ZFIN ID: ZDB-PERS-960805-111
Chitnis, Ajay
Email: chitnisa@mail.nih.gov
Affiliation: Chitnis Lab
Address: Unit on Vertebrate Neural Development Laboratory of Molecular Genetics NIH/NICHD Building 6B, Room 3B-315 9000 Rockville Pike Bethesda, MD 20892 USA
Country: United States
Phone: (301) 435-8262
Fax: (301) 496-0243

Our lab studies how interactions between cells during early development lead to the self-organization of a functional nervous system in zebrafish. The laboratory uses a combination of cellular, molecular and genetic tools to identify genetic regulatory networks that direct early development in the nervous system. We also build computational models to understand how interactions identified through biological experiments lead to the emergence of patterned development. Current projects are directed toward understanding the genetic regulatory networks that coordinate cell fate and morphogenesis during development of the zebrafish hindbrain and the lateral line system.

Faucz, F.R., Horvath, A.D., Assié, G., Almeida, M.Q., Szarek, E., Boikos, S., Angelousi, A., Levy, I., Maria, A.G., Chitnis, A., Antonescu, C., Claus, R., Bertherat, J., Plass, C., Eng, C., Stratakis, C.A. (2023) Embryonic stem cell factor FOXD3 (Genesis) defects in gastrointestinal stromal tumors. Endocrine-related cancer. 30(10):
Sinclair, J.W., Hoying, D.R., Bresciani, E., Nogare, D.D., Needle, C.D., Berger, A., Wu, W., Bishop, K., Elkahloun, A.G., Chitnis, A., Liu, P., Burgess, S.M. (2021) The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration. NPJ Regenerative medicine. 6:55
Dalle Nogare, D.E., Natesh, N., Vishwasrao, H.D., Shroff, H., Chitnis, A.B. (2020) Zebrafish Posterior Lateral Line primordium migration requires interactions between a superficial sheath of motile cells and the skin. eLIFE. 9:
Guo, M., Li, Y., Su, Y., Lambert, T., Nogare, D.D., Moyle, M.W., Duncan, L.H., Ikegami, R., Santella, A., Rey-Suarez, I., Green, D., Beiriger, A., Chen, J., Vishwasrao, H., Ganesan, S., Prince, V., Waters, J.C., Annunziata, C.M., Hafner, M., Mohler, W.A., Chitnis, A.B., Upadhyaya, A., Usdin, T.B., Bao, Z., Colón-Ramos, D., La Riviere, P., Liu, H., Wu, Y., Shroff, H. (2020) Rapid image deconvolution and multiview fusion for optical microscopy. Nature Biotechnology. 38:1337-1346
Dalle Nogare, D., Chitnis, A.B. (2019) NetLogo agent-based models as tools for understanding the self-organization of cell fate, morphogenesis and collective migration of the zebrafish posterior Lateral Line primordium. Seminars in cell & developmental biology. 100:186-198
Chitnis, A., Nogare, D.D. (2018) Time-lapse imaging beyond the diffraction limit. Methods (San Diego, Calif.). 150:32-41
Neelathi, U.M., Dalle Nogare, D., Chitnis, A.B. (2018) Cxcl12a induces snail1b expression to initiate collective migration and sequential Fgf-dependent neuromast formation in the zebrafish posterior lateral line primordium.. Development (Cambridge, England). 145(14):
Zheng, W., Wu, Y., Winter, P., Fischer, R., Nogare, D.D., Hong, A., McCormick, C., Christensen, R., Dempsey, W.P., Arnold, D.B., Zimmerberg, J., Chitnis, A., Sellers, J., Waterman, C., Shroff, H. (2017) Adaptive optics improves multiphoton super-resolution imaging. Nature Methods. 14(9):869-872
Nogare, D.D., Chitnis, A.B. (2017) A framework for understanding morphogenesis and migration of the zebrafish posterior Lateral Line primordium. Mechanisms of Development. 148:69-78
Knutsdottir, H., Zmurchok, C., Bhaskar, D., Palsson, E., Dalle Nogare, D., Chitnis, A., Edelstein-Keshet, L. (2017) Polarization and migration in the zebrafish posterior lateral line system. PLoS Computational Biology. 13:e1005451
Nogare, D.D., Nikaido, M., Somers, K., Head, J., Piotrowski, T., Chitnis, A. (2017) In toto imaging of the migrating Zebrafish lateral line primordium at single cell resolution. Developmental Biology. 422(1):14-23
Matsuda, M., Rand, K., Palardy, G., Shimizu, N., Ikeda, H., Nogare, D.D., Itoh, M., Chitnis, A.B. (2016) Epb41l5 competes with Delta as a substrate for Mib1 to coordinate specification and differentiation of neurons. Development (Cambridge, England). 143(17):3085-96
Dalle Nogare, D., Chitnis, A.B. (2015) Connecting physical cues and tissue patterning. eLIFE. 4:e11375
Palardy, G., Chitnis, A.B. (2015) Identification of the Mind Bomb1 Interaction Domain in Zebrafish DeltaD. PLoS One. 10:e0127864
Winter, P.W., York, A.G., Nogare, D.D., Ingaramo, M., Christensen, R., Chitnis, A., Patterson, G.H., Shroff, H. (2014) Two-photon instant structured illumination microscopy improves the depth penetration of super-resolution imaging in thick scattering samples. Optica. 1:181-191
Dalle Nogare, D., Somers, K., Rao, S., Matsuda, M., Reichman-Fried, M., Raz, E., Chitnis, A.B. (2014) Leading and trailing cells cooperate in collective migration of the zebrafish Posterior Lateral Line primordium. Development (Cambridge, England). 141(16):3188-96
York, A.G., Chandris, P., Nogare, D.D., Head, J., Wawrzusin, P., Fischer, R.S., Chitnis, A., and Shroff, H. (2013) Instant super-resolution imaging in live cells and embryos via analog image processing. Nature Methods. 10(11):1122-1126
Matsuda, M., Nogare, D.D., Somers, K., Martin, K., Wang, C., and Chitnis, A.B. (2013) Lef1 regulates Dusp6 to influence neuromast formation and spacing in the zebrafish posterior lateral line primordium. Development (Cambridge, England). 140(11):2387-2397
Ernst, S., Liu, K., Agarwala, S., Moratscheck, N., Avci, M.E., Nogare, D.D., Chitnis, A.B., Ronneberger, O., and Lecaudey, V. (2012) Shroom3 is required downstream of FGF signalling to mediate proneuromast assembly in zebrafish. Development (Cambridge, England). 139(24):4571-4581
Ball, E.R., Matsuda, M.M., Dye, L., Hoffmann, V., Zerfas, P.M., Szarek, E., Rich, A., Chitnis, A.B., and Stratakis, C.A. (2012) Ultra-structural identification of interstitial cells of Cajal in the zebrafish Danio rerio. Cell and tissue research. 349(2):483-491
York, A.G., Parekh, S.H., Nogare, D.D., Fischer, R.S., Temprine, K., Mione, M., Chitnis, A.B., Combs, C.A., and Shroff, H. (2012) Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy. Nature Methods. 9(7):749-754
Dong, Z., Yang, N., Yeo, S.Y., Chitnis, A., and Guo, S. (2012) Intralineage directional notch signaling regulates self-renewal and differentiation of asymmetrically dividing radial glia. Neuron. 74(1):65-78
Chitnis, A.B., Nogare, D.D., and Matsuda, M. (2012) Building the posterior lateral line system in zebrafish. Developmental Neurobiology. 72(3):234-255
Veleri, S., Bishop, K., Dalle Nogare, D.E., English, M.A., Foskett, T.J., Chitnis, A., Sood, R., Liu, P., and Swaroop, A. (2012) Knockdown of Bardet-Biedl Syndrome Gene BBS9/PTHB1 Leads to Cilia Defects. PLoS One. 7(3):e34389
Matsuda, M., and Chitnis, A.B. (2010) Atoh1a expression must be restricted by Notch signaling for effective morphogenesis of the posterior lateral line primordium in zebrafish. Development (Cambridge, England). 137(20):3477-3487
Yamamoto, M., Morita, R., Mizoguchi, T., Matsuo, H., Isoda, M., Ishitani, T., Chitnis, A.B., Matsumoto, K., Crump, J.G., Hozumi, K., Yonemura, S., Kawakami, K., and Itoh, M. (2010) Mib-Jag1-Notch signalling regulates patterning and structural roles of the notochord by controlling cell-fate decisions. Development (Cambridge, England). 137(15):2527-2537
Ma, H., Blake, T., Chitnis, A., Liu, P., and Balla, T. (2009) Crucial role of phosphatidylinositol 4-kinase III{alpha} in development of zebrafish pectoral fin is linked to phosphoinositide 3-kinase and FGF signaling. Journal of Cell Science. 122(Pt 23):4303-4310
Hava, D., Forster, U., Matsuda, M., Cui, S., Link, B.A., Eichhorst, J., Wiesner, B., Chitnis, A., and Abdelilah-Seyfried, S. (2009) Apical membrane maturation and cellular rosette formation during morphogenesis of the zebrafish lateral line. Journal of Cell Science. 122(Pt 5):687-695
So, J.H., Chun, H.S., Bae, Y.K., Kim, H.S., Park, Y.M., Huh, T.L., Chitnis, A.B., Kim, C.H., and Yeo, S.Y. (2009) Her4 is necessary for establishing peripheral projections of the trigeminal ganglia in zebrafish. Biochemical and Biophysical Research Communications. 379(1):22-26
Matsuda, M., and Chitnis, A.B. (2009) Interaction with Notch determines endocytosis of specific Delta ligands in zebrafish neural tissue. Development (Cambridge, England). 136(2):197-206
Diks, S.H., Sartori da Silva, M.A., Hillebrands, J.L., Bink, R.J., Versteeg, H.H., van Rooijen, C., Brouwers, A., Chitnis, A.B., Peppelenbosch, M.P., and Zivkovic, D. (2008) d-Asb11 is an essential mediator of canonical Delta-Notch signalling. Nature cell biology. 10(10):1190-1198
Keller, M.J., and Chitnis, A.B. (2007) Insights into the evolutionary history of the vertebrate zic3 locus from a teleost-specific zic6 gene in the zebrafish, Danio rerio. Development genes and evolution. 217(7):541-547
Yeo, S.Y., and Chitnis, A.B. (2007) Jagged-mediated Notch signaling maintains proliferating neural progenitors and regulates cell diversity in the ventral spinal cord. Proceedings of the National Academy of Sciences of the United States of America. 104(14):5913-5918
Yeo, S.Y., Kim, M., Kim, H.S., Huh, T.L., and Chitnis, A.B. (2007) Fluorescent protein expression driven by her4 regulatory elements reveals the spatiotemporal pattern of Notch signaling in the nervous system of zebrafish embryos. Developmental Biology. 301(2):555-567
Koo, B.K., Lim, H.S., Song, R., Yoon, M.J., Yoon, K.J., Moon, J.S., Kim, Y.W., Kwon, M.C., Yoo, K.W., Kong, M.P., Lee, J., Chitnis, A.B., Kim, C.H., and Kong, Y.Y. (2005) Mind bomb 1 is essential for generating functional Notch ligands to activate Notch. Development (Cambridge, England). 132(15):3459-3470
Lorent, K., Yeo, S.Y., Oda, T., Chandrasekharappa, S., Chitnis, A., Matthews, R.P., and Pack, M. (2004) Inhibition of Jagged-mediated Notch signaling disrupts zebrafish biliary development and generates multi-organ defects compatible with an Alagille syndrome phenocopy. Development (Cambridge, England). 131(22):5753-5766
Chitnis, A.B., and Itoh, M. (2004) Exploring alternative models of rostral-caudal patterning in the zebrafish neurectoderm with computer simulations. Current opinion in genetics & development. 14(4):415-421
Kikuchi, Y., Verkade, H., Reiter, J.F., Kim, C.H., Chitnis, A.B., Kuroiwa, A., and Stainier, D.Y. (2004) Notch signaling can regulate endoderm formation in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 229(4):756-762
Nojima, H., Shimizu, T., Kim, C.H., Yabe, T., Bae, Y.K., Muraoka, O., Hirata, T., Chitnis, A., Hirano, T., and Hibi, M. (2004) Genetic evidence for involvement of maternally derived Wnt canonical signaling in dorsal determination in zebrafish. Mechanisms of Development. 121(4):371-386
Bingham, S., Chaudhari, S., Vanderlaan, G., Itoh, M., Chitnis, A., and Chandrasekhar, A. (2003) Neurogenic phenotype of mind bomb mutants leads to severe patterning defects in the zebrafish hindbrain. Developmental Dynamics : an official publication of the American Association of Anatomists. 228(3):451-463
Park, S.-H., Yeo, S.-Y., Yoo, K.-W., Hong, S.-K., Lee, S., Rhee, M., Chitnis, A.B., and Kim, C.-H. (2003) Zath3, a neural basic helix-loop-helix gene, regulates early neurogenesis in the zebrafish. Biochemical and Biophysical Research Communications. 308(1):184-190
Dorsky, R.I., Itoh, M., Moon, R.T., and Chitnis, A. (2003) Two tcf3 genes cooperate to pattern the zebrafish brain. Development (Cambridge, England). 130(9):1937-1947
Geling, A., Itoh, M., Tallafuss, A., Chapouton, P., Tannhauser, B., Kuwada, J.Y., Chitnis, A.B., and Bally-Cuif, L. (2003) bHLH transcription factor Her5 links patterning to regional inhibition of neurogenesis at the midbrain-hindbrain boundary. Development (Cambridge, England). 130(8):1591-1604
Itoh, M., Kim, C.-H., Palardy, G., Oda, T., Jiang, Y.-J., Maust, D., Yeo, S.-Y., Lorick, K., Wright, G.J., Ariza-McNaughton, L., Weissman, A.M., Lewis, J., Chandrasekharappa, S.C., and Chitnis, A.B. (2003) Mind Bomb is a ubiquitin ligase that is essential for efficient activation of notch signaling by Delta. Developmental Cell. 4(1):67-82
Kim, S.-H., Shin, J., Park, H.-C., Yeo, S.-Y., Hong, S.-K., Han, S., Rhee, M., Kim, C.-H., Chitnis, A.B., and Huh, T.-L. (2002) Specification of an anterior neuroectoderm patterning by Frizzled8a-mediated Wnt8b signalling during late gastrulation in zebrafish. Development (Cambridge, England). 129(19):4443-4455
Itoh, M., Kudoh, T., Dedekian, M., Kim, C.-H., and Chitnis, A.J. (2002) A role for iro1 and iro7 in the establishment of an anteroposterior compartment of the ectoderm adjacent to the midbrain-hindbrain boundary. Development (Cambridge, England). 129(10):2317-2327
Appel, B. and Chitnis, A. (2002) Neurogenesis and specification of neuronal identity. Results and problems in cell differentiation. 40:237-251
Belting, H.G., Hauptmann, G., Meyer, D., Abdelilah-Seyfried, S., Chitnis, A., Eschbach, C., Söll, I., Thisse, C., Thisse, B., Artinger, K., Lunde, K., and Driever, W. (2001) spiel ohne grenzen/pou2 is required during establishment of the zebrafish midbrain-hindbrain boundary organizer. Development (Cambridge, England). 128(21):4165-4176
Lawson, N.D., Scheer, N., Pham, V.N., Kim, C.-H., Chitnis, A.B., Campos-Ortega, J.A., and Weinstein, B.M. (2001) Notch signaling is required for arterial-venous differentiation during embryonic vascular development. Development (Cambridge, England). 128(19):3675-3683
Dawid, I.B. and Chitnis, A.B. (2001) Lim homeobox genes and the CNS: a close relationship. Neuron. 30(2):301-303
Itoh, M. and Chitnis, A.B. (2001) Expression of proneural and neurogenic genes in the zebrafish lateral line primordium correlates with selection of hair cell fate in neuromasts. Mechanisms of Development. 102(1-2):263-266
Blake, T., Adya, N., Kim, C.H., Oates, A.C., Zon, L., Chitnis, A., Weinstein, B.M., and Liu, P.P. (2000) Zebrafish homolog of the leukemia gene CBFB: its expression during embryogenesis and its relationship to scl and gata-1 in hematopoiesis. Blood. 96(13):4178-4184
Park, H.-C., Kim, C.-H., Bae, Y.-K., Yee, S.-Y., Kim, S.-H., Hong, S.-K., Shin, J., Yoo, K.-W., Hibi, M., Hirano, T., Miki, N., Chitnis, A.B., and Huh, T.-L. (2000) Analysis of upstream elements in the HuC promoter leads to the establishment of transgenic zebrafish with fluorescent neurons. Developmental Biology. 227(2):279-293
Kim, C.H., Oda, T., Itoh, M., Jiang, D., Artinger, K.B., Chandrasekharappa, S.C., Driever, W., and Chitnis, A.B. (2000) Repressor activity of Headless/Tcf3 is essential for vertebrate head formation. Nature. 407(6806):913-916
Gothilf, Y., Coon, S.L., Toyama, R., Chitnis, A., Namboodiri, M.A.A., and Klein, D.C. (1999) Zebrafish serotonin N-acetyltransferase-2: marker for development of pineal photoreceptors and circadian clock function. Endocrinology. 140(10):4895-4903
Artinger, K.B., Chitnis, A.B., Mercola, M., and Driever, W. (1999) Zebrafish narrowminded suggests a genetic link between formation of neural crest and primary sensory neurons. Development (Cambridge, England). 126(18):3969-3979
Guo, S., Wilson, S.W., Cooke, S., Chitnis, A.B., Driever, W., and Rosenthal, A. (1999) Mutations in the zebrafish unmask shared regulatory pathways controlling the development of catecholaminergic neurons. Developmental Biology. 208:473-487
Chitnis, A.B. and Dawid, I.B. (1999) Neurogenesis in zebrafish embryos. In The Zebrafish: Biology. H.W. Detrich, L.I. Zon, and M. Westerfield, eds. Methods Cell Biol.. 59:367-386
Chitnis, A. and Kintner, C. (1996) The role of vertebrate neurogenic genes in early neurogenesis. International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience. 14:58
Chitnis, A.B., Patel, C.K., Kim, S., and Kuwada, J.Y. (1992) A specific brain tract guides follower growth cones in two regions of the zebrafish brain. Journal of neurobiology. 23:845-854
Chitnis, A.B. and Kuwada, J.Y. (1991) Elimination of a brain tract increases errors in pathfinding by follower growth cones in the zebrafish embryo. Neuron. 7:277-285
Chitnis, A.B. (1991) Pathfinding by identified growth cones in the embryonic zebrafish brain (Brachydanio rerio, brain tracts). Ph.D. Thesis.
Chitnis, A.B., Patel, C.K., and Kuwada, J.Y. (1991) A specific brain tract guides follower growth cones in two regions of the zebrafish brain. Soc. Neurosci. Abstr.. 17:40
Bernhardt, R.R., Chitnis, A.B., Lindamer, L., and Kuwada, J.Y. (1990) Identification of spinal neurons in the embryonic and larval zebrafish. The Journal of comparative neurology. 302:603-616
Chitnis, A.B. and Kuwada, J.Y. (1990) Axonogenesis in the brain of zebrafish embryos. The Journal of neuroscience : the official journal of the Society for Neuroscience. 10:1892-1905
Kuwada, J.Y., Bernhardt, R.R., and Chitnis, A.B. (1990) Pathfinding by identified growth cones in the spinal cord of zebrafish embryos. The Journal of neuroscience : the official journal of the Society for Neuroscience. 10:1299-1308
Kuwada, J.Y., Bernhardt, R.R., Chitnis, A.B., and Nguyen, N. (1989) Pathfinding by spinal growth cones in the zebrafish embryo. Soc. Neurosci. Abstr.. 15:1028
Kuwada, J.Y., Chitnis, A., and Lindamer, L.A. (1987) Stereotyped pathfinding by identified growth cones in the embryonic spinal cord. Soc. Neurosci. Abstr.. 13:1220