endoderm and various nonaxial mesoderm fates, including paraxial and intermediate mesoderm and blood precursors. We found that the activity of the T-box transcription factor Eomesodermin accounts for specification of these tissues in midway embryos. Inhibition of Eomesodermin in midway mutants severely reduces the specification of these tissues and effectively phenocopies the defects seen upon complete loss of Nodal signaling. Our results indicate that the specific combinations of transcription factors available for signal transduction play critical and separable roles in determining Nodal pathway output during mesendoderm patterning. Our findings also offer novel insights into the co-evolution of the Nodal signaling pathway, the notochord specification program, and the chordate branch of the deuterostome family of animals. Multiple signaling pathways function combinatorially to form and pattern the primary tissue layers of almost all organisms, by interacting with each other and by utilizing different pathway components to perform specific roles. Here we investigated the combinatorial aspects of the Nodal signaling pathway, which is essential for proper induction of mesoderm and endoderm in vertebrates. We identified a new mutation in the zebrafish FoxH1 gene, which encodes a Nodal pathway transcription factor, a protein that responds to Nodal signals to carry out the pathway's cellular functions by regulating target gene expression. Using this mutation, we determined that FoxH1 acts in a combinatorial fashion with two other transcription factors, called Mixer and Eomesodermin, to carry out all roles of the Nodal pathway during early development. Through genetic manipulation, we were able to identify the discrete functions regulated by different combinations of these three transcription factors. Our results indicate that the availability of specific Nodal-responsive transcription factors dictates the functions of the Nodal pathway in specific areas of the developing embryo. Our work also provides evidence that the FoxH1 family of transcription factors evolved concomitantly, and perhaps causally, with the chordate branch of animals, to which all vertebrates including humans belong.
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Putiri E, Pelegri F. The zebrafish maternal-effect gene mission impossible encodes the DEAH-box helicase Dhx16 and is essential for the expression of downstream endodermal genes. Dev Biol 2011; 353:275-89. [PMID: 21396359 PMCID: PMC3088167 DOI: 10.1016/j.ydbio.2011.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 01/26/2011] [Accepted: 03/01/2011] [Indexed: 10/18/2022]
Abstract
Early animal embryonic development requires maternal products that drive developmental processes prior to the activation of the zygotic genome at the mid-blastula transition. During and after this transition, maternal products may continue to act within incipient zygotic developmental programs. Mechanisms that control maternally-inherited products to spatially and temporally restrict developmental responses remain poorly understood, but necessarily depend on posttranscriptional regulation. We report the functional analysis and molecular identification of the zebrafish maternal-effect gene mission impossible (mis). Our studies suggest requirements for maternally-derived mis function in events that occur during gastrulation, including cell movement and the activation of some endodermal target genes. Cell transplantation experiments show that the cell movement defect is cell autonomous. Within the endoderm induction pathway, mis is not required for the activation of early zygotic genes, but is essential to implement nodal activity downstream of casanova/sox 32 but upstream of sox17 expression. Activation of nodal signaling in blastoderm explants shows that the requirement for mis function in endoderm gene induction is independent of the underlying yolk cell. Positional cloning of mis, including genetic rescue and complementation analysis, shows that it encodes the DEAH-box RNA helicase Dhx16, shown in other systems to act in RNA regulatory processes such as splicing and translational control. Analysis of a previously identified insertional dhx16 mutation shows that the zygotic component of this gene is also essential for embryonic viability. Our studies provide a striking example of the interweaving of maternal and zygotic genetic functions during the egg-to-embryo transition. Maternal RNA helicases have long been known to be involved in the development of the animal germ line, but our findings add to growing evidence that these factors may also control specific gene expression programs in somatic tissues.
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Affiliation(s)
- Emily Putiri
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, Madison, WI 53706
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, Madison, WI 53706
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46
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Marikawa Y, Alarcón VB. Establishment of trophectoderm and inner cell mass lineages in the mouse embryo. Mol Reprod Dev 2010; 76:1019-32. [PMID: 19479991 DOI: 10.1002/mrd.21057] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The first cell lineage specification in mouse embryo development is the formation of trophectoderm (TE) and inner cell mass (ICM) of the blastocyst. This article is to review and discuss the current knowledge on the cellular and molecular mechanisms of this particular event. Several transcription factors have been identified as the critical regulators of the formation or maintenance of the two cell lineages. The establishment of TE manifests as the formation of epithelium, and is dependent on many structural and regulatory components that are commonly found and that function in many epithelial tissues. Distinct epithelial features start to emerge at the late 8-cell stage, but the fates of blastomeres are not fixed as TE or ICM until around 32-cell stage. The location of blastomeres at this stage, that is, external or internal of the embryo, in effect defines the commitment towards the TE or ICM lineage, respectively. Some studies implicate the presence of a developmental bias among blastomeres at 2- or 4-cell stage, although it is unlikely to play a decisive role in the establishment of TE and ICM. The unique mode of cell lineage specification in the mouse embryo is further discussed in comparison with the formation of initial cell lineages, namely the three germ layers, in non-mammalian embryos.
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Affiliation(s)
- Yusuke Marikawa
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. Biosciences Building 163 Honolulu, HI 96813, USA.
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47
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Abstract
The endoderm germ layer contributes to the respiratory and gastrointestinal tracts and to all of their associated organs. Over the past decade, studies in vertebrate model organisms, including frog, fish, chick, and mouse, have greatly enhanced our understanding of the molecular basis of endoderm organ development. We review this progress with a focus on early stages of endoderm organogenesis including endoderm formation, gut tube morphogenesis and patterning, and organ specification. Lastly, we discuss how developmental mechanisms that regulate endoderm organogenesis are used to direct differentiation of embryonic stem cells into specific adult cell types, which function to alleviate disease symptoms in animal models.
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Affiliation(s)
- Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Research Foundation and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45229, USA.
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48
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Tremblay KD. Formation of the murine endoderm: lessons from the mouse, frog, fish, and chick. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2010; 96:1-34. [PMID: 21075338 DOI: 10.1016/b978-0-12-381280-3.00001-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The mammalian definitive endoderm arises as a simple epithelial sheet. This sheet of cells will eventually produce the innermost tube that comprises the entire digestive tract from the esophagus to the colon as well as the epithelial component of the digestive and respiratory organs including the thymus, thyroid, lung, liver, gallbladder, and pancreas. Thus a wide array of tissue types are derived from the early endodermal sheet, and understanding the morphological and molecular mechanisms used to produce this tissue is integral to understanding the development of all these organs. The goal of this chapter is to summarize what is known about the morphological and molecular mechanisms used to produce this embryonic germ layer. Although this chapter mainly focuses on the mechanisms used to generate the murine endoderm, supportive or suggestive data from other species, including chick, frog (Xenopus laevis), and the Zebrafish (Danio rerio) are also examined.
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Affiliation(s)
- Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
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49
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Pernaute B, Cañon S, Crespo M, Fernandez-Tresguerres B, Rayon T, Manzanares M. Comparison of extraembryonic expression of Eomes and Cdx2 in pregastrulation chick and mouse embryo unveils regulatory changes along evolution. Dev Dyn 2009; 239:620-9. [DOI: 10.1002/dvdy.22176] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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50
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Tiso N, Moro E, Argenton F. Zebrafish pancreas development. Mol Cell Endocrinol 2009; 312:24-30. [PMID: 19477220 DOI: 10.1016/j.mce.2009.04.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 04/28/2009] [Accepted: 04/30/2009] [Indexed: 10/20/2022]
Abstract
An accurate understanding of the molecular events governing pancreas development can have an impact on clinical medicine related to diabetes, obesity and pancreatic cancer, diseases with a high impact in public health. Until 1996, the main animal models in which pancreas formation and differentiation could be studied were mouse and, for some instances related to early development, chicken and Xenopus. Zebrafish has penetrated this field very rapidly offering a new model of investigation; by joining functional genomics, genetics and in vivo whole mount visualization, Danio rerio has allowed large scale and fine multidimensional analysis of gene functions during pancreas formation and differentiation.
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Affiliation(s)
- Natascia Tiso
- Dipartimento di Biologia, Universita' degli Studi di Padova, Via Ugo Bassi 58b, I-35121 Padova, Italy
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