Yanniv Dorone

Yanniv Dorone

San Francisco Bay Area
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About

Yanniv is a Senior Vice President at Fall Line Capital, a venture capital firm focused on…

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Experience

  • Fall Line Capital Graphic

    Fall Line Capital

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    San Mateo, California, United States

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    San Mateo, California, United States

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    Carnegie Institution of Washington, Department of Plant Biology

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Education

  • Stanford University Graphic

    Stanford University

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    Cell and molecular biology track

    Awarded the Charles Yanofsky Prize for "most outstanding graduate student working in the field of molecular biology"

    Main publication: Dorone, Yanniv, Steven Boeynaems, Eduardo Flores, Benjamin Jin, Shannon Hateley, Flavia Bossi, Elena Lazarus et al. "A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation." Cell (2021). Featured on the cover. Highlighted in Science, Nature Plants, Nature Chemical Biology…

    Cell and molecular biology track

    Awarded the Charles Yanofsky Prize for "most outstanding graduate student working in the field of molecular biology"

    Main publication: Dorone, Yanniv, Steven Boeynaems, Eduardo Flores, Benjamin Jin, Shannon Hateley, Flavia Bossi, Elena Lazarus et al. "A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation." Cell (2021). Featured on the cover. Highlighted in Science, Nature Plants, Nature Chemical Biology, PNAS, Developmental Cell and Molecular Plant.

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    Homerton College

    Plant sciences: https://www.plantsci.cam.ac.uk/teaching/plants

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    Normalien student (228 spots for 6000 candidates)

    Ranked 5th best small university in the world by the Times Higher Education: https://www.timeshighereducation.com/student/best-universities/worlds-best-small-universities

Volunteer Experience

Publications

  • Poly(A)-binding protein is an ataxin-2 chaperone that regulates biomolecular condensates

    Molecular Cell

    Biomolecular condensation underlies the biogenesis of an expanding array of membraneless assemblies, including stress granules (SGs), which form under a variety of cellular stresses. Advances have been made in understanding the molecular grammar of a few scaffold proteins that make up these phases, but how the partitioning of hundreds of SG proteins is regulated remains largely unresolved. While investigating the rules that govern the condensation of ataxin-2, an SG protein implicated in…

    Biomolecular condensation underlies the biogenesis of an expanding array of membraneless assemblies, including stress granules (SGs), which form under a variety of cellular stresses. Advances have been made in understanding the molecular grammar of a few scaffold proteins that make up these phases, but how the partitioning of hundreds of SG proteins is regulated remains largely unresolved. While investigating the rules that govern the condensation of ataxin-2, an SG protein implicated in neurodegenerative disease, we unexpectedly identified a short 14 aa sequence that acts as a condensation switch and is conserved across the eukaryote lineage. We identify poly(A)-binding proteins as unconventional RNA-dependent chaperones that control this regulatory switch. Our results uncover a hierarchy of cis and trans interactions that fine-tune ataxin-2 condensation and reveal an unexpected molecular function for ancient poly(A)-binding proteins as regulators of biomolecular condensate proteins. These findings may inspire approaches to therapeutically target aberrant phases in disease.

    See publication

  • When Phased without Water: Biophysics of Cellular Desiccation, from Biomolecules to Condensates

    ACS Chemical Reviews

    The molecular machinery that enables life has evolved in water, yet many of
    the organisms around us are able to survive even extreme desiccation. Especially remarkable
    are single-cell and sedentary organisms that rely on specialized biomolecular machinery to
    survive in environments that are routinely subjected to a near-complete lack of water. In this
    review, we zoom in on the molecular level of what is happening in the cellular environment
    under water stress. We cover the…

    The molecular machinery that enables life has evolved in water, yet many of
    the organisms around us are able to survive even extreme desiccation. Especially remarkable
    are single-cell and sedentary organisms that rely on specialized biomolecular machinery to
    survive in environments that are routinely subjected to a near-complete lack of water. In this
    review, we zoom in on the molecular level of what is happening in the cellular environment
    under water stress. We cover the various mechanisms by which biochemical components of
    the cell can dysfunction in dehydrated cells and detail the different strategies that organisms
    have evolved to eliminate or cope with these desiccation-induced perturbations. We
    specifically focus on two survival strategies: (1) the use of disordered proteins to protect the cellular environment before, during, and in the recovery from desiccation, and (2) the use of biomolecular condensates as a self-assembly mechanism that can sequester or protect specific cellular machinery in times of water stress. We provide a summary of experimental work describing the critical contributions of disordered proteins and biomolecular condensates to the cellular response to water loss and highlight their role in desiccation tolerance. Desiccation biology is an exciting area of cell biology, still far from being completely explored. Understanding it on the molecular level is bound to give us critical new insights in how life adapted/can adapt to the loss of water, spanning from the early colonization of land to how we can deal with climate change in our future.

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  • CHIQUITA1 maintains temporal transition between proliferation and differentiation in Arabidopsis thaliana

    Development

    Body size varies widely among species, populations and individuals, depending on the environment. Transitioning between proliferation and differentiation is a crucial determinant of final organ size, but how the timing of this transition is established and maintained remains unknown. Using cell proliferation markers and genetic analysis, we show that CHIQUITA1 (CHIQ1) is required to maintain the timing of the transition from proliferation to differentiation in Arabidopsis thaliana. Combining…

    Body size varies widely among species, populations and individuals, depending on the environment. Transitioning between proliferation and differentiation is a crucial determinant of final organ size, but how the timing of this transition is established and maintained remains unknown. Using cell proliferation markers and genetic analysis, we show that CHIQUITA1 (CHIQ1) is required to maintain the timing of the transition from proliferation to differentiation in Arabidopsis thaliana. Combining kinematic and cell lineage-tracking studies, we found that the number of actively dividing cells in chiquita1-1 plants decreases prematurely compared with wild-type plants, suggesting CHIQ1 maintains the proliferative capacity in dividing cells and ensures that cells divide a specific number of times. CHIQ1 belongs to a plant-specific gene family of unknown molecular function and genetically interacts with three close members of its family to control the timing of proliferation exit. Our work reveals the interdependency between cellular and organ-level processes underlying final organ size determination.

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  • Live imaging Arabidopsis thaliana embryos under different hydration conditions

    STAR Protocols

    Despite the ecological and agronomical importance of seed germination, how seeds integrate environmental signals to trigger germination remains enigmatic. Recently we reported that a protein called FLOE1 is involved in sensing and responding to water availability during germination. Here, we present a live-imaging protocol to assess the subcellular localization of a protein of interest during imbibition of desiccated Arabidopsis thaliana seeds with the goal of understanding protein dynamics…

    Despite the ecological and agronomical importance of seed germination, how seeds integrate environmental signals to trigger germination remains enigmatic. Recently we reported that a protein called FLOE1 is involved in sensing and responding to water availability during germination. Here, we present a live-imaging protocol to assess the subcellular localization of a protein of interest during imbibition of desiccated Arabidopsis thaliana seeds with the goal of understanding protein dynamics during the early stages of water uptake.

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  • Interdependent iron and phosphorus availability controls photosynthesis through retrograde signaling

    Nature Communications

    Iron deficiency hampers photosynthesis and is associated with chlorosis. We recently showed that iron deficiency-induced chlorosis depends on phosphorus availability. How plants integrate these cues to control chlorophyll accumulation is unknown. Here, we show that iron limitation downregulates photosynthesis genes in a phosphorus-dependent manner. Using transcriptomics and genome-wide association analysis, we identify two genes, PHT4;4 encoding a chloroplastic ascorbate transporter and bZIP58,…

    Iron deficiency hampers photosynthesis and is associated with chlorosis. We recently showed that iron deficiency-induced chlorosis depends on phosphorus availability. How plants integrate these cues to control chlorophyll accumulation is unknown. Here, we show that iron limitation downregulates photosynthesis genes in a phosphorus-dependent manner. Using transcriptomics and genome-wide association analysis, we identify two genes, PHT4;4 encoding a chloroplastic ascorbate transporter and bZIP58, encoding a nuclear transcription factor, which prevent the downregulation of photosynthesis genes leading to the stay-green phenotype under iron-phosphorus deficiency. Joint limitation of these nutrients induces ascorbate accumulation by activating expression of an ascorbate biosynthesis gene, VTC4, which requires bZIP58. Furthermore, we demonstrate that chloroplastic ascorbate transport prevents the downregulation of photosynthesis genes under iron-phosphorus combined deficiency through modulation of ROS homeostasis. Our study uncovers a ROS-mediated chloroplastic retrograde signaling pathway to adapt photosynthesis to nutrient availability.

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  • A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation

    Cell

    Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1…

    Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.

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  • Hydration-dependent phase separation of a prion-like protein regulates seed germination during water stress.

    SSRN

    Many organisms evolved strategies to survive and thrive under extreme desiccation. Plant seeds protect dehydrated embryos from a variety of stressors and can even lay dormant for millennia. While hydration is the key trigger that reactivates metabolism and kick-starts germination, the exact mechanism by which the embryo senses water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the…

    Many organisms evolved strategies to survive and thrive under extreme desiccation. Plant seeds protect dehydrated embryos from a variety of stressors and can even lay dormant for millennia. While hydration is the key trigger that reactivates metabolism and kick-starts germination, the exact mechanism by which the embryo senses water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that the biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We also find intragenic, intraspecific, and interspecific natural variations in phase separation propensity of FLOE1 homologs. These findings demonstrate a physiological role of phase separation in a multicellular organism and have direct implications for plant ecology and agriculture, especially the design of drought resistant crops, in the face of climate change.

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  • Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction

    BMC Genomics

    Background
    The molecular function of a gene is most commonly inferred by sequence similarity. Therefore, genes that lack sufficient sequence similarity to characterized genes (such as certain classes of transcriptional regulators) are difficult to classify using most function prediction algorithms and have remained uncharacterized.

    Results
    To identify novel transcriptional regulators systematically, we used a feature-based pipeline to screen protein families of unknown function…

    Background
    The molecular function of a gene is most commonly inferred by sequence similarity. Therefore, genes that lack sufficient sequence similarity to characterized genes (such as certain classes of transcriptional regulators) are difficult to classify using most function prediction algorithms and have remained uncharacterized.

    Results
    To identify novel transcriptional regulators systematically, we used a feature-based pipeline to screen protein families of unknown function. This method predicted 43 transcriptional regulator families in Arabidopsis thaliana, 7 families in Drosophila melanogaster, and 9 families in Homo sapiens. Literature curation validated 12 of the predicted families to be involved in transcriptional regulation. We tested 33 out of the 195 Arabidopsis putative transcriptional regulators for their ability to activate transcription of a reporter gene in planta and found twelve coactivators, five of which had no prior literature support. To investigate mechanisms of action in which the predicted regulators might work, we looked for interactors of an Arabidopsis candidate that did not show transactivation activity in planta and found that it might work with other members of its own family and a subunit of the Polycomb Repressive Complex 2 to regulate transcription.

    Conclusions
    Our results demonstrate the feasibility of assigning molecular function to proteins of unknown function without depending on sequence similarity. In particular, we identified novel transcriptional regulators using biological features enriched in transcription factors. The predictions reported here should accelerate the characterization of novel regulators.

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  • DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis

    The Plant Cell

    The rate of crossover, the reciprocal exchanges of homologous chromosomal segments, is not uniform along chromosomes differing between male and female meiocytes. To better understand the factors regulating this variable landscape, we performed a detailed genetic and epigenetic analysis of 737 crossover events in Arabidopsis thaliana. Crossovers were more frequent than expected in promoters. Three DNA motifs enriched in crossover regions and less abundant in crossover-poor pericentric regions…

    The rate of crossover, the reciprocal exchanges of homologous chromosomal segments, is not uniform along chromosomes differing between male and female meiocytes. To better understand the factors regulating this variable landscape, we performed a detailed genetic and epigenetic analysis of 737 crossover events in Arabidopsis thaliana. Crossovers were more frequent than expected in promoters. Three DNA motifs enriched in crossover regions and less abundant in crossover-poor pericentric regions were identified. One of these motifs, the CCN repeat, was previously unknown in plants. The A-rich motif was preferentially associated with promoters, while the CCN repeat and the CTT repeat motifs were preferentially associated with genes. Analysis of epigenetic modifications around the motifs showed, in most cases, a specific epigenetic architecture. For example, we show that there is a peak of nucleosome occupancy and of H3K4me3 around the CCN and CTT repeat motifs while nucleosome occupancy was lowest around the A-rich motif. Cytosine methylation levels showed a gradual decrease within ∼2 kb of the three motifs, being lowest at sites where crossover occurred. This landscape was conserved in the decreased DNA methylation1 mutant. In summary, the crossover motifs are associated with epigenetic landscapes corresponding to open chromatin and contributing to the nonuniformity of crossovers in Arabidopsis.

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  • Diploidization of meiosis in autotetraploids

    BioSciences Master Reviews

    Abstract
    Recent genome analyses indicate that genome doubling occurs frequently in eukaryotes. The presence of additional sets of chromosomes can lead to meiotic failures, which pressure polyploids to evolve into a diploid-like state. This process is called diploidization and can be broken down into two distinct types: cytological diploidization, a transition to bivalent chromosome configurations at meiosis, and genetic diploidization, the development of pairing preferences that result in…

    Abstract
    Recent genome analyses indicate that genome doubling occurs frequently in eukaryotes. The presence of additional sets of chromosomes can lead to meiotic failures, which pressure polyploids to evolve into a diploid-like state. This process is called diploidization and can be broken down into two distinct types: cytological diploidization, a transition to bivalent chromosome configurations at meiosis, and genetic diploidization, the development of pairing preferences that result in disomic inheritance. In this review, I select studies that have consolidated our understanding of diploidization. Nevertheless, little is known on this subject and only assumptions can be made.

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Patents

Honors & Awards

  • Charles Yanofsky Prize in Molecular Biology

    Stanford University

    "This goes to the most outstanding graduate student working in the field of molecular biology. It honors Professor Charles Yanofsky of the Department of Biology."

    https://biology.stanford.edu/academics/student-awards

  • Forbes 30 under 30 Europe 2019

    Forbes

    https://www.forbes.com/under30/list/2019/europe/science-healthcare/#a4fe7f95d91c

  • American Society of Plant Biologists Conviron Scholar

    American Society of Plant Biologists

    http://www.conviron.com/winners-of-the-2018-19-aspb-conviron-scholars-program

  • Stanford Graduate Fellowship In Science & Engineering-William R. and Sara Hart Kimball Fellow

    Stanford University

    https://dpb.carnegiescience.edu/article/yanniv-dorone-awarded-prestigious-graduate-fellowship-stanford

  • Joseph R. McMicking Fellowship in Biological Sciences

    Stanford University

  • Normalien Fellowship

    French Ministry of Higher Education

    https://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000023661814

Languages

  • French

    Native or bilingual proficiency

  • Hebrew

    Native or bilingual proficiency

  • English

    Full professional proficiency

  • Spanish

    Limited working proficiency

Organizations

  • Kudla Fund

    Portfolio Manager

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