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Paraiso KD, Blitz IL, Coley M, Cheung J, Sudou N, Taira M, Cho KWY. Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation. Cell Rep 2020; 27:2962-2977.e5. [PMID: 31167141 PMCID: PMC6610736 DOI: 10.1016/j.celrep.2019.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/30/2019] [Accepted: 05/01/2019] [Indexed: 01/06/2023] Open
Abstract
Elucidation of the sequence of events underlying the dynamic interaction
between transcription factors and chromatin states is essential. Maternal
transcription factors function at the top of the regulatory hierarchy to specify
the primary germ layers at the onset of zygotic genome activation (ZGA). We
focus on the formation of endoderm progenitor cells and examine the interactions
between maternal transcription factors and chromatin state changes underlying
the cell specification process. Endoderm-specific factors Otx1 and Vegt together
with Foxh1 orchestrate endoderm formation by coordinated binding to select
regulatory regions. These interactions occur before the deposition of enhancer
histone marks around the regulatory regions, and these TFs recruit RNA
polymerase II, regulate enhancer activity, and establish super-enhancers
associated with important endodermal genes. Therefore, maternal transcription
factors Otx1, Vegt, and Foxh1 combinatorially regulate the activity of
super-enhancers, which in turn activate key lineage-specifying genes during
ZGA. How do maternal transcription factors interact with chromatin regions to
coordinate the endodermal gene regulatory program? Paraiso et al. demonstrate
that combinatorial binding of maternal Otx1, Vegt, and Foxh1 to select enhancers
and super-enhancers in the genome controls endodermal cell fate specification
during zygotic gene activation.
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Affiliation(s)
- Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Masani Coley
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jessica Cheung
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Norihiro Sudou
- Department of Anatomy, Tokyo Women's Medical University, Tokyo, Japan
| | - Masanori Taira
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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Heim AE, Hartung O, Rothhämel S, Ferreira E, Jenny A, Marlow FL. Oocyte polarity requires a Bucky ball-dependent feedback amplification loop. Development 2014; 141:842-54. [PMID: 24496621 DOI: 10.1242/dev.090449] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In vertebrates, the first asymmetries are established along the animal-vegetal axis during oogenesis, but the underlying molecular mechanisms are poorly understood. Bucky ball (Buc) was identified in zebrafish as a novel vertebrate-specific regulator of oocyte polarity, acting through unknown molecular interactions. Here we show that endogenous Buc protein localizes to the Balbiani body, a conserved, asymmetric structure in oocytes that requires Buc for its formation. Asymmetric distribution of Buc in oocytes precedes Balbiani body formation, defining Buc as the earliest marker of oocyte polarity in zebrafish. Through a transgenic strategy, we determined that excess Buc disrupts polarity and results in supernumerary Balbiani bodies in a 3'UTR-dependent manner, and we identified roles for the buc introns in regulating Buc activity. Analyses of mosaic ovaries indicate that oocyte pattern determines the number of animal pole-specific micropylar cells that are associated with an egg via a close-range signal or direct cell contact. We demonstrate interactions between Buc protein and buc mRNA with two conserved RNA-binding proteins (RNAbps) that are localized to the Balbiani body: RNA binding protein with multiple splice isoforms 2 (Rbpms2) and Deleted in azoospermia-like (Dazl). Buc protein and buc mRNA interact with Rbpms2; buc and dazl mRNAs interact with Dazl protein. Cumulatively, these studies indicate that oocyte polarization depends on tight regulation of buc: Buc establishes oocyte polarity through interactions with RNAbps, initiating a feedback amplification mechanism in which Buc protein recruits RNAbps that in turn recruit buc and other RNAs to the Balbiani body.
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Affiliation(s)
- Amanda E Heim
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Gagnon JA, Mowry KL. Molecular motors: directing traffic during RNA localization. Crit Rev Biochem Mol Biol 2011; 46:229-39. [PMID: 21476929 DOI: 10.3109/10409238.2011.572861] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA localization, the enrichment of RNA in a specific subcellular region, is a mechanism for the establishment and maintenance of cellular polarity in a variety of systems. Ultimately, this results in a universal method for spatially restricting gene expression. Although the consequences of RNA localization are well-appreciated, many of the mechanisms that are responsible for carrying out polarized transport remain elusive. Several recent studies have illuminated the roles that molecular motor proteins play in the process of RNA localization. These studies have revealed complex mechanisms in which the coordinated action of one or more motor proteins can act at different points in the localization process to direct RNAs to their final destination. In this review, we discuss recent findings from several different systems in an effort to clarify pathways and mechanisms that control the directed movement of RNA.
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Affiliation(s)
- James A Gagnon
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, USA
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Nuage morphogenesis becomes more complex: two translocation pathways and two forms of nuage coexist in Drosophila germline syncytia. Cell Tissue Res 2011; 344:169-81. [PMID: 21365220 DOI: 10.1007/s00441-011-1145-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 02/03/2011] [Indexed: 12/18/2022]
Abstract
We have developed a simple and reliable method of preserving antigen immunoreactivity with concomitant excellent retention of the cell ultrastructure. Using this method, we have been able to follow the origin and developmental stages of nuage accumulations within the nurse cell/oocyte syncytium in the ovary of the fruit fly, Drosophila melanogaster, at the ultrastructural level. We have found two morphologically and biochemically distinct forms of nuage material in the nurse cell cytoplasm: translocating accumulations of nuage containing the Vasa protein, termed sponge bodies and stationary polymorphic accumulations of nuage enriched in Argonaute and Survival of motor neuron proteins. Immunogold labeling combined with confocal fluorescent and ultrastructural analyses have revealed that the Vasa-containing nuage accumulations remain closely associated with the cisternae of the endoplasmic reticulum throughout their lifetimes. The migration mechanism of the Vasa-positive nuage appears distinct from the microtubule-dependent translocation of oskar ribonucleoprotein complexes. We postulate that these two distinct nuage translocation pathways converge in the formation of the polar granules within the polar/germ plasm of the oocyte posterior pole. We also provide morphological and immunocytochemical evidence that these polymorphic nuage accumulations correspond to the recently described cytoplasmic domains termed U body-P body complexes.
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Lindeman RE, Pelegri F. Vertebrate maternal-effect genes: Insights into fertilization, early cleavage divisions, and germ cell determinant localization from studies in the zebrafish. Mol Reprod Dev 2010; 77:299-313. [PMID: 19908256 PMCID: PMC4276564 DOI: 10.1002/mrd.21128] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the earliest stages of animal development prior to the commencement of zygotic transcription, all critical cellular processes are carried out by maternally-provided molecular products accumulated in the egg during oogenesis. Disruption of these maternal products can lead to defective embryogenesis. In this review, we focus on maternal genes with roles in the fundamental processes of fertilization, cell division, centrosome regulation, and germ cell development with emphasis on findings from the zebrafish, as this is a unique and valuable model system for vertebrate reproduction.
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Affiliation(s)
- Robin E. Lindeman
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin
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Takada H, Kawana T, Ito Y, Kikuno RF, Mamada H, Araki T, Koga H, Asashima M, Taira M. The RNA-binding protein Mex3b has a fine-tuning system for mRNA regulation in early Xenopus development. Development 2009; 136:2413-22. [PMID: 19542354 DOI: 10.1242/dev.029165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Post-transcriptional control by RNA-binding proteins is a precise way to assure appropriate levels of gene expression. Here, we identify a novel mRNA regulatory system involving Mex3b (RKHD3) and demonstrate its role in FGF signaling. mex3b mRNA has a 3' long conserved UTR, named 3'LCU, which contains multiple elements for both mRNA destabilization and translational enhancement. Notably, Mex3b promotes destabilization of its own mRNA by binding to the 3'LCU, thereby forming a negative autoregulatory loop. The combination of positive regulation and negative autoregulation constitutes a fine-tuning system for post-transcriptional control. In early embryogenesis, Mex3b is involved in anteroposterior patterning of the neural plate. Consistent with this, Mex3b can attenuate FGF signaling and destabilize mRNAs for the FGF signaling components Syndecan 2 and Ets1b through their 3' UTRs. These data suggest that the 3'LCU-mediated fine-tuning system determines the appropriate level of mex3b expression, which in turn contributes to neural patterning through regulating FGF signaling.
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Affiliation(s)
- Hitomi Takada
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Yan CYI, Skourides P, Chang C, Brivanlou A. Samba, a Xenopus hnRNP expressed in neural and neural crest tissues. Dev Dyn 2009; 238:204-9. [PMID: 19097051 DOI: 10.1002/dvdy.21826] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
RNA binding proteins regulate gene expression at the posttranscriptional level and play important roles in embryonic development. Here, we report the cloning and expression of Samba, a Xenopus hnRNP that is maternally expressed and persists at least until tail bud stages. During gastrula stages, Samba is enriched in the dorsal regions. Subsequently, its expression is elevated only in neural and neural crest tissues. In the latter, Samba expression overlaps with that of Slug in migratory neural crest cells. Thereafter, Samba is maintained in the neural crest derivatives, as well as other neural tissues, including the anterior and posterior neural tube and the eyes. Overexpression of Samba in the animal pole leads to defects in neural crest migration and cranial cartilage development. Thus, Samba encodes a Xenopus hnRNP that is expressed early in neural and neural crest derivatives and may regulate crest cells migratory behavior.
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Affiliation(s)
- Chao Yun Irene Yan
- Department of Cell and Developmental Biology, Universidade de São Paulo, São Paulo, SP, Brazil.
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Messitt TJ, Gagnon JA, Kreiling JA, Pratt CA, Yoon YJ, Mowry KL. Multiple kinesin motors coordinate cytoplasmic RNA transport on a subpopulation of microtubules in Xenopus oocytes. Dev Cell 2008; 15:426-436. [PMID: 18771961 DOI: 10.1016/j.devcel.2008.06.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 06/05/2008] [Accepted: 06/26/2008] [Indexed: 12/23/2022]
Abstract
RNA localization is a widely conserved mechanism for generating cellular asymmetry. In Xenopus oocytes, microtubule-dependent transport of RNAs to the vegetal cortex underlies germ layer patterning. Although kinesin motors have been implicated in this process, the apparent polarity of the microtubule cytoskeleton has pointed instead to roles for minus-end-directed motors. To resolve this issue, we have analyzed participation of kinesin motors in vegetal RNA transport and identified a direct role for Xenopus kinesin-1. Moreover, in vivo interference and biochemical experiments reveal a key function for multiple motors, specifically kinesin-1 and kinesin-2, and suggest that these motors may interact during transport. Critically, we have discovered a subpopulation of microtubules with plus ends at the vegetal cortex, supporting roles for these kinesin motors in vegetal RNA transport. These results provide a new mechanistic basis for understanding directed RNA transport within the cytoplasm.
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Affiliation(s)
- Timothy J Messitt
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Box G-L268, Providence, RI 02912, USA
| | - James A Gagnon
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Box G-L268, Providence, RI 02912, USA
| | - Jill A Kreiling
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Box G-L268, Providence, RI 02912, USA
| | - Catherine A Pratt
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Box G-L268, Providence, RI 02912, USA
| | - Young J Yoon
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Box G-L268, Providence, RI 02912, USA
| | - Kimberly L Mowry
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Box G-L268, Providence, RI 02912, USA.
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Lee JY, Lim JM, Kim DK, Zheng YH, Moon S, Han BK, Song KD, Kim H, Han JY. Identification and gene expression profiling of the Pum1 and Pum2 members of the Pumilio family in the chicken. Mol Reprod Dev 2008; 75:184-90. [PMID: 17474090 DOI: 10.1002/mrd.20765] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Members of the Pumilio (Pum) family of RNA-binding proteins act as translational repressors and are required for germ cell development and asymmetric division. We identified the chicken Pum1 and Pum2 genes and analyzed their expression patterns in various tissues. Comparative sequence analysis of the Pum1 and Pum2 proteins from the drosophila, chicken, mouse, and human revealed a high degree of evolutionary conservation in terms of the levels of homology of the peptide sequences and the structure of Pumilio homology domain (PUM-HD), C-terminal RNA-binding domain, with similar spacing between the adjacent Pum eight tandem repeats. In addition, phylogenetic patterns of pumilio family showed that Pum 1 and 2 of chicken are more closely related to those of mouse and human than other species and Pum1 is more conserved than Pum2. Using real-time RT-PCR, the expression levels of the Pum1 and Pum2 genes were found to be highest in hatched female gonads, and high-level expression of Pum2 was detected in 12-day and hatched gonads among the various chicken embryonic tissues tested. In adult tissues, the expression levels of Pum1 and Pum2 were expressed at higher levels in the testis and muscle than in any other tissue. The characteristics of the tissue-specific expression of Pum genes suggest that Pum1 and Pum2 have effects crucially in particular stage during development of chicken gonads depending on sexual maturation.
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Affiliation(s)
- Jee Young Lee
- Department of Agricultural Biotechnology, Division of Animal Genetic Engineering, Seoul National University, Seoul, Korea
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PTB/hnRNP I is required for RNP remodeling during RNA localization in Xenopus oocytes. Mol Cell Biol 2007; 28:678-86. [PMID: 18039852 DOI: 10.1128/mcb.00999-07] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transport of specific mRNAs to defined regions within the cell cytoplasm is a fundamental mechanism for regulating cell and developmental polarity. In the Xenopus oocyte, Vg1 RNA is transported to the vegetal cytoplasm, where localized expression of the encoded protein is critical for embryonic polarity. The Vg1 localization pathway is directed by interactions between key motifs within Vg1 RNA and protein factors recognizing those RNA sequences. We have investigated how RNA-protein interactions could be modulated to trigger distinct steps in the localization pathway and found that the Vg1 RNP is remodeled during cytoplasmic RNA transport. Our results implicate two RNA-binding proteins with key roles in Vg1 RNA localization, PTB/hnRNP I and Vg1RBP/vera, in this process. We show that PTB/hnRNP I is required for remodeling of the interaction between Vg1 RNA and Vg1RBP/vera. Critically, mutations that block this remodeling event also eliminate vegetal localization of the RNA, suggesting that RNP remodeling is required for localization.
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Abstract
The body axes of the fruit fly are established in mid-oogenesis by the localization of three mRNA determinants, bicoid, oskar, and gurken, within the oocyte. General mechanisms of RNA localization and cell polarization, applicable to many cell types, have emerged from investigation of these determinants in Drosophila oogenesis. Localization of these RNAs is dependent on the germline microtubules, which reorganize to form a polarized array at mid-oogenesis in response to a signaling relay between the oocyte and the surrounding somatic follicle cells. Here we describe what is known about this microtubule reorganization and the signaling relay that triggers it. Recent studies have identified a number of ubiquitous RNA binding proteins essential for this process. So far, no targets for any of these proteins have been identified, and future work will be needed to illuminate how they function to reorganize microtubes and whether similar mechanisms also exist in other cell types.
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Affiliation(s)
- Josefa Steinhauer
- Skirball Institute for Biomolecular Medicine and Department of Developmental Genetics, New York University School of Medicine, New York, New York 10016,USA.
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Abstract
Cytoplasmic RNA localization is a means to create polarity by restricting protein expression to a discrete subcellular location. RNA localization is a multistep process that begins with the recognition of cis-acting sequences within the RNA by specific trans-factors, and RNAs are localized in ribonucleoprotein (RNP) complexes that contain both the RNA and numerous protein components. Components of the localization machinery transport the RNP complex, usually in a translationally repressed state, to a distinct subcellular region, resulting in spatially restricted gene expression. Recent efforts to identify both the cis- and trans-factors required for RNA localization have elucidated RNA-protein interactions that are remodeled during localization.
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Affiliation(s)
- Raymond A Lewis
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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Kumano G, Nishida H. Ascidian embryonic development: An emerging model system for the study of cell fate specification in chordates. Dev Dyn 2007; 236:1732-47. [PMID: 17366575 DOI: 10.1002/dvdy.21108] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The ascidian tadpole larva represents the basic body plan of all chordates in a relatively small number of cells and tissue types. Although it had been considered that ascidians develop largely in a determinative way, whereas vertebrates develop in an inductive way, recent studies at the molecular and cellular levels have uncovered several similarities in the way developmental fates are specified. In this review, we describe ascidian embryogenesis and its cell lineages, introduce several characteristics of ascidian embryos, describe recent advances in understanding of the mechanisms of cell fate specification, and discuss them in the context of what is known in vertebrates and other organisms.
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Affiliation(s)
- Gaku Kumano
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
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Röttinger E, Besnardeau L, Lepage T. Expression pattern of three putative RNA-binding proteins during early development of the sea urchin Paracentrotus lividus. Gene Expr Patterns 2006; 6:864-72. [PMID: 17061352 DOI: 10.1016/j.modgep.2006.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report the expression patterns of three transcripts encoding RNA-binding proteins during early development of the Mediterranean sea urchin Paracentrotus lividus. Two of these genes encode KH-domains RNA-binding proteins closely related to the vertebrate neuro-oncological ventral antigen 1 (Nova) and RING Finger and KH-domain (RKHD). The third encodes the sea urchin ortholog of the polypyrimidine tract binding protein (PTB). Zygotic expression of nova and rkhd starts at mesenchyme blastula stage and is restricted to the presumptive endoderm territory. During gastrulation, expression of nova is restricted to the midgut and hindgut, while expression of rkhd become more complex and includes the foregut and hindgut territories as well as previously unknown territories within the ectoderm. PTB is first expressed ubiquitously but starting at the late gastrula stage, then PTB transcripts become highly enriched in the foregut and oral ectoderm. We further report that expression of nova and rkhd in the endomesoderm is under the control of the Wnt/beta-catenin pathway and occurs in a cell-autonomous manner while expression of rkhd and PTB in the oral ectoderm is regulated by Nodal signaling.
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Affiliation(s)
- Eric Röttinger
- UMR7009/CNRS, Université de Paris VI, Biologie du Développement, Observatoire Océanologique, 06230 Villefranche sur Mer, France
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