Michael Levine

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Characterization of the transvection mediating region of the abdominal-B locus in Drosophila
    J Zhou
    Dept Mol Cell Biol, Division of Genetics, University of California, Berkeley, CA 94720, USA
    Development 126:3057-65. 1999
  2. ncbi request reprint Transcription regulation and animal diversity
    Michael Levine
    Department of Molecular and Cell Biology, Division of Genetics and Development, Center for Integrative Genomics, University of California, Berkeley, 401 Barker Hall, Berkeley, California 94720, USA
    Nature 424:147-51. 2003
  3. pmc Organization of developmental enhancers in the Drosophila embryo
    Dmitri Papatsenko
    Department of Molecular Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720 200, USA
    Nucleic Acids Res 37:5665-77. 2009
  4. ncbi request reprint Decoding cis-regulatory DNAs in the Drosophila genome
    Michele Markstein
    Department of Molecular Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, California 94720, USA
    Curr Opin Genet Dev 12:601-6. 2002
  5. ncbi request reprint A regulatory code for neurogenic gene expression in the Drosophila embryo
    Michele Markstein
    Department of Molecular and Cellular Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Development 131:2387-94. 2004
  6. pmc CtBP-independent repression in the Drosophila embryo
    Yutaka Nibu
    Division of Genetics and Development, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Mol Cell Biol 23:3990-9. 2003
  7. ncbi request reprint Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset
    Angelike Stathopoulos
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Development 129:3411-9. 2002
  8. ncbi request reprint Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo
    Angelike Stathopoulos
    Division of Genetics and Development, Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkeley, 94720, USA
    Dev Biol 280:482-93. 2005
  9. pmc Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo
    Dmitri Papatsenko
    Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, 16 Barker Hall No 3204, Berkeley, CA 94720 3204, USA
    Proc Natl Acad Sci U S A 102:4966-71. 2005
  10. ncbi request reprint Ventral dominance governs sequential patterns of gene expression across the dorsal-ventral axis of the neuroectoderm in the Drosophila embryo
    John Cowden
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Dev Biol 262:335-49. 2003

Collaborators

Detail Information

Publications80

  1. ncbi request reprint Characterization of the transvection mediating region of the abdominal-B locus in Drosophila
    J Zhou
    Dept Mol Cell Biol, Division of Genetics, University of California, Berkeley, CA 94720, USA
    Development 126:3057-65. 1999
    ..We discuss the significance of these findings with regard to Abd-B transvection and long-range enhancer-promoter interactions in mammalian globin loci...
  2. ncbi request reprint Transcription regulation and animal diversity
    Michael Levine
    Department of Molecular and Cell Biology, Division of Genetics and Development, Center for Integrative Genomics, University of California, Berkeley, 401 Barker Hall, Berkeley, California 94720, USA
    Nature 424:147-51. 2003
    ..How, then, has evolutionary diversity arisen? Emerging evidence suggests that organismal complexity arises from progressively more elaborate regulation of gene expression...
  3. pmc Organization of developmental enhancers in the Drosophila embryo
    Dmitri Papatsenko
    Department of Molecular Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720 200, USA
    Nucleic Acids Res 37:5665-77. 2009
    ..We conclude that grammar of gene control regions is pervasively used in the patterning of the Drosophila embryo...
  4. ncbi request reprint Decoding cis-regulatory DNAs in the Drosophila genome
    Michele Markstein
    Department of Molecular Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, California 94720, USA
    Curr Opin Genet Dev 12:601-6. 2002
    ..These methods change the way that cis-DNAs will be analyzed in future studies and offer the promise of unraveling complex gene networks...
  5. ncbi request reprint A regulatory code for neurogenic gene expression in the Drosophila embryo
    Michele Markstein
    Department of Molecular and Cellular Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Development 131:2387-94. 2004
    ..We discuss the prospects for deciphering regulatory codes that link primary DNA sequence information with predicted patterns of gene expression...
  6. pmc CtBP-independent repression in the Drosophila embryo
    Yutaka Nibu
    Division of Genetics and Development, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Mol Cell Biol 23:3990-9. 2003
    ..These findings provide evidence that competition is distinct from quenching and direct repression. Quenching and direct repression depend on dCtBP, whereas competition does not...
  7. ncbi request reprint Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset
    Angelike Stathopoulos
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Development 129:3411-9. 2002
    ..We discuss how the Dorsal gradient system can be modified during metazoan evolution and conclude that Dorsal-Twist interactions are distinct from the interplay between Bicoid and Hunchback, which pattern the anteroposterior axis...
  8. ncbi request reprint Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo
    Angelike Stathopoulos
    Division of Genetics and Development, Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkeley, 94720, USA
    Dev Biol 280:482-93. 2005
    ..The ventral limits of gene expression are defined by the Snail and Vnd repressors, while the dorsal border is established by the newly defined silencer element...
  9. pmc Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo
    Dmitri Papatsenko
    Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, 16 Barker Hall No 3204, Berkeley, CA 94720 3204, USA
    Proc Natl Acad Sci U S A 102:4966-71. 2005
    ..Similar motif arrangements were identified in orthologous loci in the distant mosquito genome, Anopheles gambiae. We discuss how Dorsal and Twist work either additively or synergistically to activate different target enhancers...
  10. ncbi request reprint Ventral dominance governs sequential patterns of gene expression across the dorsal-ventral axis of the neuroectoderm in the Drosophila embryo
    John Cowden
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Dev Biol 262:335-49. 2003
    ....
  11. pmc Stalled Hox promoters as chromosomal boundaries
    Vivek S Chopra
    Department of Molecular and Cellular Biology, Division of Genetics, Genomics, and Development, University of California at Berkeley, Berkeley, California 94720, USA
    Genes Dev 23:1505-9. 2009
    ..Thus, promoter-proximal stalling factors might help promote insulator-promoter interactions. We propose that stalled promoters help organize gene complexes within chromosomal loop domains...
  12. ncbi request reprint Immunity regulatory DNAs share common organizational features in Drosophila
    Kate Senger
    Department of Molecular and Cellular Biology, Division of Genetics and Development, University of California, Berkeley, Berkeley, CA 94720, USA
    Mol Cell 13:19-32. 2004
    ..Aspects of this "regulatory code" are essential for the immune response. These results suggest that immunity regulatory DNAs contain constrained organizational features, which may be a general property of eukaryotic enhancers...
  13. pmc Vectors and parameters that enhance the efficacy of RNAi-mediated gene disruption in transgenic Drosophila
    Benjamin Haley
    Center for Integrative Genomics, Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 107:11435-40. 2010
    ..These studies provide a foundation for the specific and effective use of gene silencing in transgenic Drosophila...
  14. pmc Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex
    Vincent C Calhoun
    Department of Molecular and Cell Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 100:9878-83. 2003
    ..We suggest that homotypic interactions between the tethering elements stabilize long-range T1-Scr interactions during development...
  15. doi request reprint The transcription/migration interface in heart precursors of Ciona intestinalis
    Lionel Christiaen
    Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Science 320:1349-52. 2008
    ..We propose that transcription regulation of specific effector genes determines the coordinated deployment of discrete cellular modules underlying migration...
  16. pmc Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo
    Michael W Perry
    Department of Integrative Biology, Biophysics Graduate Group, University of California, Berkeley, CA 94720 3200, USA
    Proc Natl Acad Sci U S A 108:13570-5. 2011
    ..We present different models for "enhancer synergy," whereby two enhancers with overlapping activities produce authentic patterns of gene expression...
  17. ncbi request reprint Early chordate origins of the vertebrate second heart field
    Alberto Stolfi
    Center for Integrative Genomics, Division of Genetics, Genomics and Development, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Science 329:565-8. 2010
    ..We propose that the last common ancestor of tunicates and vertebrates possessed multipotent cardiopharyngeal muscle precursors, and that their reallocation might have contributed to the emergence of the SHF...
  18. pmc Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex
    Vincent C Calhoun
    Department of Molecular and Cell Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:9243-7. 2002
    ..We suggest that the Scr450 fragment contains tethering elements that selectively recruit T1 to the Scr promoter. Tethering elements might regulate enhancer-promoter interactions at other complex genetic loci...
  19. ncbi request reprint Synchronous and stochastic patterns of gene activation in the Drosophila embryo
    Alistair N Boettiger
    Biophysics Program, University of California, Berkeley, CA 94720, USA
    Science 325:471-3. 2009
    ..Transcriptional synchrony might ensure the orderly deployment of the complex gene regulatory networks that control embryogenesis...
  20. pmc Regulation of Hox gene activity by transcriptional elongation in Drosophila
    Vivek S Chopra
    Division of Genetics, Center for Integrative Genomics, University of California, Berkeley, Berkeley, CA 94720 3200, USA
    Curr Biol 19:688-93. 2009
    ..Stalled Pol II persists in tissues where Ubx and Abd-B are silenced by the PcG complex. We propose that stalling fosters both the rapid induction and precise silencing of Hox gene expression during development...
  21. pmc Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex
    Esther Bae
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:16847-52. 2002
    ..These observations suggest that the intergenic RNAs may play a role in initiating cis regulation at the BX-C early in development...
  22. pmc Coordinate enhancers share common organizational features in the Drosophila genome
    Albert Erives
    Center for Integrative Genomics, Department of Molecular and Cell Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 101:3851-6. 2004
    ..Organized binding sites should facilitate the identification of regulatory codes that link primary DNA sequence information with predicted patterns of gene activity...
  23. pmc The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo
    Jacques P Bothma
    Biophysics Graduate Group, Center for Integrative Genomics, Division of Genetics, Genomics and Development, University of California, Berkeley, Berkeley, CA 94720, USA
    Curr Biol 21:1571-7. 2011
    ....
  24. doi request reprint Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp
    Lionel Christiaen
    Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California Berkeley, CA 94720 3200, USA
    Dev Biol 328:552-60. 2009
    ..Mutations in the Lhx3 half-site of Tbx6/Lhx3 composite elements strongly reduced the activity of a minimal Mesp enhancer. We discuss the delineation of the heart field by the synergistic action of muscle and gut determinants...
  25. pmc Transcriptional repression via antilooping in the Drosophila embryo
    Vivek S Chopra
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 109:9460-4. 2012
    ..This higher-order mechanism of transcriptional repression has broad implications for the control of gene activity in metazoan development...
  26. pmc The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo
    Vivek S Chopra
    Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, University of California, Berkeley, Berkeley, CA 94720, USA
    Mol Cell 42:837-44. 2011
    ..We suggest that this conversion of silent genes into poised genes might render differentiated cell types susceptible to switches in identity in PcG mutants...
  27. ncbi request reprint BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development
    Lionel Christiaen
    Department of Molecular and Cell Biology, University of California, Center for Integrative Genomics, Berkeley, CA, USA
    Dev Biol 340:179-87. 2010
    ..Our observations led us to propose a model for the coordination of cell migration and gene expression based on the temporal unfolding of a gene regulatory sub-network in a relevant developmental context...
  28. ncbi request reprint Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo
    Angelike Stathopoulos
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 111:687-701. 2002
    ..The new Dorsal target genes and enhancers represent one of the most extensive gene networks known for any developmental process...
  29. 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...
  30. pmc FGF3 in the floor plate directs notochord convergent extension in the Ciona tadpole
    Weiyang Shi
    Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California, Berkeley, Berkeley, CA 94720, USA
    Development 136:23-8. 2009
    ..We propose that FGF signaling coordinates CE movements by regulating PCP pathway components such as Dsh...
  31. ncbi request reprint Conservation patterns in different functional sequence categories of divergent Drosophila species
    Dmitri Papatsenko
    Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
    Genomics 88:431-42. 2006
    ..We discuss how restraining conservation patterns may help in mapping functional sequence categories and improve genome annotation...
  32. ncbi request reprint Precision of hunchback expression in the Drosophila embryo
    Michael W Perry
    Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720 3200, USA
    Curr Biol 22:2247-52. 2012
    ..We propose that this repression helps ensure precision of the anterior Hb border in response to variations in the Bicoid gradient...
  33. ncbi request reprint FGF signaling establishes the anterior border of the Ciona neural tube
    Eileen Wagner
    Center for Integrative Genomics, Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
    Development 139:2351-9. 2012
    ..Inhibition of FGF signaling leads to expanded expression of FoxC, the loss of ZicL, and truncation of the anterior neural tube...
  34. pmc miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data
    David Hendrix
    Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, 142 LSA 3200, Berkeley, CA 94720 3200, USA
    Genome Biol 11:R39. 2010
    ..This program was applied to the simple chordate Ciona intestinalis and identified nearly 400 putative miR loci...
  35. doi request reprint Neuronal subtype specification in the spinal cord of a protovertebrate
    Alberto Stolfi
    Center for Integrative Genomics, Division of Genetics, Genomics and Development, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Development 138:995-1004. 2011
    ..These experiments demonstrate the connection between transcriptional regulation and the neuronal subtype diversity underlying swimming behavior in a simple chordate...
  36. ncbi request reprint Uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis
    Brad Davidson
    Department of Molecular and Cellular Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA
    Development 132:4811-8. 2005
    ..We discuss the implications of Tbx6-Mesp interactions for the evolution of cardiac mesoderm in invertebrates and vertebrates...
  37. ncbi request reprint Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis
    Weiyang Shi
    Department of Molecular and Cell Biology, Division of Genetics and Development, Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
    Genome Res 15:1668-74. 2005
    ....
  38. pmc A simplified miRNA-based gene silencing method for Drosophila melanogaster
    Benjamin Haley
    Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, Berkeley, Berkeley, California 94720, USA
    Dev Biol 321:482-90. 2008
    ..As proof of concept, this method was used for the efficient silencing of dpp gene activity in the adult wing, and the analysis of the general RNA Polymerase II (Pol II) elongation factor, Nelf-E...
  39. ncbi request reprint Identification of a rudimentary neural crest in a non-vertebrate chordate
    Philip Barron Abitua
    Center for Integrative Genomics, Division of Genetics, Genomics and Development, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nature 492:104-7. 2012
    ..We propose that the co-option of mesenchyme determinants, such as Twist, into the neural plate ectoderm was crucial to the emergence of the vertebrate 'new head'...
  40. ncbi request reprint Control of intercalation is cell-autonomous in the notochord of Ciona intestinalis
    David N Keys
    Department of Molecular and Cell Biology, University of California, 401 Barker Hall, Berkeley, California 94720, USA
    Dev Biol 246:329-40. 2002
    ..Finally, this study establishes the Ciona embryo as an effective in vivo system for the study of the molecular control of morphogenetic cell movements in chordates...
  41. pmc Neural-specific elongation of 3' UTRs during Drosophila development
    Valérie Hilgers
    Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California, Berkeley, CA 94720 3200, USA
    Proc Natl Acad Sci U S A 108:15864-9. 2011
    ..These findings suggest a previously unknown mode of posttranscriptional regulation that may contribute to the complexity of neurogenesis or neural function...
  42. ncbi request reprint Whole-genome analysis of Drosophila gastrulation
    Angelike Stathopoulos
    Dept of MCB, Division of Genetics, University of California, Berkeley, California 94720 3204, USA
    Curr Opin Genet Dev 14:477-84. 2004
    ..Recent work has yielded insights into how these signaling pathways control gastrulation, particularly in the context of the Dorsal-mediated gene regulation network..
  43. ncbi request reprint Development: lights, camera, action--the Drosophila embryo goes live!
    Jacques Bothma
    Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, University of California, Berkeley, USA
    Curr Biol 23:R965-7. 2013
    ..Live imaging of developmental gene expression in Drosophila embryos opens up exciting new prospects for understanding gene regulation during development. ..
  44. pmc ELAV mediates 3' UTR extension in the Drosophila nervous system
    Valérie Hilgers
    Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California at Berkeley, Berkeley, California 94720, USA
    Genes Dev 26:2259-64. 2012
    ..We propose that this mechanism for coordinating 3' UTR extension may be generally used in a variety of cellular processes...
  45. ncbi request reprint Shadow enhancers foster robustness of Drosophila gastrulation
    Michael W Perry
    Department of Integrative Biology, University of California Berkeley, CA 94720, USA
    Curr Biol 20:1562-7. 2010
    ..These results suggest that shadow enhancers represent a novel mechanism of canalization whereby complex developmental processes "bring about one definite end-result regardless of minor variations in conditions" [6]...
  46. doi request reprint Neural tube patterning by Ephrin, FGF and Notch signaling relays
    Alberto Stolfi
    Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Development 138:5429-39. 2011
    ..This MG regulatory network provides a foundation for elucidating the genetic and cellular basis of a model chordate central pattern generator...
  47. pmc Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles
    Dmitri Papatsenko
    Department of Molecular and Cell Biology, Division of Genetics Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, California, United States of America
    PLoS Biol 9:e1000584. 2011
    ..We propose that gene clustering by local temporal discordance can be used for the de novo identification of the gene batteries underlying morphological diversity...
  48. pmc Evolving enhancer-promoter interactions within the tinman complex of the flour beetle, Tribolium castaneum
    Jessica Doran Cande
    Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California at Berkeley, Berkeley, CA 94720, USA
    Development 136:3153-60. 2009
    ..Given the high frequency of genome rearrangements in insects, it is possible that such enhancer switching might be widely used in the diversification of the arthropods...
  49. pmc Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo
    Yury Goltsev
    Department of Mol Cell Biology, Division of Genetics Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Dev Biol 330:462-70. 2009
    ..melanogaster. We discuss how evolutionary modifications in the well-defined dorsal-ventral patterning network led to the wholesale deployment of the cuticle biosynthesis pathway in early embryos of A. gambiae...
  50. ncbi request reprint Whole-genome expression profiles identify gene batteries in Drosophila
    Angelike Stathopoulos
    Department of Molecular and Cellular Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA
    Dev Cell 3:464-5. 2002
    ....
  51. pmc pyramus and thisbe: FGF genes that pattern the mesoderm of Drosophila embryos
    Angelike Stathopoulos
    Department of Molecular and Cell Biology, Division of Genetics and Development, University of California, Berkeley 94720 3204, USA
    Genes Dev 18:687-99. 2004
    ..It is therefore possible to describe FGF signaling and other aspects of gastrulation as a direct manifestation of discrete threshold readouts of the Dorsal gradient...
  52. doi request reprint Morphogen gradients: limits to signaling or limits to measurement?
    Jacques P Bothma
    Biophysics Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA
    Curr Biol 20:R232-4. 2010
    ..Recent quantitative studies agree on the temporal dynamics of the gradient, but disagree on its spatial limits...
  53. pmc Looping back to leap forward: transcription enters a new era
    Michael Levine
    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94707, USA Electronic address
    Cell 157:13-25. 2014
    ..We review progress in unraveling one of the outstanding mysteries of modern biology: the dynamic communication of remote enhancers with target promoters in the specification of cellular identity. ..
  54. ncbi request reprint Computational identification of regulatory DNAs underlying animal development
    Dmitri Papatsenko
    Department of Molecular and Cellular Biology, Division of Genetics and Development, University of California, Berkeley, California 94720, USA
    Nat Methods 2:529-34. 2005
  55. ncbi request reprint Analyzing gene regulation in ascidian embryos: new tools for new perspectives
    Anna Di Gregorio
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California at Berkeley, 94720 3204, USA
    Differentiation 70:132-9. 2002
    ..Here we review the past and present uses of electroporation in ascidian development, and speculate on potential future uses...
  56. ncbi request reprint Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle
    Anna Di Gregorio
    Department of Molecular and Cell Biology, University of California, 401 Barker Hall, Berkeley, California 94720 3204, USA
    Dev Biol 244:385-95. 2002
    ..Taken together, these observations suggest that tail formation in ascidian larvae requires not only signaling from notochord to muscle cells, but also a "retrograde" signal from muscle cells to notochord...
  57. pmc Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    Benjamin P Berman
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:757-62. 2002
    ..We tested one of the newly identified clusters, mapping upstream of the gap gene giant (gt), and show that it acts as an enhancer that recapitulates the posterior expression pattern of gt...
  58. ncbi request reprint The Snail repressor positions Notch signaling in the Drosophila embryo
    John Cowden
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Development 129:1785-93. 2002
    ..We suggest that these dual activities of Snail, repression of Notch target genes and stimulation of Notch signaling, help define precise lines of sim expression within the neurogenic ectoderm...
  59. ncbi request reprint Mechanisms of transcriptional precision in animal development
    Mounia Lagha
    Center for Integrative Genomics, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Trends Genet 28:409-16. 2012
    ..We propose that such regulatory mechanisms provide population fitness and 'fine-tune' the spatial and temporal control of gene expression...
  60. ncbi request reprint Coordinate regulation of an extended chromosome domain
    Vincent C Calhoun
    Department of Molecular and Cell Biology, Division of Genetics and Development, University of California Berkeley, Berkeley, CA 94720, USA
    Cell 113:278-80. 2003
    ..The GCR provides an explanation for the colinear genetic linkage and expression of individual Hox genes within developing limbs...
  61. ncbi request reprint Dorsal gradient networks in the Drosophila embryo
    Angelike Stathopoulos
    Department of Molecular and Cellular Biology, Division of Genetics and Development, University of California, Berkeley 94720 3204, USA
    Dev Biol 246:57-67. 2002
    ....
  62. ncbi request reprint Activation, proliferation and commitment of endogenous stem/progenitor cells to the oligodendrocyte lineage by TS1 in a rat model of dysmyelination
    Araceli Espinosa-Jeffrey
    Mental Retardation Research Center, Semel Institute for Neuroscience and Human Behavior and Department of Neurobiology, University of California, Los Angeles, 90095 7332, USA
    Dev Neurosci 28:488-98. 2006
    ..This strategy offers for the first time the possibility of myelin restoration to treat myelin disorders...
  63. ncbi request reprint Isolation of Individual Cells and Tissues from Electroporated Sea Squirt (Ciona) Embryos by Fluorescence-Activated Cell Sorting (FACS)
    Lionel Christiaen
    Molecular and Cell Biology Department, University of California, Berkeley, California 94720, USA
    CSH Protoc 2009:pdb.prot5349. 2009
    ..This method permits the identification of effector genes responsible for changes in cell shape, polarity, or motility in a given tissue...
  64. ncbi request reprint Whole-Mount In Situ Hybridization on Sea Squirt (Ciona intestinalis) Embryos
    Lionel Christiaen
    Molecular and Cell Biology Department, University of California, Berkeley, California 94720, USA
    CSH Protoc 2009:pdb.prot5348. 2009
    ....
  65. ncbi request reprint Microinjection of Morpholino Oligos and RNAs in Sea Squirt (Ciona) Embryos
    Lionel Christiaen
    Molecular and Cell Biology Department, University of California, Berkeley, California 94720, USA
    CSH Protoc 2009:pdb.prot5347. 2009
    ..Injection can also be performed in unfertilized eggs to inhibit maternal genes. Microinjection also permits DiI labeling and lineage tracing...
  66. ncbi request reprint X-gal Staining of Electroporated Sea Squirt (Ciona) Embryos
    Lionel Christiaen
    Molecular and Cell Biology Department, University of California, Berkeley, California 94720, USA
    CSH Protoc 2009:pdb.prot5346. 2009
    ..g., tissue-specific enhancer) fused to the lacZ reporter gene. Green fluorescent protein (GFP) reporter genes can be directly visualized in living embryos and larvae, although fixed preparations can use aspects of this protocol...
  67. ncbi request reprint Electroporation of Transgenic DNAs in the Sea Squirt Ciona
    Lionel Christiaen
    Molecular and Cell Biology Department, University of California, Berkeley, California 94720, USA
    CSH Protoc 2009:pdb.prot5345. 2009
    ..Finally, structure-function relationships can be examined by expressing dominant-negative or constitutively active forms of specific proteins using appropriate cell-specific enhancers...
  68. ncbi request reprint Isolation of sea squirt (ciona) gametes, fertilization, dechorionation, and development
    Lionel Christiaen
    Molecular and Cell Biology Department, University of California, Berkeley, California 94720, USA
    CSH Protoc 2009:pdb.prot5344. 2009
    ..Any solutions that come into contact with embryos should be prepared in absolutely clean glassware with the highest quality water...
  69. pmc Genome-wide identification of tissue-specific enhancers in the Ciona tadpole
    Naoe Harafuji
    Department of Molecular and Cell Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:6802-5. 2002
    ..We discuss the prospects of creating a regulatory atlas of the Ciona genome, whereby every enhancer is identified for every gene...
  70. pmc Evolutionary origins of the vertebrate heart: Specification of the cardiac lineage in Ciona intestinalis
    Brad Davidson
    Department of Molecular and Cell Biology, Division of Genetics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 100:11469-73. 2003
    ..We discuss the possibility that the germ line also influences the specification of the vertebrate heart...
  71. doi request reprint Paused RNA polymerase II as a developmental checkpoint
    Michael Levine
    Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, Center for Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 145:502-11. 2011
    ..I review the implications of this mechanism of gene activation with respect to the orderly unfolding of complex gene networks governing animal development...
  72. pmc Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo
    Michele Markstein
    Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:763-8. 2002
    ..These results suggest that bioinformatics can be used to identify novel target genes and associated regulatory DNAs in a gene network...
  73. pmc Promoter elements associated with RNA Pol II stalling in the Drosophila embryo
    David A Hendrix
    Department Molecular and Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 105:7762-7. 2008
    ..We discuss different models for Pol II binding and gene activation in the early embryo...
  74. pmc Dual regulation by the Hunchback gradient in the Drosophila embryo
    Dmitri Papatsenko
    Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, and Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 105:2901-6. 2008
    ..Computational simulations suggest that repression results from the dimerization of Hb monomers on the DNA template...
  75. pmc Spatial regulation of microRNA gene expression in the Drosophila embryo
    Frederic Biemar
    Division of Genetics and Development, Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 102:15907-11. 2005
    ..These results provide evidence that restricted activities of the 8-miR and miR-1 miRNAs are mediated by classical tissue-specific enhancers...
  76. doi request reprint Shadow enhancers as a source of evolutionary novelty
    Joung Woo Hong
    Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Science 321:1314. 2008
  77. pmc Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array
    Frederic Biemar
    Division of Genetics and Development, Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 103:12763-8. 2006
    ..We discuss the potential functions of these recently identified genes and suggest that intronic enhancers are a common feature of the DV gene network...
  78. pmc DEAF-1 regulates immunity gene expression in Drosophila
    Darien E Reed
    Helen Diller Family Comprehensive Cancer Center and Cancer Research Institute, University of California, San Francisco, CA 94115 0128, USA
    Proc Natl Acad Sci U S A 105:8351-6. 2008
    ..The coexpression of DEAF-1 with Dorsal, Dif, and Relish results in the synergistic activation of transcription. We propose that DEAF-1 is a regulator of Drosophila immunity...
  79. pmc Full-length human mutant huntingtin with a stable polyglutamine repeat can elicit progressive and selective neuropathogenesis in BACHD mice
    Michelle Gray
    Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California 90095, USA
    J Neurosci 28:6182-95. 2008
    ..In summary, the BACHD model constitutes a novel and robust in vivo paradigm for the investigation of HD pathogenesis and treatment...
  80. ncbi request reprint Striatal potassium channel dysfunction in Huntington's disease transgenic mice
    Marjorie A Ariano
    Mental Retardation Research Center, NPI Room 58 258, 760 Westwood Plaza, University of California, Los Angeles, CA 90095, USA
    J Neurophysiol 93:2565-74. 2005
    ..Attenuation in K+ conductances and channel subunit expression contribute to altered electrophysiological properties of MSNs and may partially account for selective cellular vulnerability in the striatum...