Michael Levine

University of California, Berkeley, Berkeley, California, United States

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Publications (99)1069.41 Total impact

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    ABSTRACT: Recent evidence suggests that ascidian pigment cells are related to neural crest-derived melanocytes of vertebrates. Using live-imaging, we determine a revised cell lineage of the pigment cells in Ciona intestinalis embryos. The neural precursors undergo successive rounds of anterior-posterior (A-P) oriented cell divisions, starting at the blastula 64-cell stage. A previously unrecognized fourth A-P oriented cell division in the pigment cell lineage leads to the generation of the post-mitotic pigment cell precursors. We provide evidence that MEK/ERK signals are required for pigment cell specification until approximately 30 minutes after the final cell division has taken place. Following each of the four A-P oriented cell divisions, ERK1/2 is differentially activated in the posterior sister cells, into which the pigment cell lineage segregates. Eph/ephrin signals are critical during the third A-P oriented cell division to spatially restrict ERK1/2 activation to the posterior daughter cell. Targeted inhibition of Eph/ephrin signals results in, at neurula stages, anterior expansion of both ERK1/2 activation and a pigment cell lineage marker and subsequently, at larval stages, supernumerary pigment cells. We discuss the implications of these findings with respect to the evolution of the vertebrate neural crest.
    Developmental biology. 07/2014;
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    ABSTRACT: There is considerable information about the spatial regulation of gene expression during pattern formation in animal development. Significantly less is known about temporal control, in part due to our inability to analyze gene activity in real time. Using a recently developed approach for the visualization of gene expression in living Drosophila embryos, we examined the well-known even-skipped stripe 2 expression pattern. Surprisingly, we observe that this classic pattern is quite transient and generated by discontinuous surges of transcriptional activity in individual cells. These results challenge a purely static framework for dissecting developmental programs and emphasize the importance of the dynamic features of pattern formation.
    Proceedings of the National Academy of Sciences 07/2014; 111(29):10598. · 9.81 Impact Factor
  • Michael Levine
    Science (New York, N.Y.). 07/2014; 345(6194):277.
  • Michael Levine
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    ABSTRACT: Lucas et al. report the visualization of V(D)J recombination of the immunoglobulin heavy-chain gene (Igh) in living pro-B cells. Despite the huge distances separating V coding sequences from D-J sequences (∼2 Mb), the authors document an astonishingly rapid rate of remote associations. The key to speed is contraction of the Igh chromosomal domain. These findings provide a foundation for understanding long-range regulatory interactions in a variety of developmental processes, including the patterning of vertebrate limbs.
    07/2014; 158(2):243–244.
  • Michael Levine, Claudia Cattoglio, Robert Tjian
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    ABSTRACT: Comparative genome analyses reveal that organismal complexity scales not with gene number but with gene regulation. Recent efforts indicate that the human genome likely contains hundreds of thousands of enhancers, with a typical gene embedded in a milieu of tens of enhancers. Proliferation of cis-regulatory DNAs is accompanied by increased complexity and functional diversification of transcriptional machineries recognizing distal enhancers and core promoters and by the high-order spatial organization of genetic elements. 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.
    Cell 03/2014; 157(1):13-25. · 31.96 Impact Factor
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    Jacques Bothma, Michael Levine
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    ABSTRACT: Live imaging of developmental gene expression in Drosophila embryos opens up exciting new prospects for understanding gene regulation during development.
    Current biology: CB 11/2013; 23(21):R965-7. · 10.99 Impact Factor
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    ABSTRACT: ERK1/2 MAP kinase exhibits a highly dynamic activation pattern in developing embryos, which largely depends on fibroblast growth factor (FGF) signals. In ascidian embryos, FGF-dependent activation of ERK1/2 occurs differentially between sister cells during marginal zone and neural lineage patterning. Selective attenuation of FGF signals by localised ephrin/Eph signals accounts for this differential ERK activation, which controls the binary fate choice of each sibling cell pair. Here, we show that p120 Ras GTPase-activating protein (p120RasGAP) is a crucial mediator of these ephrin/Eph signals. First, inhibition of p120RasGAP has a similar effect to inhibition of ephrin/Eph function during marginal zone and neural patterning. Second, p120RasGAP acts epistatically to ephrin/Eph signals. Third, p120RasGAP physically associates with Eph3 in an ephrin-dependent manner. This study provides the first in vivo evidence that the functional association between Eph and RasGAP controls the spatial extent of FGF-activated ERK.
    Development 09/2013; · 6.60 Impact Factor
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    Alistair Nicol Boettiger, Michael Levine
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    ABSTRACT: Transcription is commonly held to be a highly stochastic process, resulting in considerable heterogeneity of gene expression among the different cells in a population. Here, we employ quantitative in situ hybridization methods coupled with high-resolution imaging assays to measure the expression of snail, a developmental patterning gene necessary for coordinating the invagination of the mesoderm during gastrulation of the Drosophila embryo. Our measurements of steady-state mRNAs suggest that there is very little variation in snail expression across the different cells that make up the mesoderm and that synthesis approaches the kinetic limits of Pol II processivity. We propose that rapid transcription kinetics and negative autoregulation are responsible for the remarkable homogeneity of snail expression and the coordination of mesoderm invagination.
    Cell Reports 01/2013; · 7.21 Impact Factor
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    Michael Levine
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    ABSTRACT: Computer simulations and quantitative imaging of Drosophila embryos have been used to recreate the dynamic activities of a complex transcriptional enhancer.
    eLife Sciences 01/2013; 2:e01135. · 8.52 Impact Factor
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    ABSTRACT: Neural crest arises at the neural plate border, expresses a core set of regulatory genes and produces a diverse array of cell types, including ectomesenchyme derivatives that elaborate the vertebrate head. The evolution of neural crest has been proposed to be a key event leading to the appearance of new cell types that fostered the transition from filter feeding to active predation in ancestral vertebrates. However, the origin of neural crest remains controversial, as homologous cell types have not been unambiguously identified in non-vertebrate chordates. Here we show that the tunicate Ciona intestinalis possesses a cephalic melanocyte lineage (a9.49) similar to neural crest that can be reprogrammed into migrating 'ectomesenchyme' by the targeted misexpression of Twist (also known as twist-like 2). Our results suggest that the neural crest melanocyte regulatory network pre-dated the divergence of tunicates and vertebrates. 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'.
    Nature 11/2012; · 38.60 Impact Factor
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    ABSTRACT: Activation of the gap gene hunchback (hb) by the maternal Bicoid gradient is one of the most intensively studied gene regulatory interactions in animal development. Most efforts to understand this process have focused on the classical Bicoid target enhancer located immediately upstream of the P2 promoter [1-12]. However, hb is also regulated by a recently identified distal shadow enhancer as well as a neglected "stripe" enhancer, which mediates expression in both central and posterior regions of cellularizing embryos [13, 14]. Here, we employ BAC transgenesis and quantitative imaging methods to investigate the individual contributions of these different enhancers to the dynamic hb expression pattern. These studies reveal that the stripe enhancer is crucial for establishing the definitive border of the anterior Hb expression pattern, just beyond the initial border delineated by Bicoid. Removal of this enhancer impairs dynamic expansion of hb expression and results in variable cuticular defects in the mesothorax (T2) due to abnormal patterns of segmentation gene expression. The stripe enhancer is subject to extensive regulation by gap repressors, including Kruppel, Knirps, and Hb itself. We propose that this repression helps ensure precision of the anterior Hb border in response to variations in the Bicoid gradient.
    Current biology: CB 10/2012; · 10.99 Impact Factor
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    Valérie Hilgers, Sandra B Lemke, Michael Levine
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    ABSTRACT: Post-transcriptional gene regulation is prevalent in the nervous system, where multiple tiers of regulatory complexity contribute to the development and function of highly specialized cell types. Whole-genome studies in Drosophila have identified several hundred genes containing long 3' extensions in neural tissues. We show that ELAV (embryonic-lethal abnormal visual system) is a key mediator of these neural-specific extensions. Misexpression of ELAV results in the ectopic synthesis of long messenger RNAs (mRNAs) in transgenic embryos. RNA immunoprecipitation assays suggest that ELAV directly binds the proximal polyadenylation signals of many target mRNAs. Finally, ELAV is sufficient to suppress 3' end formation at a strong polyadenylation signal when tethered to a synthetic RNA. We propose that this mechanism for coordinating 3' UTR extension may be generally used in a variety of cellular processes.
    Genes & development 09/2012; 26(20):2259-64. · 12.08 Impact Factor
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    Vivek S Chopra, Nikki Kong, Michael Levine
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    ABSTRACT: Transcriptional repressors are thought to inhibit gene expression by interfering with the binding or function of RNA Polymerase II, perhaps by promoting local chromatin condensation. Here, we present evidence for a distinctive mechanism of repression, whereby sequence-specific repressors prevent the looping of distal enhancers to the promoter. Particular efforts focus on the Snail repressor, which plays a conserved role in promoting epithelial-mesenchyme transitions in both invertebrates and vertebrates, including mesoderm invagination in Drosophila, neural crest migration in vertebrates, and tumorigenesis in mammals. Chromosome conformation capture experiments were used to examine enhancer looping at Snail target genes in wild-type and mutant embryos. These studies suggest that the Snail repressor blocks the formation of fruitful enhancer-promoter interactions when bound to a distal enhancer. This higher-order mechanism of transcriptional repression has broad implications for the control of gene activity in metazoan development.
    Proceedings of the National Academy of Sciences 05/2012; 109(24):9460-4. · 9.81 Impact Factor
  • Eileen Wagner, Michael Levine
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    ABSTRACT: The Ciona tadpole is constructed from simple, well-defined cell lineages governed by provisional gene networks that have been defined via extensive gene disruption assays. Here, we examine the patterning of the anterior neural plate, which produces placodal derivatives such as the adhesive palps and stomodeum, as well as the sensory vesicle (simple brain) of the Ciona tadpole. Evidence is presented that the doublesex-related gene DMRT is expressed throughout the anterior neural plate of neurulating embryos. It leads to the activation of FoxC and ZicL in the palp placode and anterior neural tube, respectively. This differential expression depends on FGF signaling, which inhibits FoxC expression in the anterior neural tube. Inhibition of FGF signaling leads to expanded expression of FoxC, the loss of ZicL, and truncation of the anterior neural tube.
    Development 05/2012; 139(13):2351-9. · 6.60 Impact Factor
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    Emma Farley, Michael Levine
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    ABSTRACT: Enhancers mediate localized patterns of gene expression during development. A common feature of "traditional" enhancers is the presence of clustered binding motifs for sequence-specific transcription factors (TFs). In this issue of Genes & Development, Kvon and colleagues (pp. 908-913) present new evidence that HOT (highly occupied transcription) DNAs direct specific patterns of gene expression, despite being depleted for TF-binding motifs.
    Genes & development 05/2012; 26(9):873-6. · 12.08 Impact Factor
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    Mounia Lagha, Jacques P Bothma, Michael Levine
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    ABSTRACT: We review recently identified mechanisms of transcriptional control that ensure reliable and reproducible patterns of gene expression in natural populations of developing embryos, despite inherent fluctuations in gene regulatory processes, variations in genetic backgrounds and exposure to diverse environmental conditions. These mechanisms are not responsible for switching genes on and off. Instead, they control the fine-tuning of gene expression and ensure regulatory precision. Several such mechanisms are discussed, including redundant binding sites within transcriptional enhancers, shadow enhancers, and 'poised' enhancers and promoters, as well as the role of 'redundant' gene interactions within regulatory networks. We propose that such regulatory mechanisms provide population fitness and 'fine-tune' the spatial and temporal control of gene expression.
    Trends in Genetics 04/2012; 28(8):409-16. · 9.77 Impact Factor
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    ABSTRACT: The motor ganglion (MG) controls the rhythmic swimming behavior of the Ciona intestinalis tadpole. Despite its cellular simplicity (five pairs of neurons), the MG exhibits conservation of transcription factor expression with the spinal cord of vertebrates. Evidence is presented that the developing MG is patterned by sequential Ephrin/FGF/MAPK and Delta/Notch signaling events. FGF/MAPK attenuation by a localized EphrinAb signal specifies posterior neuronal subtypes, which in turn relay a Delta2/Notch signal that specifies anterior fates. This short-range relay is distinct from the patterning of the vertebrate spinal cord, which is a result of opposing BMP and Shh morphogen gradients. Nonetheless, both mechanisms lead to localized expression of related homeodomain codes for the specification of distinct neuronal subtypes. This MG regulatory network provides a foundation for elucidating the genetic and cellular basis of a model chordate central pattern generator.
    Development 12/2011; 138(24):5429-39. · 6.60 Impact Factor
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    ABSTRACT: Cholinergic motor neurons are defined by the coexpression of a battery of genes encoding proteins that act sequentially to synthesize, package and degrade acetylcholine and reuptake its breakdown product, choline. How expression of these critical motor neuron identity determinants is controlled and coordinated is not understood. We show here that, in the nematode Caenorhabditis elegans, all members of the cholinergic gene battery, as well as many other markers of terminal motor neuron fate, are co-regulated by a shared cis-regulatory signature and a common trans-acting factor, the phylogenetically conserved COE (Collier, Olf, EBF)-type transcription factor UNC-3. UNC-3 initiated and maintained expression of cholinergic fate markers and was sufficient to induce cholinergic fate in other neuron types. UNC-3 furthermore operated in negative feedforward loops to induce the expression of transcription factors that repress individual UNC-3-induced terminal fate markers, resulting in diversification of motor neuron differentiation programs in specific motor neuron subtypes. A chordate ortholog of UNC-3, Ciona intestinalis COE, was also both required and sufficient for inducing a cholinergic fate. Thus, UNC-3 is a terminal selector for cholinergic motor neuron differentiation whose function is conserved across phylogeny.
    Nature Neuroscience 11/2011; 15(2):205-14. · 15.25 Impact Factor
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    Jacques P Bothma, Joe Magliocco, Michael Levine
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    ABSTRACT: The development of the precellular Drosophila embryo is characterized by exceptionally rapid transitions in gene activity, with broadly distributed maternal regulatory gradients giving way to precise on/off patterns of gene expression within a one-hour window, between two and three hours after fertilization [1]. Transcriptional repression plays a pivotal role in this process, delineating sharp expression patterns (e.g., pair-rule stripes) within broad domains of gene activation. As many as 20 different sequence-specific repressors have been implicated in this process, yet the mechanisms by which they silence gene expression have remained elusive [2]. Here we report the development of a method for the quantitative visualization of transcriptional repression. We focus on the Snail repressor, which establishes the boundary between the presumptive mesoderm and neurogenic ectoderm [3]. We find that elongating Pol II complexes complete transcription after the onset of Snail repression. As a result, moderately sized genes (e.g., the 22 kb sog locus) are fully silenced only after tens of minutes of repression. We propose that this "repression lag" imposes a severe constraint on the regulatory dynamics of embryonic patterning and further suggest that posttranscriptional regulators, like microRNAs, are required to inhibit unwanted transcripts produced during protracted periods of gene silencing.
    Current biology: CB 09/2011; 21(18):1571-7. · 10.99 Impact Factor
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    ABSTRACT: The 3' termini of eukaryotic mRNAs influence transcript stability, translation efficiency, and subcellular localization. Here we report that a subset of developmental regulatory genes, enriched in critical RNA-processing factors, exhibits synchronous lengthening of their 3' UTRs during embryogenesis. The resulting UTRs are up to 20-fold longer than those found on typical Drosophila mRNAs. The large mRNAs emerge shortly after the onset of zygotic transcription, with several of these genes acquiring additional, phased UTR extensions later in embryogenesis. We show that these extended 3' UTR sequences are selectively expressed in neural tissues and contain putative recognition motifs for the translational repressor, Pumilio, which also exhibits the 3' lengthening phenomenon documented in this study. These findings suggest a previously unknown mode of posttranscriptional regulation that may contribute to the complexity of neurogenesis or neural function.
    Proceedings of the National Academy of Sciences 09/2011; 108(38):15864-9. · 9.81 Impact Factor

Publication Stats

6k Citations
1,069.41 Total Impact Points

Institutions

  • 1999–2014
    • University of California, Berkeley
      • • Department of Molecular and Cell Biology
      • • Division of Genetics, Genomics and Development
      • • Center for Integrative Genomics
      Berkeley, California, United States
  • 2013
    • Harvard University
      Cambridge, Massachusetts, United States
  • 2011
    • Mount Sinai School of Medicine
      • Black Family Stem Cell Institute
      Manhattan, NY, United States
  • 2009
    • Brigham and Women's Hospital
      • Department of Medicine
      Boston, MA, United States
  • 2003–2009
    • Kyoto University
      • Department of Zoology
      Kyoto, Kyoto-fu, Japan
    • Weill Cornell Medical College
      New York City, New York, United States
    • Howard Hughes Medical Institute
      Ashburn, Virginia, United States
  • 2007
    • Whitehead Institute for Biomedical Research
      Cambridge, Massachusetts, United States
  • 2005
    • California Institute of Technology
      • Division of Biology
      Pasadena, CA, United States
  • 2002
    • University of Chicago
      Chicago, Illinois, United States