E H Davidson

Summary

Affiliation: California Institute of Technology
Country: USA

Publications

  1. ncbi request reprint Developmental gene network analysis
    Roger Revilla-i-Domingo
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Int J Dev Biol 47:695-703. 2003
  2. doi request reprint Emerging properties of animal gene regulatory networks
    Eric H Davidson
    Division of Biology 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nature 468:911-20. 2010
  3. pmc Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
    C Titus Brown
    Division of Biological Sciences, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Bioinformatics 6:70. 2005
  4. pmc Evolutionary bioscience as regulatory systems biology
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, 91125, USA
    Dev Biol 357:35-40. 2011
  5. ncbi request reprint A genomic regulatory network for development
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Science 295:1669-78. 2002
  6. ncbi request reprint The sea urchin genome: where will it lead us?
    Eric H Davidson
    Division of Biology, 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Science 314:939-40. 2006
  7. pmc Properties of developmental gene regulatory networks
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 105:20063-6. 2008
  8. ncbi request reprint A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Dev Biol 246:162-90. 2002
  9. doi request reprint An integrated view of precambrian eumetazoan evolution
    E H Davidson
    Division of Biology 156 29, California Institute of Technology, Pasasdena, CA 91125, USA
    Cold Spring Harb Symp Quant Biol 74:65-80. 2009
  10. pmc Network design principles from the sea urchin embryo
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Curr Opin Genet Dev 19:535-40. 2009

Detail Information

Publications107 found, 100 shown here

  1. ncbi request reprint Developmental gene network analysis
    Roger Revilla-i-Domingo
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Int J Dev Biol 47:695-703. 2003
    ....
  2. doi request reprint Emerging properties of animal gene regulatory networks
    Eric H Davidson
    Division of Biology 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nature 468:911-20. 2010
    ..The structural organization of various kinds of GRN reflects their roles in the life process, and causally illuminates both developmental and evolutionary process...
  3. pmc Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
    C Titus Brown
    Division of Biological Sciences, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Bioinformatics 6:70. 2005
    ..Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes...
  4. pmc Evolutionary bioscience as regulatory systems biology
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, 91125, USA
    Dev Biol 357:35-40. 2011
    ..These are created by the logic outputs of network subcircuits, and in modern animals these outputs are impervious to continuous adaptive variation unlike genes operating more peripherally in the network...
  5. ncbi request reprint A genomic regulatory network for development
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Science 295:1669-78. 2002
    ..Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time...
  6. ncbi request reprint The sea urchin genome: where will it lead us?
    Eric H Davidson
    Division of Biology, 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Science 314:939-40. 2006
    ..The sequence will accelerate progress toward complete understanding of the genomic regulatory system that controls developmental specification and morphogenetic function, thus illuminating basic developmental process in all animals...
  7. pmc Properties of developmental gene regulatory networks
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 105:20063-6. 2008
    ....
  8. ncbi request reprint A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Dev Biol 246:162-90. 2002
    ..Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages...
  9. doi request reprint An integrated view of precambrian eumetazoan evolution
    E H Davidson
    Division of Biology 156 29, California Institute of Technology, Pasasdena, CA 91125, USA
    Cold Spring Harb Symp Quant Biol 74:65-80. 2009
    ....
  10. pmc Network design principles from the sea urchin embryo
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Curr Opin Genet Dev 19:535-40. 2009
    ..These subcircuits are dedicated to specific developmental functions, unlike simpler 'motifs', and may indicate a repertoire of specific devices of which developmental gene regulatory networks are composed...
  11. pmc Regulatory gene networks and the properties of the developmental process
    Eric H Davidson
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 100:1475-80. 2003
    ..Gene regulatory networks make it possible to explain the process of development in causal terms and eventually will enable the redesign of developmental regulatory circuitry to achieve different outcomes...
  12. ncbi request reprint Gene regulatory networks and the evolution of animal body plans
    Eric H Davidson
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Science 311:796-800. 2006
    ..Conservation of phyletic body plans may have been due to the retention since pre-Cambrian time of GRN kernels, which underlie development of major body parts...
  13. ncbi request reprint R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres
    Roger Revilla-i-Domingo
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 274:438-51. 2004
    ..In addition, we introduce new methodological tools for quantitative measurement of the output of expression constructs that promise to be of general value for cis-regulatory analysis in sea urchin embryos...
  14. ncbi request reprint SpMyb functions as an intramodular repressor to regulate spatial expression of CyIIIa in sea urchin embryos
    J A Coffman
    Stowers Institute for Medical Research, California Institute of Technology, Pasadena 91125, USA
    Development 124:4717-27. 1997
    ..purpuratus member of the myb family of transcription factors. Through interactions within the middle module, SpMyb functions to repress activation of CyIIIa in the oral ectoderm and skeletogenic mesenchyme...
  15. ncbi request reprint Evidence for a mesodermal embryonic regulator of the sea urchin CyIIa gene
    E L Martin
    Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
    Dev Biol 236:46-63. 2001
    ..The finding of a single protein target site that recapitulates CyIIa expression in both primary and secondary mesenchyme cells suggests the existence of a pan-mesodermal gene expression program in the sea urchin embryo...
  16. ncbi request reprint Specification of cell fate in the sea urchin embryo: summary and some proposed mechanisms
    E H Davidson
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Development 125:3269-90. 1998
    ..The requirements for postembryonic adult body plan formation in the larval rudiment include engagement of a new level of genetic regulatory apparatus, exemplified by the Hox gene complex...
  17. ncbi request reprint SpRunt-1, a new member of the runt domain family of transcription factors, is a positive regulator of the aboral ectoderm-specific CyIIIA gene in sea urchin embryos
    J A Coffman
    Division of Biology 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Dev Biol 174:43-54. 1996
    ..These results are discussed with reference to known features of the runt domain family of transcription factors...
  18. ncbi request reprint Expression pattern of Brachyury and Not in the sea urchin: comparative implications for the origins of mesoderm in the basal deuterostomes
    K J Peterson
    Division of Biology, California Institute of Technology, Pasadena, California, 91125, USA
    Dev Biol 207:419-31. 1999
    ..Finally, Brachyury appears to be an excellent marker for the progeny of the set-aside cells of the sea urchin embryo...
  19. ncbi request reprint Expression and function of blimp1/krox, an alternatively transcribed regulatory gene of the sea urchin endomesoderm network
    Carolina B Livi
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 293:513-25. 2006
    ..The MASO perturbation analysis also revealed blimp1/krox inputs into other genes of the endomesoderm regulatory network...
  20. ncbi request reprint Gene regulatory factors of the sea urchin embryo. II. Two dissimilar proteins, P3A1 and P3A2, bind to the same target sites that are required for early territorial gene expression
    C Hoog
    Division of Biology, California Institute of Technology, Pasadena 91125
    Development 112:351-64. 1991
    ..The P3A1 and P3A2 factors could function as regulatory antagonists, having evolved similar target specificities from dissimilar DNA-binding domains...
  21. ncbi request reprint Expression of AmHNF6, a sea star orthologue of a transcription factor with multiple distinct roles in sea urchin development
    Ochan Otim
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Gene Expr Patterns 5:381-6. 2005
    ..This terminal phase of expression has remained unchanged since the divergence of these two taxa half a billion years ago...
  22. ncbi request reprint Maternal and embryonic provenance of a sea urchin embryo transcription factor, SpZ12-1
    D G Wang
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Mol Mar Biol Biotechnol 4:148-53. 1995
    ..SpZ12-1 probably functions at several developmental stages and is evidently of both maternal and embryonic provenance...
  23. ncbi request reprint Complexity and organization of DNA-protein interactions in the 5'-regulatory region of an endoderm-specific marker gene in the sea urchin embryo
    C H Yuh
    Division of Biology 156 29, California Institute of Technology, Pasadena 91125
    Mech Dev 47:165-86. 1994
    ..The high complexity of the Endo16 gene regulatory system may be characteristic for genes that are spatially regulated in early embryonic development...
  24. ncbi request reprint SpZ12-1, a negative regulator required for spatial control of the territory-specific CyIIIa gene in the sea urchin embryo
    D G Wang
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Development 121:1111-22. 1995
    ..CAT in skeletogenic mesenchyme and is likely to be the trans factor that mediates this repression...
  25. ncbi request reprint Correct Expression of spec2a in the sea urchin embryo requires both Otx and other cis-regulatory elements
    C H Yuh
    Division of Biology, California Institute of Biology, Pasadena, California 91125, USA
    Dev Biol 232:424-38. 2001
    ..The spec2a enhancer thus consists of closely linked activator and repressor elements that function collectively to cause expression of the spec2a gene in the aboral ectoderm...
  26. ncbi request reprint Spatial expression of Hox cluster genes in the ontogeny of a sea urchin
    C Arenas-Mena
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Development 127:4631-43. 2000
    ..The spatial expression patterns of the Hox genes illuminate the evolutionary process by which the pentameral echinoderm body plan emerged from a bilateral ancestor...
  27. ncbi request reprint SpHmx, a sea urchin homeobox gene expressed in embryonic pigment cells
    P Martinez
    Division of Biology 156 29, California Institute of Technology, Pasadena 91125, USA
    Dev Biol 181:213-22. 1997
    ..This more general expression resolves to a dramatic pigment cell-specific pattern in prism and pluteus stages. SpHmx apparently encodes a cell-type-specific transcription factor of embryonic pigment cells...
  28. ncbi request reprint Activation of pmar1 controls specification of micromeres in the sea urchin embryo
    Paola Oliveri
    Division of Biology, 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 258:32-43. 2003
    ..Each of the tests we describe supports the placement and function of Pmar1 in the endomesoderm GRN model...
  29. ncbi request reprint Regulation of spblimp1/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula
    Carolina B Livi
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Gene Expr Patterns 7:1-7. 2007
    ..Its sequence contains binding sites for Brn1/2/4, Otx, and Blimp1/Krox itself, as predicted in a prior regulatory network analysis...
  30. pmc Exclusive developmental functions of gatae cis-regulatory modules in the Strongylocentrorus purpuratus embryo
    Pei Yun Lee
    Division of Biology, California Institute of Technology, 1200 E California Blvd, Mail Code 156 29, Pasadena, CA 9112, USA
    Dev Biol 307:434-45. 2007
    ..In addition, they imply a functional cis-regulatory module exclusion, whereby only a single module can associate with the basal promoter and drive gene expression at any given time...
  31. ncbi request reprint SpGCF1, a sea urchin embryo DNA-binding protein, exists as five nested variants encoded by a single mRNA
    R W Zeller
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Dev Biol 169:713-27. 1995
    ..Since proline-rich regions often serve as transcriptional activation domains, the five SpGCF1 proteins apparently possess different "activation potentials."..
  32. ncbi request reprint Complete sequence of SpHox8 and its linkage in the single Hox gene cluster of Strongylocentrotus purpuratus
    P Martinez
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    J Mol Evol 44:371-7. 1997
    ..SpHox8 is a single-copy gene, and there is only one Hox gene cluster per genome in S. purpuratus...
  33. ncbi request reprint Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development
    Meredith Howard-Ashby
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 300:74-89. 2006
    ..The results demonstrate that homeodomain transcription factors participate in multiple and diverse developmental functions, in that they are used at a range of time points and in every territory of the developing embryo...
  34. ncbi request reprint The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development
    Stefan C Materna
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 300:108-20. 2006
    ..These genes may execute important regulatory functions in development. However, the functional meaning of the majority of this large gene family remains undefined...
  35. ncbi request reprint Expression of AmKrox, a starfish ortholog of a sea urchin transcription factor essential for endomesodermal specification
    Veronica F Hinman
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Gene Expr Patterns 3:423-6. 2003
    ..In the early bipinnaria larva transcripts are detected in the midgut and hindgut. Despite differences in early development of sea urchins and starfish, the expression of these Krox transcription factors is highly conserved...
  36. ncbi request reprint SM37, a skeletogenic gene of the sea urchin embryo linked to the SM50 gene
    Y H Lee
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Dev Growth Differ 41:303-12. 1999
    ..This gene was regulated coordinately with SM50 during development, and like SM50 was expressed exclusively in skeletogenic mesenchyme lineages...
  37. ncbi request reprint Sea urchin genes expressed in activated coelomocytes are identified by expressed sequence tags. Complement homologues and other putative immune response genes suggest immune system homology within the deuterostomes
    L C Smith
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    J Immunol 156:593-602. 1996
    ..Many of the ESTs identified in this study represent the types of genes expected to be used in lower deuterostome immune functions...
  38. ncbi request reprint Themes from a NASA workshop on gene regulatory processes in development and evolution
    E H Davidson
    Division of Biology 156 29, California Institute of Technology, Pasadena, California 91125, USA
    J Exp Zool 285:104-15. 1999
    ..J. Exp. Zool. (Mol. Dev. Evol. ) 285:104-115, 1999...
  39. ncbi request reprint Sea urchin Forkhead gene family: phylogeny and embryonic expression
    Qiang Tu
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 300:49-62. 2006
    ..The sea urchin fox genes clearly execute many different regulatory functions, and almost all of them participate in the process of embryonic development...
  40. pmc Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network
    Jongmin Nam
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 306:860-9. 2007
    ....
  41. ncbi request reprint cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network
    Takuya Minokawa
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 288:545-58. 2005
    ..In a second regulatory region, which initiates expression in micromere and macromere descendant cells early in cleavage, Tcf1 sites act to repress ectopic transcription in prospective ectoderm cells...
  42. ncbi request reprint Expression and function of a starfish Otx ortholog, AmOtx: a conserved role for Otx proteins in endoderm development that predates divergence of the eleutherozoa
    Veronica F Hinman
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Mech Dev 120:1165-76. 2003
    ..The function of Otx proteins in endodermal development at least predated the evolution of the free-living echinoderms (Eleutherozoa)...
  43. ncbi request reprint Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening
    Cristina Calestani
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Development 130:4587-96. 2003
    ..The results suggest that S. purpuratus pks, fmo and sult could belong to a differentiation gene battery of pigment cells...
  44. ncbi request reprint SpHnf6, a transcription factor that executes multiple functions in sea urchin embryogenesis
    Ochan Otim
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 273:226-43. 2004
    ..Neither oral ectoderm regulatory functions nor ciliated band formation occur normally in the absence of hnf6 expression...
  45. ncbi request reprint A view from the genome: spatial control of transcription in sea urchin development
    E H Davidson
    Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
    Curr Opin Genet Dev 9:530-41. 1999
    ....
  46. ncbi request reprint New approaches towards an understanding of deuterostome immunity
    J P Rast
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Curr Top Microbiol Immunol 248:3-16. 2000
  47. pmc Organization and expression of multiple actin genes in the sea urchin
    R H Scheller
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Mol Cell Biol 1:609-28. 1981
    ....
  48. ncbi request reprint Confocal quantification of cis-regulatory reporter gene expression in living sea urchin
    Sagar Damle
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 299:543-50. 2006
    ..The outcome is a validated method for accurately counting GFP molecules in given cells in reporter gene transfer experiments, as we demonstrate by use of an expression construct expressed exclusively in skeletogenic cells...
  49. ncbi request reprint Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus
    Meredith Howard-Ashby
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 300:90-107. 2006
    ..The observations suggest assignment of many regulatory genes to specific developmental sub-networks, including endomesodermal, oral, aboral, and apical...
  50. pmc A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres
    Roger Revilla-i-Domingo
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 104:12383-8. 2007
    ..As logically required, blockade of hesC mRNA translation and global overexpression of pmar1 mRNA have the same effect, which is to cause all of the cells of the embryo to express micromere-specific genes...
  51. ncbi request reprint Expression of a gene encoding a Gata transcription factor during embryogenesis of the starfish Asterina miniata
    Veronica F Hinman
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Gene Expr Patterns 3:419-22. 2003
    ..These observations show that despite differences in the early specification processes of the endomesoderm in starfish and sea urchins, gatae factors are expressed very similarly in these two taxa...
  52. pmc Building developmental gene regulatory networks
    Enhu Li
    Division of Biology, California Institute of Technology, Pasadena, California 911025, USA
    Birth Defects Res C Embryo Today 87:123-30. 2009
    ..The explanatory power of the GRN was shown in the lineage specification of sea urchin endomesoderm. Acquiring such networks is essential for a systematic and mechanistic understanding of the developmental process...
  53. ncbi request reprint Spdeadringer, a sea urchin embryo gene required separately in skeletogenic and oral ectoderm gene regulatory networks
    Gabriele Amore
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 261:55-81. 2003
    ....
  54. ncbi request reprint cis-Regulatory control circuits in development
    Meredith L Howard
    Division of Biology 156 29, California Institute of Technology, Pasadena 91125, USA
    Dev Biol 271:109-18. 2004
    ..At this higher level of organization, common bilaterian strategies for specifying progenitor fields, locking down regulatory states, and driving development forward emerge...
  55. pmc Functional cis-regulatory genomics for systems biology
    Jongmin Nam
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 107:3930-5. 2010
    ..This approach will qualitatively alter the practice of GRN construction as well as validation, and will impact many additional areas of regulatory system biology...
  56. pmc A sea urchin genome project: sequence scan, virtual map, and additional resources
    R A Cameron
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Proc Natl Acad Sci U S A 97:9514-8. 2000
    ..The accumulated STC data and an expanding expressed sequence tag database (at present including >12, 000 sequences) have been reported to GenBank and are accessible on public web sites...
  57. doi request reprint The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage
    Isabelle S Peter
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 340:188-99. 2010
    ..Here we integrate the architecture of regulatory interactions with the spatial restriction of regulatory gene expression to model the logic control of endoderm development...
  58. doi request reprint Genomic control of patterning
    Isabelle S Peter
    California Institute of Technology, Pasadena, 91125, USA
    Int J Dev Biol 53:707-16. 2009
    ....
  59. pmc Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring
    Joel Smith
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 106:18291-6. 2009
    ..Genomically encoded backup control circuitry thus provides the mechanism underlying a specific example of the regulative development for which the sea urchin embryo has long been famous...
  60. ncbi request reprint Deciphering the underlying mechanism of specification and differentiation: the sea urchin gene regulatory network
    Smadar Ben-Tabou de-Leon
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Sci STKE 2006:pe47. 2006
    ..It demonstrates how the static physical genomic components define functional connections between the various regulatory genes that act together to conduct the dynamical developmental program...
  61. ncbi request reprint Gene regulation: gene control network in development
    Smadar Ben-Tabou de-Leon
    Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
    Annu Rev Biophys Biomol Struct 36:191. 2007
    ....
  62. pmc Modularity and design principles in the sea urchin embryo gene regulatory network
    Isabelle S Peter
    California Institute of Technology, Division of Biology, Pasadena, CA 91125, USA
    FEBS Lett 583:3948-58. 2009
    ..Network structure not only specifies the linkages constituting the genomic regulatory code for development, but also indicates the various regulatory requirements of regional developmental processes...
  63. doi request reprint Modeling the dynamics of transcriptional gene regulatory networks for animal development
    Smadar Ben-Tabou de-Leon
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 325:317-28. 2009
    ..Model simulations display the effects of mutation of binding sites, or perturbation of upstream gene expression. The model is a generally useful tool for understanding gene regulation and the dynamics of cell fate specification...
  64. doi request reprint Flexibility of transcription factor target site position in conserved cis-regulatory modules
    R Andrew Cameron
    Division of Biology and the Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 336:122-35. 2009
    ..Their conservation is probably due to the necessity for interaction of proximally bound transcription factors, while a facilitated form of sequence conversion might be the mechanism of site position change...
  65. ncbi request reprint Development. Built to run, not fail
    Paola Oliveri
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Science 315:1510-1. 2007
  66. pmc Information processing at the foxa node of the sea urchin endomesoderm specification network
    Smadar Ben Tabou de-Leon
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 107:10103-8. 2010
    ..This study shed light on the mesoderm-endoderm fate decision and provides a functional explanation, in terms of the genomic regulatory code, for the spatial and temporal expression of a key developmental control gene...
  67. pmc The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example
    Hamid Bolouri
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 340:170-8. 2010
    ....
  68. pmc A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo
    Yi Hsien Su
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 329:410-21. 2009
    ....
  69. pmc A basal deuterostome genome viewed as a natural experiment
    R Andrew Cameron
    Beckman Institute 139 74, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, United States
    Gene 406:1-7. 2007
    ..The gene sets of the sea urchin place it firmly among the deuterostomes and indicate that various gene family-specific expansions and contractions characterize the evolution of animal genomes rather than the invention of new genes...
  70. pmc Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo
    Joel Smith
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 105:20089-94. 2008
    ..Thus the specific cis-regulatory linkages of the gene regulatory network encode the coordinated spatial expression of Wnt and Notch signaling as they sweep outward across the vegetal plate of the embryo...
  71. pmc High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development
    Stefan C Materna
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Gene Expr Patterns 10:177-84. 2010
    ..The data are available via an interactive website for quick plotting of selected time courses...
  72. doi request reprint A new method, using cis-regulatory control, for blocking embryonic gene expression
    Joel Smith
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 318:360-5. 2008
    ..This method thus provides the opportunity to study regulatory requirements of skeletogenesis after ingression, and may be similarly useful in many other developmental contexts...
  73. ncbi request reprint Repression of mesodermal fate by foxa, a key endoderm regulator of the sea urchin embryo
    Paola Oliveri
    Division of Biology, 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Development 133:4173-81. 2006
    ..These experiments show that the foxa gene is a component of three distinct embryonic gene regulatory networks...
  74. pmc Quantitative imaging of cis-regulatory reporters in living embryos
    Ivan J Dmochowski
    Divisions of Biology and Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 99:12895-900. 2002
    ..Confocal laser scanning microscopy data collection from a single sea urchin blastula required less than 2 min, thereby allowing gene expression in dozens of embryos to be monitored in parallel with high spatial and temporal resolution...
  75. ncbi request reprint An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network
    Chiou Hwa Yuh
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 269:536-51. 2004
    ..We thus demonstrate directly the structure/function relationships of the genomic regulatory code, at this key node of the endomesoderm GRN...
  76. ncbi request reprint cis-Regulatory activity of randomly chosen genomic fragments from the sea urchin
    R Andrew Cameron
    Division of Biology 156 29, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA
    Gene Expr Patterns 4:205-13. 2004
    ..On further analysis one isolate was shown to contain a gut specific element as well as one that controls expression in the secondary mesenchyme cells...
  77. ncbi request reprint Expression patterns of four different regulatory genes that function during sea urchin development
    Takuya Minokawa
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Gene Expr Patterns 4:449-56. 2004
    ....
  78. ncbi request reprint Gene regulatory network controlling embryonic specification in the sea urchin
    Paola Oliveri
    Division of Biology 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Curr Opin Genet Dev 14:351-60. 2004
    ..The network includes almost 50 genes, and these are organized in subcircuits, each of which executes a particular regulatory function...
  79. ncbi request reprint Expression of Spgatae, the Strongylocentrotus purpuratus ortholog of vertebrate GATA4/5/6 factors
    Pei Yun Lee
    Division of Biology, California Institute of Technology, 1200 E California Blvd, Mail Code 156 29, Pasadena, CA 91125, USA
    Gene Expr Patterns 5:161-5. 2004
    ..Towards the end of embryogenesis, expression in the hindgut decreases. The terminal pattern of expression is in midgut plus coelomic pouches...
  80. ncbi request reprint Gene regulatory network analysis in sea urchin embryos
    Paola Oliveri
    Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
    Methods Cell Biol 74:775-94. 2004
    ..As the results crystallize together, we can begin to see how far this powerful combination of methods and ideas is going to carry us...
  81. ncbi request reprint New early zygotic regulators expressed in endomesoderm of sea urchin embryos discovered by differential array hybridization
    Andrew Ransick
    Division of Biology 156 29, California Institute of Technology, Pasadena 91125, USA
    Dev Biol 246:132-47. 2002
    ....
  82. pmc An evolutionary constraint: strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules
    R Andrew Cameron
    Division of Biology and Center for Computational Regulatory Genomics of the Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 102:11769-74. 2005
    ..The result helps to explain the patterns of evolutionary sequence divergence characteristic of cis-regulatory DNA...
  83. ncbi request reprint cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification
    Andrew Ransick
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 297:587-602. 2006
    ..While these Su(H) target sites provide the cis-regulatory architecture with the core of an N signaling transcriptional response switch, both the on and off outputs from this module require additional inputs...
  84. ncbi request reprint cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo
    Gabriele Amore
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 293:555-64. 2006
    ....
  85. ncbi request reprint Unusual gene order and organization of the sea urchin hox cluster
    R Andrew Cameron
    Division of Biology and the Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
    J Exp Zool B Mol Dev Evol 306:45-58. 2006
    ..Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex...
  86. ncbi request reprint Origins of immunity: transcription factors and homologues of effector genes of the vertebrate immune system expressed in sea urchin coelomocytes
    Z Pancer
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Immunogenetics 49:773-86. 1999
    ..We conclude that the vertebrate immune system has evolved by inserting new genes into old gene regulatory networks dedicated to immunity...
  87. ncbi request reprint Gene regulatory factors of the sea urchin embryo. I. Purification by affinity chromatography and cloning of P3A2, a novel DNA-binding protein
    F J Calzone
    Division of Biology, California Institute of Technology, Pasadena 91125
    Development 112:335-50. 1991
    ..The results reported demonstrate that it might be possible to purify most of these regulatory proteins, or any other specific DNA-binding proteins of the sea urchin embryo, by using the simple procedures described for P3A2...
  88. ncbi request reprint How embryos work: a comparative view of diverse modes of cell fate specification
    E H Davidson
    Division of Biology, California Institute of Technology, Pasadena 91125
    Development 108:365-89. 1990
    ....
  89. pmc SpCoel1: a sea urchin profilin gene expressed specifically in coelomocytes in response to injury
    L C Smith
    Division of Biology, California Institute of Technology, Pasadena 91125
    Mol Biol Cell 3:403-14. 1992
    ....
  90. pmc Developmental gene regulatory network architecture across 500 million years of echinoderm evolution
    Veronica F Hinman
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 100:13356-61. 2003
    ..Evolutionary changes in the GRNs since divergence are limited sharply to certain cis-regulatory elements, whereas others have persisted unaltered...
  91. pmc The genome of the sea urchin Strongylocentrotus purpuratus
    Erica Sodergren
    Science 314:941-52. 2006
    ..This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes...
  92. pmc Transcriptional regulatory cascades in development: initial rates, not steady state, determine network kinetics
    Hamid Bolouri
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
    Proc Natl Acad Sci U S A 100:9371-6. 2003
    ..The kinetics of such developmental systems thus depend mainly on the initial output rates of genes activated in response to the advent of new transcription factors...
  93. ncbi request reprint The last common bilaterian ancestor
    Douglas H Erwin
    Department of Paleobiology, National Museum of Natural History, Washington, D C 20560, USA
    Development 129:3021-32. 2002
    ..This reconstruction alters expectations for Neoproterozoic fossil remains that could illustrate the pathways of bilaterian evolution...
  94. ncbi request reprint A regulatory gene network that directs micromere specification in the sea urchin embryo
    Paola Oliveri
    Division of Biology 156 29, California Institute of Technology, Pasadena 91125, USA
    Dev Biol 246:209-28. 2002
    ..More generally, the regulatory network subelement emerging from this work shows how the specificity of micromere function depends on continuing global regulatory interactions, as well as on early localized inputs...
  95. ncbi request reprint brachyury Target genes in the early sea urchin embryo isolated by differential macroarray screening
    Jonathan P Rast
    Division of Biology 156 29, California Institute of Technology, Pasadena 91125, USA
    Dev Biol 246:191-208. 2002
    ..These results and other data suggest that the brachyury gene transduces information about the state of endodermal specification to genes that modulate morphogenesis and genes that perform terminal functions in the gut...
  96. ncbi request reprint Paleogenomics of echinoderms
    David J Bottjer
    Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089 0740, USA
    Science 314:956-60. 2006
    ..purpuratus genome and are likely to be the same genes that were involved with stereom formation in the earliest echinoderms some 520 million years ago...
  97. ncbi request reprint The transcriptome of the sea urchin embryo
    Manoj P Samanta
    Systemix Institute, Los Altos, CA 94024, USA
    Science 314:960-2. 2006
    ..The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process...
  98. pmc Gene regulatory networks for development
    Michael Levine
    Department of Molecular and Cell Biology, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:4936-42. 2005
    ..Here, we survey salient points of these networks, by using as reference those governing specification of the endomesoderm in sea urchin embryos and dorsal-ventral patterning in the Drosophila embryo...
  99. ncbi request reprint The regulatory genome and the computer
    Sorin Istrail
    Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA
    Dev Biol 310:187-95. 2007
    ..The genomic computer controls spatial gene expression in the development of the body plan, and its appearance in remote evolutionary time must be considered to have been a founding requirement for animal grade life...
  100. ncbi request reprint Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins
    Veronica F Hinman
    Department of Biological Sciences, Carnegie Mellon University, PA 15213, USA
    Dev Biol 312:584-95. 2007
    ..Finally, inter-specific gene transfer experiments confirm this scenario and demonstrate evolution occurring at the level of sequence changes to the cis-regulatory module...
  101. pmc Evolutionary plasticity of developmental gene regulatory network architecture
    Veronica F Hinman
    Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
    Proc Natl Acad Sci U S A 104:19404-9. 2007
    ..An emergent theme is that subcircuit design may be preserved even while the identity of genes performing given roles changes because of alteration in their cis-regulatory control systems...

Research Grants46

  1. GENE LIBRARY RESOURCE FOR THE SEA URCHIN S. PURPURATUS
    Eric H Davidson; Fiscal Year: 2010
    ..And we present the bioinformatics tools and databases of genomic sequence collections to the experimentalist. All of the individual goals detailed above are direct responses to this view. ..
  2. Computational Model of Gene Regulatory Program
    Eric Davidson; Fiscal Year: 2007
    ..abstract_text> ..
  3. Regulatory Genomics: BAC-GFP Library of Control Genes
    Eric Davidson; Fiscal Year: 2007
    ..Numerous letters from outside investigators attesting interest in this facility are included as an Appendix to this application. ..
  4. GENE LIBRARY RESOURCE FOR THE SEA URCHIN S. PURPURATUS
    Eric Davidson; Fiscal Year: 2005
    ..And we present the bioinformatics tools and databases of genomic sequence collections to the experimentalist. All of the individual goals detailed above are direct responses to this view. ..
  5. GENE LIBRARY RESOURCE FOR THE SEA URCHIN S. PURPURATUS
    Eric Davidson; Fiscal Year: 2006
    ..And we present the bioinformatics tools and databases of genomic sequence collections to the experimentalist. All of the individual goals detailed above are direct responses to this view. ..
  6. GLOBAL GENE REGULATORY NETWORKS FOR SPECIFIC CELL TYPES OF THE SEA URCHIN EMBRYO
    Eric H Davidson; Fiscal Year: 2010
    ..Our practice must get beyond struggling to ameliorate effects rather than altering causes. This research shows the way to discovery of structure and function in causal genomic control systems. ..
  7. Computational Model of Gene Regulatory Program
    Eric Davidson; Fiscal Year: 2009
    ..abstract_text> ..
  8. GENE LIBRARY RESOURCE FOR THE SEA URCHIN S. PURPURATUS
    Eric Davidson; Fiscal Year: 2009
    ..And we present the bioinformatics tools and databases of genomic sequence collections to the experimentalist. All of the individual goals detailed above are direct responses to this view. ..
  9. Computational Model of Gene Regulatory Program
    Eric H Davidson; Fiscal Year: 2010
    ....
  10. GENE LIBRARY RESOURCE FOR SEA URCHIN S. PURPURATUS
    Eric Davidson; Fiscal Year: 2004
    ..abstract_text> ..
  11. HOMOZYGOUS SEA URCHIN AS A POTENTIAL RESEARCH RESOURCE
    Eric Davidson; Fiscal Year: 1993
    ....
  12. COMPUTATIONAL MODEL OF GENE REGULATORY PROGRAM
    Eric Davidson; Fiscal Year: 2003
    ..The model will ultimately constitute a quantitative computational analysis of a genomic regulatory network, defined at the DNA sequence level, the function of which is to organize a complex, major process in animal development. ..
  13. GENE LIBRARY RESOURCE FOR THE SEA URCHIN S. PURPURATUS
    Eric Davidson; Fiscal Year: 2003
    ..In addition, the investigators need to carry out several unique computational analyses that reflect the particular features of the S. purpuratus genome. ..
  14. HOMOZYGOUS SEA URCHIN AS A POTENTIAL RESEARCH RESOURCE
    Eric Davidson; Fiscal Year: 2003
    ..purpuratus is a heritable trait, and carry out other investigations on genetic aspects of sex in S. purpuratus. ..