ZFIN ID: ZDB-PERS-971001-7
Holley, Scott
Email: scott.holley@yale.edu
URL: http://www.yale.edu/holleylab
Affiliation: Holley Lab
Address: Department of Molecular, Cellular and Developmental Biology Yale University P.O. Box 208103 New Haven, CT 06520-8103 USA
Country: United States
Phone: (203) 432-3230
Fax: 203-432-5690

Somites are segmentally repeated mesodermal structures within the vertebrate embryo that give rise to the vertebrae and muscle of the trunk and tail. A recent large-scale screen for developmental mutants of the zebrafish, Danio rerio, identified mutations in five complementation groups that affect the anterior-posterior pattern of the somites: fused somites (fss), beamter (bea), after eight (aei), deadly seven (des) and white tail (wit). Both embryological and molecular genetic techniques are being used to further characterize the role that fss, bea, aei, and des play in somitogenesis and to identify the affected genes. Moreover, cross-species experiments will be used to elucidate the extent of any evolutionary conservation of the regulatory networks involved in segmentation. Thus, this analysis is aimed at both understanding the mechanism by which the paraxial mesoderm is segmented in the zebrafish and determining the extent of conservation between species of genetic regulatory networks involved in segmentation.

Genuth, M.A., Kojima, Y., Jülich, D., Kiryu, H., Holley, S.A. (2023) Automated time-lapse data segmentation reveals in vivo cell state dynamics. Science advances. 9:eadf1814eadf1814
Samarasinghe, K.T.G., An, E., Genuth, M.A., Chu, L., Holley, S.A., Crews, C.M. (2022) OligoTRAFTACs: A generalizable method for transcription factor degradation. RSC chemical biology. 3:1144-1153
Smith, S.J., Holley, S.A. (2021) The eye tugs and the nose follows: how inter-tissue adhesion directs olfactory development. EMBO reports. 23(2):e54396
Sun, G., Guillon, E., Holley, S.A. (2021) Integrin intra-heterodimer affinity inversely correlates with integrin activatability. Cell Reports. 35:109230
Samarasinghe, K.T.G., Jaime-Figueroa, S., Burgess, M., Nalawansha, D.A., Dai, K., Hu, Z., Bebenek, A., Holley, S.A., Crews, C.M. (2021) Targeted degradation of transcription factors by TRAFTACs: TRAnscription Factor TArgeting Chimeras. Cell chemical biology. 28(5):648-661.e5
Genuth, M.A., Holley, S.A. (2020) Mechanics as a Means of Information Propagation in Development. BioEssays : news and reviews in molecular, cellular and developmental biology. 42(11):e2000121
Guillon, E., Das, D., Jülich, D., Hassan, A.R., Geller, H., Holley, S. (2020) Fibronectin is a smart adhesive that both influences and responds to the mechanics of early spinal column development. eLIFE. 9:
Das, D., Jülich, D., Schwendinger-Schreck, J., Guillon, E., Lawton, A.K., Dray, N., Emonet, T., O'Hern, C.S., Shattuck, M.D., Holley, S.A. (2019) Organization of Embryonic Morphogenesis via Mechanical Information. Developmental Cell. 49(6):829-839.e5
Das, D., Chatti, V., Emonet, T., Holley, S.A. (2017) Patterned Disordered Cell Motion Ensures Vertebral Column Symmetry. Developmental Cell. 42:170-180.e5
McMillen, P., Chatti, V., Jülich, D., Holley, S.A. (2016) A Sawtooth Pattern of Cadherin 2 Stability Mechanically Regulates Somite Morphogenesis. Current biology : CB. 26(4):542-9
Jülich, D., Cobb, G., Melo, A.M., McMillen, P., Lawton, A.K., Mochrie, S.G., Rhoades, E., Holley, S.A. (2015) Cross-Scale Integrin Regulation Organizes ECM and Tissue Topology. Developmental Cell. 34(1):33-44
Schwendinger-Schreck, J., Kang, Y., Holley, S.A. (2014) Modeling the Zebrafish Segmentation Clock's Gene Regulatory Network Constrained by Expression Data Suggests Evolutionary Transitions Between Oscillating and Non-Oscillating Transcription. Genetics. 197(2):725-38
Dray, N., Lawton, A., Nandi, A., Jülich, D., Emonet, T., and Holley, S.A. (2013) Cell-Fibronectin Interactions Propel Vertebrate Trunk Elongation via Tissue Mechanics. Current biology : CB. 23(14):1335-41
Lawton, A.K., Nandi, A., Stulberg, M.J., Dray, N., Sneddon, M.W., Pontius, W., Emonet, T., and Holley, S.A. (2013) Regulated tissue fluidity steers zebrafish body elongation. Development (Cambridge, England). 140(3):573-582
Stulberg, M.J., Lin, A., Zhao, H., and Holley, S.A. (2012) Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud. Developmental Biology. 369(2):298-307
Trofka, A., Schwendinger-Schreck, J., Brend, T., Pontius, W., Emonet, T., and Holley, S.A. (2012) The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub. Development (Cambridge, England). 139(5):940-947
Neklesa, T.K., Tae, H.S., Schneekloth, A.R., Stulberg, M.J., Corson, T.W., Sundberg, T.B., Raina, K., Holley, S.A., and Crews, C.M. (2011) Small-molecule hydrophobic tagging-induced degradation of HaloTag fusion proteins. Nature Chemical Biology. 7(8):538-43
Brend, T., and Holley, S.A. (2009) Expression of the oscillating gene her1 is directly regulated by hairy/enhancer of split, T-box, and suppressor of hairless proteins in the zebrafish segmentation clock. Developmental Dynamics : an official publication of the American Association of Anatomists. 238(11):2745-2759
Jülich, D., Mould, A.P., Koper, E., and Holley, S.A. (2009) Control of extracellular matrix assembly along tissue boundaries via Integrin and Eph/Ephrin signaling. Development (Cambridge, England). 136(17):2913-2921
Brend, T., and Holley, S.A. (2009) Zebrafish whole mount high-resolution double fluorescent in situ hybridization. Journal of visualized experiments : JoVE. (25)
Mara, A., Schroeder, J., and Holley, S.A. (2008) Two deltaC splice-variants have distinct signaling abilities during somitogenesis and midline patterning. Developmental Biology. 318(1):126-132
Zhang, L., Kendrick, C., Jülich, D., and Holley, S.A. (2008) Cell cycle progression is required for zebrafish somite morphogenesis but not segmentation clock function. Development (Cambridge, England). 135(12):2065-2070
Mara, A., and Holley, S.A. (2007) Oscillators and the emergence of tissue organization during zebrafish somitogenesis. Trends in cell biology. 17(12):593-599
Li, G., Liu, T., Nie, J., Guo, L., Malicki, J., Mara, A., Holley, S.A., Xia, W., and Wong, S.T. (2007) Detection of blob objects in microscopic zebrafish images based on gradient vector diffusion. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 71(10):835-845
Holley, S.A. (2007) The genetics and embryology of zebrafish metamerism. Developmental Dynamics : an official publication of the American Association of Anatomists. 236(6):1422-1449
Mara, A., Schroeder, J., Chalouni, C., and Holley, S.A. (2007) Priming, initiation and synchronization of the segmentation clock by deltaD and deltaC. Nature cell biology. 9(5):523-530
Geisler, R., Rauch, G.J., Geiger-Rudolph, S., Albrecht, A., van Bebber, F., Berger, A., Busch-Nentwich, E., Dahm, R., Dekens, M.P., Dooley, C., Elli, A.F.,Gehring, I., Geiger, H., Geisler, M., Glaser, S., Holley, S., Huber, M., Kerr, A., Kirn, A., Knirsch, M., Konantz, M., Kuchler, A.M., Maderspacher, F., Neuhauss, S.C., Nicolson, T., Ober, E.A., Praeg, E., Ray, R., Rentzsch, B., Rick, J.M., Rief, E., Schauerte, H.E., Schepp, C.P., Schonberger, U., Schonthaler, H.B., Seiler, C., Sidi, S., Söllner, C., Wehner, A., Weiler, C., Nüsslein-Volhard, C. (2007) Large-scale mapping of mutations affecting zebrafish development. BMC Genomics. 8(1):11
Holley, S.A. (2006) Anterior-posterior differences in vertebrate segments: specification of trunk and tail somites in the zebrafish blastula. Genes & Development. 20(14):1831-1837
Julich, D., Hwee, Lim C., Round, J., Nicolaije, C., Schroeder, J., Davies, A., Geisler, R., Lewis, J., Jiang, Y.J., Holley, S.A., Tübingen 2000 Screen Consortium. (2005) beamter/deltaC and the role of Notch ligands in the zebrafish somite segmentation, hindbrain neurogenesis and hypochord differentiation. Developmental Biology. 286(2):391-404
Jülich, D., Geisler, R., Tübingen 2000 Screen Consortium, and Holley, S.A. (2005) Integrinalpha5 and Delta/Notch Signaling Have Complementary Spatiotemporal Requirements during Zebrafish Somitogenesis. Developmental Cell. 8(4):575-586
Holley, S.A. and Takeda, H. (2002) Catching a wave: the oscillator and wavefront that create the zebrafish somite. Seminars in cell & developmental biology. 13(6):481-486
Holley, S.A., Jülich, D., Rauch, G.J., Geisler, R., and Nüsslein-Volhard, C. (2002) her1 and the notch pathway function within the oscillator mechanism that regulates zebrafish somitogenesis. Development (Cambridge, England). 129(5):1175-1183
Prince, V.E., Holley, S.A., Bally-Cuif, L., Prabhakaran, B., Oates, A.C., Ho, R.K., and Vogt, T.F. (2001) Zebrafish lunatic fringe demarcates segmental boundaries. Mechanisms of Development. 105(1-2):175-180
Holley, S.A., Geisler, R., and Nüsslein-Volhard, C. (2000) Control of her1 expression during zebrafish somitogenesis by a Delta-dependent oscillator and an independent wave-front activity. Genes & Development. 14(13):1678-1690
Holley, S.A. and Nüsslein-Volhard, C. (2000) Somitogenesis in Zebrafish. Current topics in developmental biology. 47:248-277
Geisler, R., Rauch, G.J., Baier, H., van Bebber, F., Brobeta, L., Dekens, M.P., Finger, K., Fricke, C., Gates, M.A., Geiger, H., Geiger-Rudolph, S., Gilmour, D., Glaser, S., Gnugge, L., Habeck, H., Hingst, K., Holley, S., Keenan, J., Kirn, A., Knaut, H., Lashkari, D., Maderspacher, F., Martyn, U., Neuhauss, S., Neumann, C., Nicolson, T., Pelegri, F., Ray, R., Rick, J.M., Roehl, H., Roeser, T., Schauerte, H.E., Schier, A.F., Schönberger, U., Schönthaler, H.-B., Schulte-Merker, S., Seydler, C., Talbot, W.S., Weiler, C., Nüsslein-Volhard, C., and Haffter, P. (1999) A radiation hybrid map of the zebrafish genome. Nature Genetics. 23(1):86-89
van Eeden, F.J.M., Holley, S.A., Haffter, P., and Nüsslein-Volhard, C. (1998) Zebrafish segmentation and pair-rule patterning. Developmental genetics. 23:65-76
Holley, S.A. and Ferguson, E.L. (1997) Fish are like flies are like frogs: conservation of dorsal- ventral patterning mechanisms. BioEssays : news and reviews in molecular, cellular and developmental biology. 19(4):281-284

Scott A. Holley, Jeffrey L. Neul, Liliana Attisano, Jeffrey L. Wrana, Yoshiki Sasai, Michael B. O’Conner, Eddy M. De Robertis, and Edwin L. Ferguson. The Xenopus Dorsalizing Factor noggin Ventralizes Drosphila Embryos by Preventing DPP from Activating Its Receptor. Cell 86, 607-617 (1996).

Scott A. Holley, P. David Jackson, Yoshiki Sasai, Bin Lu, Eddy M. De Robertis, F. Michael Hoffmann, Edwin L. Ferguson. A conserved system for dorsal-ventral patterning in insects and vertebrates involving sog and chordin. Nature 376, 249-253 (1995).