Honors & Awards

  • HFSP Fellow, Human Frontier Science Program (2014-2017)
  • Damon Runyon Fellow, Damon Runyon Cancer Research Foundation (2013-2014)
  • Rothschild Fellowship, Yad Hanadiv (2013-2014)

Professional Education

  • Bachelor of Science, University Of The Negev (2006)
  • Master of Science, Weizmann Institute Of Science (2008)
  • Doctor of Philosophy, Weizmann Institute Of Science (2012)

Stanford Advisors

Current Research and Scholarly Interests

Aging is the primary risk factor for many human pathologies, including cardiovascular and neurodegenerative diseases, cancer, and diabetes. Yet, understanding how organisms age remains one of the biggest challenges in biology. Due to their short lifespan, non-vertebrate model systems (yeast, worms, and flies) have been widely used in experimental aging research. These studies revealed that the aging rate can be manipulated by genetic and environmental interventions, thus, underscoring that aging is not merely due to wear and tear. Rather, it is a complex trait that can be regulated by conserved mechanisms. However, the lack of short-lived vertebrate models for genetic studies has significantly limited our understanding of vertebrate aging, including the role of vertebrate-specific genes (e.g. IL8 and APOE), organs (e.g. bones and blood), and physiological processes (e.g. adaptive immunity).

We used the shortest-lived vertebrate model, the African turquoise killifish, to develop the first genetic platform for rapid exploration of vertebrate aging. This platform included a sequenced genome, CRISPR/Cas9-based genome editing, and mutant fish for many aging- and disease-relates genes. We focused on mutants for the protein subunit of telomerase, which displayed the fastest onset of telomere-related pathologies among vertebrate models. This genome-to-phenotype platform represents a unique resource for studying vertebrate aging and disease in a high-throughput manner and for investigating candidates arising from human genome-wide studies.

All Publications

  • Efficient genome engineering approaches for the short-lived African turquoise killifish. Nature protocols Harel, I., Valenzano, D. R., Brunet, A. 2016; 11 (10): 2010-2028


    A central challenge in experimental aging research is the lack of short-lived vertebrate models for genetic studies. Here we present a comprehensive protocol for efficient genome engineering in the African turquoise killifish (Nothobranchius furzeri), which is the shortest-lived vertebrate in captivity with a median life span of 4-6 months. By taking advantage of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease (CRISPR/Cas9) system and the turquoise killifish genome, this platform enables the generation of knockout alleles via nonhomologous end joining (NHEJ) and knock-in alleles via homology-directed repair (HDR). We include guidelines for guide RNA (gRNA) target design, embryo injection and hatching, germ-line transmission and for minimizing off-target effects. We also provide strategies for Tol2-based transgenesis and large-scale husbandry conditions that are critical for success. Because of the fast life cycle of the turquoise killifish, stable lines can be generated as rapidly as 2-3 months, which is much faster than other fish models. This protocol provides powerful genetic tools for studying vertebrate aging and aging-related diseases.

    View details for DOI 10.1038/nprot.2016.103

    View details for PubMedID 27658015

  • The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan CELL Valenzano, D. R., Benayoun, B. A., Singh, P. P., Zhang, E., Etter, P. D., Hu, C., Clement-Ziza, M., Willemsen, D., Cui, R., Harel, I., Machado, B. E., Yee, M., Sharp, S. C., Bustamante, C. D., Beyer, A., Johnson, E. A., Brunet, A. 2015; 163 (6): 1539-1554


    Lifespan is a remarkably diverse trait ranging from a few days to several hundred years in nature, but the mechanisms underlying the evolution of lifespan differences remain elusive. Here we de novo assemble a reference genome for the naturally short-lived African turquoise killifish, providing a unique resource for comparative and experimental genomics. The identification of genes under positive selection in this fish reveals potential candidates to explain its compressed lifespan. Several aging genes are under positive selection in this short-lived fish and long-lived species, raising the intriguing possibility that the same gene could underlie evolution of both compressed and extended lifespans. Comparative genomics and linkage analysis identify candidate genes associated with lifespan differences between various turquoise killifish strains. Remarkably, these genes are clustered on the sex chromosome, suggesting that short lifespan might have co-evolved with sex determination. Our study provides insights into the evolutionary forces that shape lifespan in nature.

    View details for DOI 10.1016/j.cell.2015.11.008

    View details for Web of Science ID 000366044800024

    View details for PubMedID 26638078

    View details for PubMedCentralID PMC4684691

  • Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events NATURE BIOTECHNOLOGY Tilgner, H., Jahanbani, F., Blauwkamp, T., Moshrefi, A., Jaeger, E., Chen, F., Harel, I., Bustamante, C. D., Rasmussen, M., Snyder, M. P. 2015; 33 (7): 736-742


    Alternative splicing shapes mammalian transcriptomes, with many RNA molecules undergoing multiple distant alternative splicing events. Comprehensive transcriptome analysis, including analysis of exon co-association in the same molecule, requires deep, long-read sequencing. Here we introduce an RNA sequencing method, synthetic long-read RNA sequencing (SLR-RNA-seq), in which small pools (≤1,000 molecules/pool, ≤1 molecule/gene for most genes) of full-length cDNAs are amplified, fragmented and short-read-sequenced. We demonstrate that these RNA sequences reconstructed from the short reads from each of the pools are mostly close to full length and contain few insertion and deletion errors. We report many previously undescribed isoforms (human brain: ∼13,800 affected genes, 14.5% of molecules; mouse brain ∼8,600 genes, 18% of molecules) and up to 165 human distant molecularly associated exon pairs (dMAPs) and distant molecularly and mutually exclusive pairs (dMEPs). Of 16 associated pairs detected in the mouse brain, 9 are conserved in human. Our results indicate conserved mechanisms that can produce distant but phased features on transcript and proteome isoforms.

    View details for DOI 10.1038/nbt.3242

    View details for Web of Science ID 000358396100029

  • A platform for rapid exploration of aging and diseases in a naturally short-lived vertebrate. Cell Harel, I., Benayoun, B. A., Machado, B., Singh, P. P., Hu, C., Pech, M. F., Valenzano, D. R., Zhang, E., Sharp, S. C., Artandi, S. E., Brunet, A. 2015; 160 (5): 1013-1026

    View details for DOI 10.1016/j.cell.2015.01.038

    View details for PubMedID 25684364

  • The African Turquoise Killifish: A Model for Exploring Vertebrate Aging and Diseases in the Fast Lane. Cold Spring Harbor symposia on quantitative biology Harel, I., Brunet, A. 2015; 80: 275-279


    Why and how organisms age remains a mystery, and it defines one of the biggest challenges in biology. Aging is also the primary risk factor for many human pathologies, such as cancer, diabetes, cardiovascular diseases, and neurodegenerative diseases. Thus, manipulating the aging rate and potentially postponing the onset of these devastating diseases could have a tremendous impact on human health. Recent studies, relying primarily on nonvertebrate short-lived model systems, have shown the importance of both genetic and environmental factors in modulating the aging rate. However, relatively little is known about aging in vertebrates or what processes may be unique and specific to these complex organisms. Here we discuss how advances in genomics and genome editing have significantly expanded our ability to probe the aging process in a vertebrate system. We highlight recent findings from a naturally short-lived vertebrate, the African turquoise killifish, which provides an attractive platform for exploring mechanisms underlying vertebrate aging and age-related diseases.

    View details for DOI 10.1101/sqb.2015.80.027524

    View details for PubMedID 26642856

  • Head Muscle Development Craniofacial Muscles: A New Framework for Understanding the Effector Side of Craniofacial Muscle Control Harel, I., Tzahor, E. Springer. 2013: 11–28
  • Pharyngeal mesoderm regulatory network controls cardiac and head muscle morphogenesis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Harel, I., Maezawa, Y., Avraham, R., Rinon, A., Ma, H., Cross, J. W., Leviatan, N., Hegesh, J., Roy, A., Jacob-Hirsch, J., Rechavi, G., Carvajal, J., Tole, S., Kioussi, C., Quaggin, S., Tzahor, E. 2012; 109 (46): 18839-18844


    The search for developmental mechanisms driving vertebrate organogenesis has paved the way toward a deeper understanding of birth defects. During embryogenesis, parts of the heart and craniofacial muscles arise from pharyngeal mesoderm (PM) progenitors. Here, we reveal a hierarchical regulatory network of a set of transcription factors expressed in the PM that initiates heart and craniofacial organogenesis. Genetic perturbation of this network in mice resulted in heart and craniofacial muscle defects, revealing robust cross-regulation between its members. We identified Lhx2 as a previously undescribed player during cardiac and pharyngeal muscle development. Lhx2 and Tcf21 genetically interact with Tbx1, the major determinant in the etiology of DiGeorge/velo-cardio-facial/22q11.2 deletion syndrome. Furthermore, knockout of these genes in the mouse recapitulates specific cardiac features of this syndrome. We suggest that PM-derived cardiogenesis and myogenesis are network properties rather than properties specific to individual PM members. These findings shed new light on the developmental underpinnings of congenital defects.

    View details for DOI 10.1073/pnas.1208690109

    View details for Web of Science ID 000311576300048

    View details for PubMedID 23112163

  • The actin regulator N-WASp is required for muscle-cell fusion in mice PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Gruenbaum-Cohen, Y., Harel, I., Umansky, K., Tzahor, E., Snapper, S. B., Shilo, B., Schejter, E. D. 2012; 109 (28): 11211-11216


    A fundamental aspect of skeletal myogenesis involves extensive rounds of cell fusion, in which individual myoblasts are incorporated into growing muscle fibers. Here we demonstrate that N-WASp, a ubiquitous nucleation-promoting factor of branched microfilament arrays, is an essential contributor to skeletal muscle-cell fusion in developing mouse embryos. Analysis both in vivo and in primary satellite-cell cultures, shows that disruption of N-WASp function does not interfere with the program of skeletal myogenic differentiation, and does not affect myoblast motility, morphogenesis and attachment capacity. N-WASp-deficient myoblasts, however, fail to fuse. Furthermore, our analysis suggests that myoblast fusion requires N-WASp activity in both partners of a fusing myoblast pair. These findings reveal a specific role for N-WASp during mammalian myogenesis. WASp-family elements appear therefore to act as universal mediators of the myogenic cell-cell fusion mechanism underlying formation of functional muscle fibers, in both vertebrate and invertebrate species.

    View details for DOI 10.1073/pnas.1116065109

    View details for Web of Science ID 000306642100042

    View details for PubMedID 22736793

  • The occipital lateral plate mesoderm is a novel source for vertebrate neck musculature DEVELOPMENT Theis, S., Patel, K., Valasek, P., Otto, A., Pu, Q., Harel, I., Tzahor, E., Tajbakhsh, S., Christ, B., Huang, R. 2010; 137 (17): 2961-2971


    In vertebrates, body musculature originates from somites, whereas head muscles originate from the cranial mesoderm. Neck muscles are located in the transition between these regions. We show that the chick occipital lateral plate mesoderm has myogenic capacity and gives rise to large muscles located in the neck and thorax. We present molecular and genetic evidence to show that these muscles not only have a unique origin, but additionally display a distinct temporal development, forming later than any other muscle group described to date. We further report that these muscles, found in the body of the animal, develop like head musculature rather than deploying the programme used by the trunk muscles. Using mouse genetics we reveal that these muscles are formed in trunk muscle mutants but are absent in head muscle mutants. In concordance with this conclusion, their connective tissue is neural crest in origin. Finally, we provide evidence that the mechanism by which these neck muscles develop is conserved in vertebrates.

    View details for DOI 10.1242/dev.049726

    View details for Web of Science ID 000280780900017

    View details for PubMedID 20699298

  • Epidermal progenitors give rise to Merkel cells during embryonic development and adult homeostasis JOURNAL OF CELL BIOLOGY Van Keymeulen, A., Mascre, G., Youseff, K. K., Harel, I., Michaux, C., De Geest, N., Szpalski, C., Achouri, Y., Bloch, W., Hassan, B. A., Blanpain, C. 2009; 187 (1): 91-100


    Merkel cells (MCs) are located in the touch-sensitive area of the epidermis and mediate mechanotransduction in the skin. Whether MCs originate from embryonic epidermal or neural crest progenitors has been a matter of intense controversy since their discovery >130 yr ago. In addition, how MCs are maintained during adulthood is currently unknown. In this study, using lineage-tracing experiments, we show that MCs arise through the differentiation of epidermal progenitors during embryonic development. In adults, MCs undergo slow turnover and are replaced by cells originating from epidermal stem cells, not through the proliferation of differentiated MCs. Conditional deletion of the Atoh1/Math1 transcription factor in epidermal progenitors results in the absence of MCs in all body locations, including the whisker region. Our study demonstrates that MCs arise from the epidermis by an Atoh1-dependent mechanism and opens new avenues for study of MC functions in sensory perception, neuroendocrine signaling, and MC carcinoma.

    View details for DOI 10.1083/jcb.200907080

    View details for Web of Science ID 000270452800012

    View details for PubMedID 19786578

  • Distinct Origins and Genetic Programs of Head Muscle Satellite Cells DEVELOPMENTAL CELL Harel, I., Nathan, E., Tirosh-Finkel, L., Zigdon, H., Guimaraes-Camboa, N., Evans, S. M., Tzahor, E. 2009; 16 (6): 822-832


    Adult skeletal muscle possesses a remarkable regenerative capacity, due to the presence of satellite cells, adult muscle stem cells. We used fate-mapping techniques in avian and mouse models to show that trunk (Pax3(+)) and cranial (MesP1(+)) skeletal muscle and satellite cells derive from separate genetic lineages. Similar lineage heterogeneity is seen within the head musculature and satellite cells, due to their shared, heterogenic embryonic origins. Lineage tracing experiments with Isl1Cre mice demonstrated the robust contribution of Isl1(+) cells to distinct jaw muscle-derived satellite cells. Transplantation of myofiber-associated, Isl1-derived satellite cells into damaged limb muscle contributed to muscle regeneration. In vitro experiments demonstrated the cardiogenic nature of cranial- but not trunk-derived satellite cells. Finally, overexpression of Isl1 in the branchiomeric muscles of chick embryos inhibited skeletal muscle differentiation in vitro and in vivo, suggesting that this gene plays a role in the specification of cardiovascular and skeletal muscle stem cell progenitors.

    View details for DOI 10.1016/j.devcel.2009.05.007

    View details for Web of Science ID 000267203700009

    View details for PubMedID 19531353

  • The contribution of Islet1-expressing splanchnic mesoderm cells to distinct branchiomeric muscles reveals significant heterogeneity in head muscle development DEVELOPMENT Nathan, E., Monovich, A., Tirosh-Finkel, L., Harrelson, Z., Rousso, T., Rinon, A., Harel, I., Evans, S. M., Tzahor, E. 2008; 135 (4): 647-657


    During embryogenesis, paraxial mesoderm cells contribute skeletal muscle progenitors, whereas cardiac progenitors originate in the lateral splanchnic mesoderm (SpM). Here we focus on a subset of the SpM that contributes to the anterior or secondary heart field (AHF/SHF), and lies adjacent to the cranial paraxial mesoderm (CPM), the precursors for the head musculature. Molecular analyses in chick embryos delineated the boundaries between the CPM, undifferentiated SpM progenitors of the AHF/SHF, and differentiating cardiac cells. We then revealed the regionalization of branchial arch mesoderm: CPM cells contribute to the proximal region of the myogenic core, which gives rise to the mandibular adductor muscle. SpM cells contribute to the myogenic cells in the distal region of the branchial arch that later form the intermandibular muscle. Gene expression analyses of these branchiomeric muscles in chick uncovered a distinct molecular signature for both CPM- and SpM-derived muscles. Islet1 (Isl1) is expressed in the SpM/AHF and branchial arch in both chick and mouse embryos. Lineage studies using Isl1-Cre mice revealed the significant contribution of Isl1(+) cells to ventral/distal branchiomeric (stylohyoid, mylohyoid and digastric) and laryngeal muscles. By contrast, the Isl1 lineage contributes to mastication muscles (masseter, pterygoid and temporalis) to a lesser extent, with virtually no contribution to intrinsic and extrinsic tongue muscles or extraocular muscles. In addition, in vivo activation of the Wnt/beta-catenin pathway in chick embryos resulted in marked inhibition of Isl1, whereas inhibition of this pathway increased Isl1 expression. Our findings demonstrate, for the first time, the contribution of Isl1(+) SpM cells to a subset of branchiomeric skeletal muscles.

    View details for DOI 10.1242/dev.007989

    View details for Web of Science ID 000252679600005

    View details for PubMedID 18184728