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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 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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2
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Wen JWH, Winklbauer R. Ingression-type cell migration drives vegetal endoderm internalisation in the Xenopus gastrula. eLife 2017; 6:e27190. [PMID: 28826499 PMCID: PMC5589415 DOI: 10.7554/elife.27190] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/08/2017] [Indexed: 12/30/2022] Open
Abstract
During amphibian gastrulation, presumptive endoderm is internalised as part of vegetal rotation, a large-scale movement that encompasses the whole vegetal half of the embryo. It has been considered a gastrulation process unique to amphibians, but we show that at the cell level, endoderm internalisation exhibits characteristics reminiscent of bottle cell formation and ingression, known mechanisms of germ layer internalisation. During ingression proper, cells leave a single-layered epithelium. In vegetal rotation, the process occurs in a multilayered cell mass; we refer to it as ingression-type cell migration. Endoderm cells move by amoeboid shape changes, but in contrast to other instances of amoeboid migration, trailing edge retraction involves ephrinB1-dependent macropinocytosis and trans-endocytosis. Moreover, although cells are separated by wide gaps, they are connected by filiform protrusions, and their migration depends on C-cadherin and the matrix protein fibronectin. Cells move in the same direction but at different velocities, to rearrange by differential migration.
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Affiliation(s)
- Jason WH Wen
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Rudolf Winklbauer
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
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3
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Suzuki A, Yoshida H, van Heeringen SJ, Takebayashi-Suzuki K, Veenstra GJC, Taira M. Genomic organization and modulation of gene expression of the TGF-β and FGF pathways in the allotetraploid frog Xenopus laevis. Dev Biol 2017; 426:336-359. [DOI: 10.1016/j.ydbio.2016.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/10/2016] [Accepted: 09/19/2016] [Indexed: 12/13/2022]
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4
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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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5
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Riddiford N, Schlosser G. Dissecting the pre-placodal transcriptome to reveal presumptive direct targets of Six1 and Eya1 in cranial placodes. eLife 2016; 5. [PMID: 27576864 PMCID: PMC5035141 DOI: 10.7554/elife.17666] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/29/2016] [Indexed: 11/13/2022] Open
Abstract
The pre-placodal ectoderm, marked by the expression of the transcription factor Six1 and its co-activator Eya1, develops into placodes and ultimately into many cranial sensory organs and ganglia. Using RNA-Seq in Xenopus laevis we screened for presumptive direct placodal target genes of Six1 and Eya1 by overexpressing hormone-inducible constructs of Six1 and Eya1 in pre-placodal explants, and blocking protein synthesis before hormone-inducing nuclear translocation of Six1 or Eya1. Comparing the transcriptome of explants with non-induced controls, we identified hundreds of novel Six1/Eya1 target genes with potentially important roles for placode development. Loss-of-function studies confirmed that target genes encoding known transcriptional regulators of progenitor fates (e.g. Sox2, Hes8) and neuronal/sensory differentiation (e.g. Ngn1, Atoh1, Pou4f1, Gfi1) require Six1 and Eya1 for their placodal expression. Our findings provide insights into the gene regulatory network regulating placodal neurogenesis downstream of Six1 and Eya1 suggesting new avenues of research into placode development and disease.
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Affiliation(s)
- Nick Riddiford
- School of Natural Sciences, National University of Ireland, Galway, Ireland.,Regenerative Medicine Institute (REMEDI), National University of Ireland, Galway, Ireland
| | - Gerhard Schlosser
- School of Natural Sciences, National University of Ireland, Galway, Ireland.,Regenerative Medicine Institute (REMEDI), National University of Ireland, Galway, Ireland
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6
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Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing. Dev Biol 2016; 426:429-441. [PMID: 27209239 DOI: 10.1016/j.ydbio.2016.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/11/2016] [Accepted: 05/11/2016] [Indexed: 12/19/2022]
Abstract
During early vertebrate embryogenesis, cell fate specification is often coupled with cell acquisition of specific adhesive, polar and/or motile behaviors. In Xenopus gastrulae, tissues fated to form different axial structures display distinct motility. The cells in the early organizer move collectively and directionally toward the animal pole and contribute to anterior mesendoderm, whereas the dorsal and the ventral-posterior trunk tissues surrounding the blastopore of mid-gastrula embryos undergo convergent extension and convergent thickening movements, respectively. While factors regulating cell lineage specification have been described in some detail, the molecular machinery that controls cell motility is not understood in depth. To gain insight into the gene battery that regulates both cell fates and motility in particular embryonic tissues, we performed RNA sequencing (RNA-seq) to investigate differentially expressed genes in the early organizer, the dorsal and the ventral marginal zone of Xenopus gastrulae. We uncovered many known signaling and transcription factors that have been reported to play roles in embryonic patterning during gastrulation. We also identified many uncharacterized genes as well as genes that encoded extracellular matrix (ECM) proteins or potential regulators of actin cytoskeleton. Co-expression of a selected subset of the differentially expressed genes with activin in animal caps revealed that they had distinct ability to block activin-induced animal cap elongation. Most of these factors did not interfere with mesodermal induction by activin, but an ECM protein, EFEMP2, inhibited activin signaling and acted downstream of the activated type I receptor. By focusing on a secreted protein kinase PKDCC1, we showed with overexpression and knockdown experiments that PKDCC1 regulated gastrulation movements as well as anterior neural patterning during early Xenopus development. Overall, our studies identify many differentially expressed signaling and cytoskeleton regulators in different embryonic regions of Xenopus gastrulae and imply their functions in regulating cell fates and/or behaviors during gastrulation.
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7
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Gao L, Zhu X, Chen G, Ma X, Zhang Y, Khand AA, Shi H, Gu F, Lin H, Chen Y, Zhang H, He L, Tao Q. A novel role for Ascl1 in the regulation of mesendoderm formation via HDAC-dependent antagonism of VegT. Development 2015; 143:492-503. [PMID: 26700681 PMCID: PMC4760308 DOI: 10.1242/dev.126292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/16/2015] [Indexed: 01/02/2023]
Abstract
Maternally expressed proteins function in vertebrates to establish the major body axes of the embryo and to establish a pre-pattern that sets the stage for later-acting zygotic signals. This pre-patterning drives the propensity of Xenopus animal cap cells to adopt neural fates under various experimental conditions. Previous studies found that the maternally expressed transcription factor, encoded by the Xenopus achaete scute-like gene ascl1, is enriched at the animal pole. Asc1l is a bHLH protein involved in neural development, but its maternal function has not been studied. Here, we performed a series of gain- and loss-of-function experiments on maternal ascl1, and present three novel findings. First, Ascl1 is a repressor of mesendoderm induced by VegT, but not of Nodal-induced mesendoderm. Second, a previously uncharacterized N-terminal domain of Ascl1 interacts with HDAC1 to inhibit mesendoderm gene expression. This N-terminal domain is dispensable for its neurogenic function, indicating that Ascl1 acts by different mechanisms at different times. Ascl1-mediated repression of mesendoderm genes was dependent on HDAC activity and accompanied by histone deacetylation in the promoter regions of VegT targets. Finally, maternal Ascl1 is required for animal cap cells to retain their competence to adopt neural fates. These results establish maternal Asc1l as a key factor in establishing pre-patterning of the early embryo, acting in opposition to VegT and biasing the animal pole to adopt neural fates. The data presented here significantly extend our understanding of early embryonic pattern formation. Summary: The proneural factor ASCL1 recruits HDAC1 to repress VegT-induced, but not Nodal-induced, mesendoderm formation via a previously uncharacterized N-terminal domain.
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Affiliation(s)
- Li Gao
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Xuechen Zhu
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Geng Chen
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Xin Ma
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Zhang
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Aftab A Khand
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Huijuan Shi
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Fei Gu
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Hao Lin
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Yuemeng Chen
- Tianjin Normal University College of Life Science, Binshuixidao (extension line) 393, Xinqing District, Tianjin 300387, China
| | - Haiyan Zhang
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Lei He
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Qinghua Tao
- MOE Key Laboratory of Protein Sciences, Tsinghua University School of Life Sciences, Beijing 100084, China
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8
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Sun G, Hu Z, Min Z, Yan X, Guan Z, Su H, Fu Y, Ma X, Chen YG, Zhang MQ, Tao Q, Wu W. Small C-terminal Domain Phosphatase 3 Dephosphorylates the Linker Sites of Receptor-regulated Smads (R-Smads) to Ensure Transforming Growth Factor β (TGFβ)-mediated Germ Layer Induction in Xenopus Embryos. J Biol Chem 2015; 290:17239-49. [PMID: 26013826 DOI: 10.1074/jbc.m115.655605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 01/27/2023] Open
Abstract
Germ layer induction is one of the earliest events shortly after fertilization that initiates body formation of vertebrate embryos. In Xenopus, the maternally deposited transcriptional factor VegT promotes the expression of zygotic Nodal/Activin ligands that further form a morphogen gradient along the vegetal-animal axis and trigger the induction of the three germ layers. Here we found that SCP3 (small C-terminal domain phosphatase 3) is maternally expressed and vegetally enriched in Xenopus embryos and is essential for the timely induction of germ layers. SCP3 is required for the full activation of Nodal/Activin and bone morphogenetic protein signals and functions via dephosphorylation in the linker regions of receptor-regulated Smads. Consistently, the linker regions of receptor-regulated Smads are heavily phosphorylated in fertilized eggs, and this phosphorylation is gradually removed when embryos approach the midblastula transition. Knockdown of maternal SCP3 attenuates these dephosphorylation events and the activation of Nodal/Activin and bone morphogenetic protein signals after midblastula transition. This study thus suggested that the maternal SCP3 serves as a vegetally enriched, intrinsic factor to ensure a prepared status of Smads for their activation by the upcoming ligands during germ layer induction of Xenopus embryos.
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Affiliation(s)
- Guanni Sun
- From the MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhirui Hu
- the Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China
| | - Zheying Min
- the School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohua Yan
- the State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China, and
| | - Zhenpo Guan
- From the MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hanxia Su
- From the MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu Fu
- From the MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaopeng Ma
- the Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China
| | - Ye-Guang Chen
- the State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China, and
| | - Michael Q Zhang
- the Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China, the Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas 75080
| | - Qinghua Tao
- the School of Life Sciences, Tsinghua University, Beijing 100084, China,
| | - Wei Wu
- From the MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing 100084, China,
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9
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Ogino H, Ochi H. Resources and transgenesis techniques for functional genomics in Xenopus. Dev Growth Differ 2009; 51:387-401. [PMID: 19382936 DOI: 10.1111/j.1440-169x.2009.01098.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recent developments in genomic resources and high-throughput transgenesis techniques have allowed Xenopus to 'metamorphose' from a classic model for embryology to a leading-edge experimental system for functional genomics. This process has incorporated the fast-breeding diploid frog, Xenopus tropicalis, as a new model-system for vertebrate genomics and genetics. Sequencing of the X. tropicalis genome is nearly complete, and its comparison with mammalian sequences offers a reliable guide for the genome-wide prediction of cis-regulatory elements. Unique cDNA sets have been generated for both X. tropicalis and X. laevis, which have facilitated non-redundant, systematic gene expression screening and comprehensive gene expression analysis. A variety of transgenesis techniques are available for both X. laevis and X. tropicalis, and the appropriate procedure may be chosen depending on the purpose for which it is required. Effective use of these resources and techniques will help to reveal the overall picture of the complex wiring of gene regulatory networks that control vertebrate development.
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Affiliation(s)
- Hajime Ogino
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan.
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10
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Macindoe I, Glockner L, Vukasin P, Stennard FA, Costa MW, Harvey RP, Mackay JP, Sunde M. Conformational stability and DNA binding specificity of the cardiac T-box transcription factor Tbx20. J Mol Biol 2009; 389:606-18. [PMID: 19414016 DOI: 10.1016/j.jmb.2009.04.056] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 04/22/2009] [Accepted: 04/25/2009] [Indexed: 11/25/2022]
Abstract
The transcription factor Tbx20 acts within a hierarchy of T-box factors in lineage specification and morphogenesis in the mammalian heart and is mutated in congenital heart disease. T-box family members share a approximately 20-kDa DNA-binding domain termed the T-box. The question of how highly homologous T-box proteins achieve differential transcriptional control in heart development, while apparently binding to the same DNA sequence, remains unresolved. Here we show that the optimal DNA recognition sequence for the T-box of Tbx20 corresponds to a T-half-site. Furthermore, we demonstrate using purified recombinant domains that distinct T-boxes show significant differences in the affinity and kinetics of binding and in conformational stability, with the T-box of Tbx20 displaying molten globule character. Our data highlight unique features of Tbx20 and suggest mechanistic ways in which cardiac T-box factors might interact synergistically and/or competitively within the cardiac regulatory network.
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Affiliation(s)
- Ingrid Macindoe
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia
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11
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Faunes F, Sánchez N, Castellanos J, Vergara IA, Melo F, Larraín J. Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression. Genome Biol 2009; 10:R15. [PMID: 19210784 PMCID: PMC2688288 DOI: 10.1186/gb-2009-10-2-r15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 11/25/2008] [Accepted: 02/11/2009] [Indexed: 11/12/2022] Open
Abstract
Comparison of dorsal and ventral transcriptomes of Xenopus tropicalis gastrulae using serial analysis of gene expression provides at least 86 novel differentially expressed transcripts. Background Recent evidence from global studies of gene expression indicates that transcriptomes are more complex than expected. Xenopus has been typically used as a model organism to study early embryonic development, particularly dorso-ventral patterning. In order to identify novel transcripts involved in dorso-ventral patterning, we compared dorsal and ventral transcriptomes of Xenopus tropicalis at the gastrula stage using serial analysis of gene expression (SAGE). Results Of the experimental tags, 54.5% were confidently mapped to transcripts and 125 showed a significant difference in their frequency of occurrence between dorsal and ventral libraries. We selected 20 differentially expressed tags and assigned them to specific transcripts using bioinformatics and reverse SAGE. Five mapped to transcripts with known dorso-ventral expression and the frequency of appearance for these tags in each library is in agreement with the expression described by other methods. The other 15 tags mapped to transcripts with no previously described asymmetric expression along the dorso-ventral axis. The differential expression of ten of these novel transcripts was validated by in situ hybridization and/or RT-PCR. We can estimate that this SAGE experiment provides a list of at least 86 novel transcripts with differential expression along the dorso-ventral axis. Interestingly, the expression of some novel transcripts was independent of β-catenin. Conclusions Our SAGE analysis provides a list of novel transcripts with differential expression in the dorso-ventral axis and a large number of orphan tags that can be used to identify novel transcripts and to improve the current annotation of the X. tropicalis genome.
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Affiliation(s)
- Fernando Faunes
- Center for Cell Regulation and Pathology and Center for Aging and Regeneration, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, 8331150, Chile
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12
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Tazumi S, Yabe S, Yokoyama J, Aihara Y, Uchiyama H. PMesogenin1 and 2 function directly downstream of Xtbx6 in Xenopus somitogenesis and myogenesis. Dev Dyn 2009; 237:3749-61. [PMID: 19035338 DOI: 10.1002/dvdy.21791] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
T-box transcription factor tbx6 and basic-helix-loop-helix transcription factor pMesogenin1 are reported to be involved in paraxial mesodermal differentiation. To clarify the relationship between these genes in Xenopus laevis, we isolated pMesogenin2, which showed high homology with pMesogenin1. Both pMesogenin1 and 2 appeared to be transcriptional activators and were induced by a hormone-inducible version of Xtbx6 without secondary protein synthesis in animal cap assays. The pMesogenin2 promoter contained three potential T-box binding sites with which Xtbx6 protein was shown to interact, and a reporter gene construct containing these sites was activated by Xtbx6. Xtbx6 knockdown reduced pMesogenin1 and 2 expressions, but not vice versa. Xtbx6 and pMesogenin1 and 2 knockdowns caused similar phenotypic abnormalities including somite malformation and ventral body wall muscle hypoplasia, suggesting that Xtbx6 is a direct regulator of pMesogenin1 and 2, which are both involved in somitogenesis and myogenesis including that of body wall muscle in Xenopus laevis.
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Affiliation(s)
- Shunsuke Tazumi
- International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Japan
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13
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Smith J, Wardle F, Loose M, Stanley E, Patient R. Germ layer induction in ESC--following the vertebrate roadmap. ACTA ACUST UNITED AC 2008; Chapter 1:Unit 1D.1. [PMID: 18785165 DOI: 10.1002/9780470151808.sc01d01s1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Controlled differentiation of pluripotential cells takes place routinely and with great success in developing vertebrate embryos. It therefore makes sense to take note of how this is achieved and use this knowledge to control the differentiation of embryonic stem cells (ESCs). An added advantage is that the differentiated cells resulting from this process in embryos have proven functionality and longevity. This unit reviews what is known about the embryonic signals that drive differentiation in one of the most informative of the vertebrate animal models of development, the amphibian Xenopus laevis. It summarizes their identities and the extent to which their activities are dose-dependent. The unit details what is known about the transcription factor responses to these signals, describing the networks of interactions that they generate. It then discusses the target genes of these transcription factors, the effectors of the differentiated state. Finally, how these same developmental programs operate during germ layer formation in the context of ESC differentiation is summarized.
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Affiliation(s)
- Jim Smith
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
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14
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Spagnoli FM, Brivanlou AH. The Gata5 target, TGIF2, defines the pancreatic region by modulating BMP signals within the endoderm. Development 2007; 135:451-61. [PMID: 18094028 DOI: 10.1242/dev.008458] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mechanisms underlying regional specification of distinct organ precursors within the endoderm, including the liver and pancreas, are still poorly understood. This is particularly true for stages between endoderm formation and the initiation of organogenesis. In this report, we have investigated these intermediate steps downstream of the early endodermal factor Gata5, which progressively lead to the induction of pancreatic fate. We have identified TGIF2 as a novel Gata5 target and demonstrate its function in the establishment of the pancreatic region within dorsal endoderm in Xenopus. TGIF2 acts primarily by restricting BMP signaling in the endoderm to allow pancreatic formation. Consistently, we found that blocking BMP signaling by independent means also perturbs the establishment of pancreatic identity in the endoderm. Previous findings demonstrated a crucial role for BMP signaling in determining dorsal/ventral fates in ectoderm and mesoderm. Our results now extend this trend to the endoderm and identify TGIF2 as the molecular link between dorsoventral patterning of the endoderm and pancreatic specification.
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Affiliation(s)
- Francesca M Spagnoli
- Laboratory of Molecular Vertebrate Embryology, The Rockefeller University, New York, NY 10021, USA
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15
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Abstract
Xenopus tropicalis is rapidly being adopted as a model organism for developmental biology research and has enormous potential for increasing our understanding of how embryonic development is controlled. In recent years there has been a well-organized initiative within the Xenopus community, funded largely through the support of the National Institutes of Health in the US, to develop X. tropicalis as a new genetic model system with the potential to impact diverse fields of research. Concerted efforts have been made both to adapt established methodologies for use in X. tropicalis and to develop new techniques. A key resource to come out of these efforts is the genome sequence, produced by the US Department of Energy's Joint Genome Institute and made freely available to the community in draft form for the past three years. In this review, we focus on how advances in X. tropicalis genetics coupled with the sequencing of its genome are likely to form a foundation from which we can build a better understanding of the genetic control of vertebrate development and why, when we already have other vertebrate genetic models, we should want to develop genetic analysis in the frog.
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Affiliation(s)
- Chris Showell
- Carolina Cardiovascular Biology Center and Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Frank L. Conlon
- Carolina Cardiovascular Biology Center and Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina
- Correspondence to: Frank L. Conlon, 220 Fordham Hall, Medical Drive, Chapel Hill, NC 27599-3280., E-mail:
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Laflamme M, Robichaud GA. Gene Suppression Technologies in High-Throughput Analysis: Front- and Back-side Applications. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 11:129-42. [PMID: 17594233 DOI: 10.1089/omi.2007.4321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Our understanding of gene function and gene interactions has changed dramatically with the development of high-throughput systems. It now seems clear that any given gene interacts with a number of different partners, and in a number of different molecular pathways. Traditionally, gene function has been studied using animal knockout systems or naturally occurring mutants. RNA-based gene suppression systems for example, RNA interference or ribozymes, offer a number of advantages over the traditional systems, including ease of use, high specificity, and efficacy in nearly any biological system, and the ability to perform large-scale screens. Since their advent in the mid-1990s, DNA microarrays have been the choice for genome-wide expression analysis. The synergistic effect from the combined use of RNA-based gene suppression and molecular profiling is providing researchers with vast amounts of data. As a result, we are rapidly gaining an understanding of gene interactions and function. This review will focus primarily on gene inactivation systems that have been proven worthy of use in molecular pathway analysis when combined with microarray analysis.
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Affiliation(s)
- Mark Laflamme
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada.
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17
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Yan B, Moody SA. The competence of Xenopus blastomeres to produce neural and retinal progeny is repressed by two endo-mesoderm promoting pathways. Dev Biol 2007; 305:103-19. [PMID: 17428460 PMCID: PMC1892348 DOI: 10.1016/j.ydbio.2007.01.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 01/11/2007] [Accepted: 01/31/2007] [Indexed: 10/23/2022]
Abstract
Only a subset of cleavage stage blastomeres in the Xenopus embryo is competent to contribute cells to the retina; ventral vegetal blastomeres do not form retina even when provided with neuralizing factors or transplanted to the most retinogenic position of the embryo. These results suggest that endogenous maternal factors in the vegetal region repress the ability of blastomeres to form retina. Herein we provide three lines of evidence that two vegetal-enriched maternal factors (VegT, Vg1), which are known to promote endo-mesodermal fates, negatively regulate which cells are competent to express anterior neural and retinal fates. First, both molecules can repress the ability of dorsal-animal retinogenic blastomeres to form retina, converting the lineage from neural/retinal to non-neural ectodermal and endo-mesodermal fates. Second, reducing the endogenous levels of either factor in dorsal-animal retinogenic blastomeres expands expression of neural/retinal genes and enlarges the retina. The dorsal-animal repression of neural/retinal fates by VegT and Vg1 is likely mediated by Sox17alpha and Derriere but not by XNr1. VegT and Vg1 likely exert their effects on neural/retinal fates through at least partially independent pathways because Notch1 can reverse the effects of VegT and Derriere but not those of Vg1 or XNr1. Third, reduction of endogenous VegT and/or Vg1 in ventral vegetal blastomeres can induce a neural fate, but only allows expression of a retinal fate when both BMP and Wnt signaling pathways are concomitantly repressed.
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Affiliation(s)
- Bo Yan
- Department of Anatomy and Cell Biology, The George Washington University Medical Center, 2300 Eye Street, N.W., Washington, DC 20037, USA
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18
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Bennett JT, Joubin K, Cheng S, Aanstad P, Herwig R, Clark M, Lehrach H, Schier AF. Nodal signaling activates differentiation genes during zebrafish gastrulation. Dev Biol 2007; 304:525-40. [PMID: 17306247 PMCID: PMC1885460 DOI: 10.1016/j.ydbio.2007.01.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2006] [Revised: 12/17/2006] [Accepted: 01/04/2007] [Indexed: 01/10/2023]
Abstract
Nodal signals induce mesodermal and endodermal progenitors during vertebrate development. To determine the role of Nodal signaling at a genomic level, we isolated Nodal-regulated genes by expression profiling using macroarrays and gene expression databases. Putative Nodal-regulated genes were validated by in situ hybridization screening in wild type and Nodal signaling mutants. 46 genes were identified, raising the currently known number of Nodal-regulated genes to 72. Based on their expression patterns along the dorsoventral axis, most of these genes can be classified into two groups. One group is expressed in the dorsal margin, whereas the other group is expressed throughout the margin. In addition to transcription factors and signaling components, the screens identified several new functional classes of Nodal-regulated genes, including cytoskeletal components and molecules involved in protein secretion or endoplasmic reticulum stress. We found that x-box binding protein-1 (xbp1) is a direct target of Nodal signaling and required for the terminal differentiation of the hatching gland, a specialized secretory organ whose specification is also dependent on Nodal signaling. These results indicate that Nodal signaling regulates not only specification genes but also differentiation genes.
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Affiliation(s)
- James T. Bennett
- Developmental Genetics Program, Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York, NY 10016, USA
| | - Katherine Joubin
- Developmental Genetics Program, Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York, NY 10016, USA
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Cheng
- Developmental Genetics Program, Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York, NY 10016, USA
- Department of Radiation Oncology New York University School of Medicine, New York, NY 10016, USA
| | - Pia Aanstad
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Ralf Herwig
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | - Matthew Clark
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | - Hans Lehrach
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | - Alexander F. Schier
- Developmental Genetics Program, Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York, NY 10016, USA
- Department of Molecular and Cellular Biology, Harvard Stem Cell Institute, Center for Brain Science, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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19
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Evolution of the mechanisms and molecular control of endoderm formation. Mech Dev 2007; 124:253-78. [PMID: 17307341 DOI: 10.1016/j.mod.2007.01.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 12/24/2006] [Accepted: 01/03/2007] [Indexed: 01/13/2023]
Abstract
Endoderm differentiation and movements are of fundamental importance not only for subsequent morphogenesis of the digestive tract but also to enable normal patterning and differentiation of mesoderm- and ectoderm-derived organs. This review defines the tissues that have been called endoderm in different species, their cellular origin and their movements. We take a comparative approach to ask how signaling pathways leading to embryonic and extraembryonic endoderm differentiation have emerged in different organisms, how they became integrated and point to specific gaps in our knowledge that would be worth filling. Lastly, we address whether the gastrulation movements that lead to endoderm internalization are coupled with its differentiation.
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20
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Zorn AM, Wells JM. Molecular Basis of Vertebrate Endoderm Development. INTERNATIONAL REVIEW OF CYTOLOGY 2007; 259:49-111. [PMID: 17425939 DOI: 10.1016/s0074-7696(06)59002-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The embryonic endoderm gives rise to the epithelial lining of the digestive and respiratory systems and organs such as the thyroid, lungs, liver, gallbladder, and pancreas. Studies in Xenopus, zebrafish, and mice have revealed a conserved molecular pathway controlling vertebrate endoderm development. The TGFbeta/Nodal signaling pathway is at the top of this molecular hierarchy and controls the expression of a number of key transcription factors including Mix-like homeodomain proteins, Gata zinc finger factors, Sox HMG domain proteins, and Fox forkhead factors. Here we review the function of these molecules comparing and contrasting their roles in each model organism. Finally, we will describe how our understanding of the molecular pathway governing endoderm development in embryos is being used to differentiate embryonic stem cells in vitro along endodermal lineages, with the ultimate goal of making therapeutically useful tissue.
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Affiliation(s)
- Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Research, Foundation and University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
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21
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Sipe CW, Saha MS. The use of microarray technology in nonmammalian vertebrate systems. Methods Mol Biol 2007; 382:1-16. [PMID: 18220221 DOI: 10.1007/978-1-59745-304-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Among vertebrates, the mammalian systems that are frequently used to investigate questions related to human health have gained the most benefit from microarray technology to date. However, it is clear that biological investigations and the generalized conclusions drawn from them, can only be enhanced by including organisms in which specific processes can be readily studied because of their genetic, physiological, or developmental disposition. As a result, the field of functional genomics has recently begun to embrace a number of other vertebrate species. This review summarizes the current state of microarray technology in a subset of these vertebrate organisms, including Xenopus, Rana, zebrafish, killifish (Fundulus sp.), medaka (Oryzias latipes), Atlantic salmon, and rainbow trout. A summary of various applications of microarray technology and a brief introduction to the steps involved in carrying out a microarray experiment are also presented.
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Affiliation(s)
- Conor W Sipe
- Department of Biology, College of William and Mary, Williamsburg, VA, USA
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22
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Li S, Shin Y, Cho KWY, Merzdorf CS. The Xfeb gene is directly upregulated by Zic1 during early neural development. Dev Dyn 2006; 235:2817-27. [PMID: 16871635 DOI: 10.1002/dvdy.20896] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The transcription factor Zic1 plays important roles in patterning the neural plate in early vertebrate development. However, few genes that are regulated by Zic1 are known. We have identified a new direct downstream target gene of Zic1 that we have named Xfeb. Xfeb is a member of the pathogenesis-related (PR) protein superfamily and contains five tandem SCP domains. The sequence of Xfeb suggests that it may possess serine protease activity. Xfeb is expressed in the presumptive hindbrain region during neurula stages and in somite tissues later in development. Xfeb represses the hindbrain gene hoxB1 and the anterior neural gene otx2, suggesting that Xfeb is involved in regionalizing the neural plate, possibly by ensuring a posterior expression limit for otx2.
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Affiliation(s)
- Shuzhao Li
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana, USA
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23
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Sinner D, Kirilenko P, Rankin S, Wei E, Howard L, Kofron M, Heasman J, Woodland HR, Zorn AM. Global analysis of the transcriptional network controlling Xenopus endoderm formation. Development 2006; 133:1955-66. [PMID: 16651540 DOI: 10.1242/dev.02358] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A conserved molecular pathway has emerged controlling endoderm formation in Xenopus zebrafish and mice. Key genes in this pathway include Nodal ligands and transcription factors of the Mix-like paired homeodomain class, Gata4-6 zinc-finger factors and Sox17 HMG domain proteins. Although a linear epistatic pathway has been proposed, the precise hierarchical relationships between these factors and their downstream targets are largely unresolved. Here, we have used a combination of microarray analysis and loss-of-function experiments to examine the global regulatory network controlling Xenopus endoderm formation. We identified over 300 transcripts enriched in the gastrula endoderm, including most of the known endoderm regulators and over a hundred uncharacterized genes. Surprisingly only 10% of the endoderm transcriptome is regulated as predicted by the current linear model. We find that Nodal genes, Mixer and Sox17 have both shared and distinct sets of downstream targets, and that a number of unexpected autoregulatory loops exist between Sox17 and Gata4-6, between Sox17 and Bix1/Bix2/Bix4, and between Sox17 and Xnr4. Furthermore, we find that Mixer does not function primarily via Sox17 as previously proposed. These data provides new insight into the complexity of endoderm formation and will serve as valuable resource for establishing a complete endoderm gene regulatory network.
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Affiliation(s)
- Débora Sinner
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45299, USA
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24
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Abstract
Vertebrate mesoderm induction is one of the classical problems in developmental biology. Various developmental biology approaches, particularly in Xenopus and zebrafish, have identified many of the key factors that are involved in this process and have provided major insights into how these factors interact as part of a signalling and transcription-factor network. These data are beginning to be refined by high-throughput approaches such as microarray assays. Future challenges include understanding how the prospective mesodermal cells integrate the various signals they receive and how they resolve this information to regulate their morphogenetic behaviours and cell-fate decisions.
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Affiliation(s)
- David Kimelman
- Department of Biochemistry, Box 357350, University of Washington, Seattle, Washington 98195-7350, USA.
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25
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Dingwell KS, Smith JC. Tes regulates neural crest migration and axial elongation in Xenopus. Dev Biol 2006; 293:252-67. [PMID: 16554046 DOI: 10.1016/j.ydbio.2006.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 02/03/2006] [Indexed: 11/20/2022]
Abstract
Tes is a member of an emerging family of proteins sharing a set of protein motifs referred to as PET-LIM domains. PET-LIM proteins such as Prickle regulate cell behavior during gastrulation in Xenopus and zebrafish, and to ask whether Tes is also involved in controlling cell behavior, we isolated its Xenopus orthologue. Xtes is expressed as a maternal transcript that is maintained at low levels until neurula stages when expression is elevated in the head and axial structures. Depletion of Xtes leads to a foreshortened head and severe defects in axis elongation. The anterior defect is due in part to the inhibition of cranial neural crest migration while the defects in elongation may be due to perturbation of expression of XFGF8, Xdelta-1 and Xcad-3 and thereby to disruption of posterior somitogenesis. Finally, we note that simultaneous depletion of Xtes and Xenopus Prickle results in axial defects that are more severe than those resulting from depletion of Xtes alone, suggesting that the two proteins act together to control axial elongation.
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Affiliation(s)
- Kevin S Dingwell
- Wellcome Trust and Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, and Department of Zoology, University of Cambridge, Cambridge CB2 1QR, UK
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26
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Dickinson K, Leonard J, Baker JC. Genomic profiling of mixer and Sox17beta targets during Xenopus endoderm development. Dev Dyn 2006; 235:368-81. [PMID: 16278889 PMCID: PMC4510981 DOI: 10.1002/dvdy.20636] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The transcription factors Mixer and Sox17beta have well-characterized roles in endoderm specification during Xenopus embryogenesis. In order to more thoroughly understand the mechanisms by which these endodermal regulators act, we expressed Mixer and Sox17beta in naïve ectodermal tissue and, using oligonucleotide-based microarrays, compared their genomic transcriptional profile to that of unaffected tissue. Using this approach, we identified 71 transcripts that are upregulated by Mixer or Sox17beta, 63 of which have previously uncharacterized roles in endoderm development. Furthermore, an in situ hybridization screen using antisense probes for several of these clones identified six targets of Mixer and/or Sox17beta that are expressed in the endoderm during gastrula stages, providing new and regional markers of the endoderm. Our results contribute further insight into the functions of Mixer and Sox17beta and bring us closer to understanding at the molecular level the pathways that regulate endoderm development.
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Affiliation(s)
| | | | - Julie C. Baker
- Corresponding Author, Julie C. Baker, Genetics Department, Stanford University, 300 Pasteur Drive, MC 5120, Stanford, CA 94062, 650-723-1082, 650-725-1534 (fax),
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27
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Abstract
Research using Xenopus laevis has made enormous contributions to our understanding of vertebrate development, control of the eukaryotic cell cycle and the cytoskeleton. One limitation, however, has been the lack of systematic genetic studies in Xenopus to complement molecular and cell biological investigations. Work with the closely related diploid frog Xenopus tropicalis is beginning to address this limitation. Here, we review the resources that will make genetic studies using X. tropicalis a reality.
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Affiliation(s)
- Samantha Carruthers
- Vertebrate Development and Genetics, The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
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28
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Sartor MA, Zorn AM, Schwanekamp JA, Halbleib D, Karyala S, Howell ML, Dean GE, Medvedovic M, Tomlinson CR. A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res 2006; 34:185-200. [PMID: 16397297 PMCID: PMC1325202 DOI: 10.1093/nar/gkj413] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The recent sequencing of a large number of Xenopus tropicalis expressed sequences has allowed development of a high-throughput approach to study Xenopus global RNA gene expression. We examined the global gene expression similarities and differences between the historically significant Xenopus laevis model system and the increasingly used X.tropicalis model system and assessed whether an X.tropicalis microarray platform can be used for X.laevis. These closely related species were also used to investigate a more general question: is there an association between mRNA sequence divergence and differences in gene expression levels? We carried out a comprehensive comparison of global gene expression profiles using microarrays of different tissues and developmental stages of X.laevis and X.tropicalis. We (i) show that the X.tropicalis probes provide an efficacious microarray platform for X.laevis, (ii) describe methods to compare interspecies mRNA profiles that correct differences in hybridization efficiency and (iii) show independently of hybridization bias that as mRNA sequence divergence increases between X.laevis and X.tropicalis differences in mRNA expression levels also increase.
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Affiliation(s)
- Maureen A. Sartor
- University of Cincinnati, Department of Environmental HealthCincinnati, OH, 45267-0056, USA
- Division of Biostatistics and Epidemiology, Children's HospitalCincinnati, OH 45229-3039, USA
- Center for Environmental Genetics, Children's HospitalCincinnati, OH 45229-3039, USA
| | - Aaron M. Zorn
- Division of Developmental Biology, Children's HospitalCincinnati, OH 45229-3039, USA
| | - Jennifer A. Schwanekamp
- University of Cincinnati, Department of Environmental HealthCincinnati, OH, 45267-0056, USA
- Division of Environmental Genetics and Molecular Toxicology, Children's HospitalCincinnati, OH 45229-3039, USA
| | - Danielle Halbleib
- University of Cincinnati, Department of Environmental HealthCincinnati, OH, 45267-0056, USA
- Division of Environmental Genetics and Molecular Toxicology, Children's HospitalCincinnati, OH 45229-3039, USA
| | - Saikumar Karyala
- University of Cincinnati, Department of Environmental HealthCincinnati, OH, 45267-0056, USA
- Division of Environmental Genetics and Molecular Toxicology, Children's HospitalCincinnati, OH 45229-3039, USA
| | | | - Gary E. Dean
- Protein Express, Inc.9940 Reading Road, Cincinnati, OH 45241, USA
- Department of Molecular Genetics, Biochemistry and Microbiology, University of CincinnatiCincinnati, OH, 45267-0524, USA
| | - Mario Medvedovic
- University of Cincinnati, Department of Environmental HealthCincinnati, OH, 45267-0056, USA
- Division of Biostatistics and Epidemiology, Children's HospitalCincinnati, OH 45229-3039, USA
- Center for Environmental Genetics, Children's HospitalCincinnati, OH 45229-3039, USA
- Center for Genome Information, Children's HospitalCincinnati, OH 45229-3039, USA
- Hyacinth Genomics, LLC3431 Stettinius Avenue, Cincinnati, OH 45208, USA
| | - Craig R. Tomlinson
- University of Cincinnati, Department of Environmental HealthCincinnati, OH, 45267-0056, USA
- Division of Environmental Genetics and Molecular Toxicology, Children's HospitalCincinnati, OH 45229-3039, USA
- Center for Environmental Genetics, Children's HospitalCincinnati, OH 45229-3039, USA
- Hyacinth Genomics, LLC3431 Stettinius Avenue, Cincinnati, OH 45208, USA
- To whom correspondence should be addressed. Tel: +1 603 650 7936; Fax: +1 603 650 6122; Email addresses:
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29
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Abstract
Mesoderm and endoderm formation in Xenopus involves the coordinated efforts of maternally and zygotically expressed transcription factors together with growth factor signalling, including members of the TGFbeta and wnt families. In this review we discuss our current state of knowledge of these pathways, and describe in more detail some of the transcription factor-DNA interactions that are involved in mesendoderm formation.
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Affiliation(s)
- Fiona C Wardle
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
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30
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Abstract
Xenopus genomics, or Xenomics for short, is coming of age. Indeed, biological insight into processes such as growth factor signaling and patterning of the early embryo is now being gained by combining the value of Xenopus as a model organism for cell and developmental biology with genomic approaches. In this review I address these recent advances and explore future possibilities gained from combining this powerful experimental system with genomic approaches, as well as how our quest to understand basic biological principles will be greatly facilitated though the marriage of Xenopus and genomics.
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Affiliation(s)
- Enrique Amaya
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CB2 1QN, United Kingdom.
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31
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Affiliation(s)
- J C Smith
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road, Cambridge CB2 1QN, UK.
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32
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Koide T, Hayata T, Cho KWY. Xenopus as a model system to study transcriptional regulatory networks. Proc Natl Acad Sci U S A 2005; 102:4943-8. [PMID: 15795378 PMCID: PMC555977 DOI: 10.1073/pnas.0408125102] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Indexed: 11/18/2022] Open
Abstract
Development is controlled by a complex series of events requiring sequential gene activation. Understanding the logic of gene networks during development is necessary for a complete understanding of how genes contribute to phenotype. Pioneering work initiated in the sea urchin and Drosophila has demonstrated that reasonable transcriptional regulatory network diagrams representing early development in multicellular animals can be generated through use of appropriate genomic, genetic, and biochemical tools. Establishment of similar regulatory network diagrams for vertebrate development is a necessary step. The amphibian Xenopus has long been used as a model for vertebrate early development and has contributed greatly to the elucidation of gene regulation. Because the best and most extensively studied transcriptional regulatory network in Xenopus is that underlying the formation and function of Spemann's organizer, we describe the current status of our understanding of this gene regulatory network and its relationship to mesodermal patterning. Seventy-four transcription factors currently known to be expressed in the mesoendoderm of Xenopus gastrula were characterized according to their modes of action, DNA binding consensus sequences, and target genes. Among them, nineteen transcription factors were characterized sufficiently in detail, allowing us to generate a gene regulatory network diagram. Additionally, we discuss recent amphibian work using a combined DNA microarray and bioinformatics approach that promises to accelerate regulatory network studies.
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Affiliation(s)
- Tetsuya Koide
- Developmental Biology Center and the Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
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33
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Baldessari D, Shin Y, Krebs O, König R, Koide T, Vinayagam A, Fenger U, Mochii M, Terasaka C, Kitayama A, Peiffer D, Ueno N, Eils R, Cho KW, Niehrs C. Global gene expression profiling and cluster analysis in Xenopus laevis. Mech Dev 2005; 122:441-75. [PMID: 15763214 DOI: 10.1016/j.mod.2004.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2004] [Revised: 10/04/2004] [Accepted: 11/07/2004] [Indexed: 01/12/2023]
Abstract
We have undertaken a large-scale microarray gene expression analysis using cDNAs corresponding to 21,000 Xenopus laevis ESTs. mRNAs from 37 samples, including embryos and adult organs, were profiled. Cluster analysis of embryos of different stages was carried out and revealed expected affinities between gastrulae and neurulae, as well as between advanced neurulae and tadpoles, while egg and feeding larvae were clearly separated. Cluster analysis of adult organs showed some unexpected tissue-relatedness, e.g. kidney is more related to endodermal than to mesodermal tissues and the brain is separated from other neuroectodermal derivatives. Cluster analysis of genes revealed major phases of co-ordinate gene expression between egg and adult stages. During the maternal-early embryonic phase, genes maintaining a rapidly dividing cell state are predominantly expressed (cell cycle regulators, chromatin proteins). Genes involved in protein biosynthesis are progressively induced from mid-embryogenesis onwards. The larval-adult phase is characterised by expression of genes involved in metabolism and terminal differentiation. Thirteen potential synexpression groups were identified, which encompass components of diverse molecular processes or supra-molecular structures, including chromatin, RNA processing and nucleolar function, cell cycle, respiratory chain/Krebs cycle, protein biosynthesis, endoplasmic reticulum, vesicle transport, synaptic vesicle, microtubule, intermediate filament, epithelial proteins and collagen. Data filtering identified genes with potential stage-, region- and organ-specific expression. The dataset was assembled in the iChip microarray database, , which allows user-defined queries. The study provides insights into the higher order of vertebrate gene expression, identifies synexpression groups and marker genes, and makes predictions for the biological role of numerous uncharacterized genes.
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Affiliation(s)
- Danila Baldessari
- Division of Molecular Embryology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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34
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Chalmers AD, Goldstone K, Smith JC, Gilchrist M, Amaya E, Papalopulu N. A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis. Mech Dev 2004; 122:355-63. [PMID: 15763212 DOI: 10.1016/j.mod.2004.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Accepted: 09/27/2004] [Indexed: 11/18/2022]
Abstract
Microarrays have great potential for the study of developmental biology. As a model system Xenopus is well suited for making the most of this potential. However, Xenopus laevis has undergone a genome wide duplication meaning that most genes are represented by two paralogues. This causes a number of problems. Most importantly the presence of duplicated genes mean that a X. laevis microarray will have less or even half the coverage of a similar sized microarray from the closely related but diploid frog Xenopus tropicalis. However, to date, X. laevis is the most commonly used amphibian system for experimental embryology. Therefore, we have tested if a microarray based on sequences from X. tropicalis will work across species using RNA from X. laevis. We produced a pilot oligonucleotide microarray based on sequences from X. tropicalis. The microarray was used to identify genes whose expression levels changed during early X. tropicalis development. The same assay was then carried out using RNA from X. laevis. The cross species experiments gave similar results to those using X. tropicalis RNA. This was true at the whole microarray level and for individual genes, with most genes giving similar results using RNA from X. laevis and X. tropicalis. Furthermore, the overlap in genes identified between a X. laevis and a X. tropicalis set of experiments was only 12% less than the overlap between two sets of X. tropicalis experiments. Therefore researchers can work with X. laevis and still make use of the advantages offered by X. tropicalis microarrays.
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Affiliation(s)
- Andrew D Chalmers
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, CB2 1QR, Cambridge, UK.
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