ZFIN Person: Roy, Sudipto

ZFIN ID: ZDB-PERS-001220-3

ZFIN ID: ZDB-PERS-001220-3

Roy, Sudipto

Email:	sudiptor@imcb.a-star.edu.sg
URL:	http://www.imcb.a-star.edu.sg/research/research_group/development_biology/6000000107_article.html
Affiliation:	Sudipto Roy Lab
Address:	Institute of Molecular and Cell Biology Proteos, 61 Biopolis Drive Singapore, 138673 Singapore
Country:	Singapore
Phone:	+65-6586-9744 (Office), -9741 (Lab)
Fax:	+65-6779-1117
ORCID ID:

BIOGRAPHY AND RESEARCH INTERESTS

Our laboratory investigates the cellular and genetic mechanisms that determine pattern during myogenesis and neurogenesis. We use a combination of genetic, molecular and cell biological techniques in the zebrafish and the fruit fly Drosophila to analyse these processes. Much of our current work focuses on the u-boot and iguana mutations that affect distinct steps in the Hedgehog-mediated induction of distinct muscle cells in the somite as well as cell-types in the neural tube of the zebrafish embryo. Our work on Drosophila centres around dissecting the developmental events involved in the specification of the adult muscle fibres of the fly and the segregation of cell fates in the embryonic nervous system.

PUBLICATIONS

Rayamajhi, D., Ege, M., Ukhanov, K., Ringers, C., Zhang, Y., Jung, I., D'Gama, P.P., Li, S.S., Cosacak, M.I., Kizil, C., Park, H.C., Yaksi, E., Martens, J.R., Brody, S.L., Jurisch-Yaksi, N., Roy, S. (2024) The forkhead transcription factor Foxj1 controls vertebrate olfactory cilia biogenesis and sensory neuron differentiation. PLoS Biology. 22:e3002468e3002468

Makrogkikas, S., Cheng, R.K., Lu, H., Roy, S. (2023) A conserved function of Pkhd1l1, a mammalian hair cell stereociliary coat protein, in regulating hearing in zebrafish. Journal of neurogenetics. 37(3):85-92

Mendieta-Serrano, M.A., Dhar, S., Ng, B.H., Narayanan, R., Lee, J.J.Y., Ong, H.T., Toh, P.J.Y., Röllin, A., Roy, S., Saunders, T.E. (2022) Slow muscles guide fast myocyte fusion to ensure robust myotome formation despite the high spatiotemporal stochasticity of fusion events. Developmental Cell. 57(17):2095-2110.e5

Mytlis, A., Kumar, V., Qiu, T., Deis, R., Hart, N., Levy, K., Masek, M., Shawahny, A., Ahmad, A., Eitan, H., Nather, F., Adar-Levor, S., Birnbaum, R.Y., Elia, N., Bachmann-Gagescu, R., Roy, S., Elkouby, Y.M. (2022) Control of meiotic chromosomal bouquet and germ cell morphogenesis by the zygotene cilium. Science (New York, N.Y.). 376(6599):eabh3104

Szenker-Ravi, E., Ott, T., Khatoo, M., de Bellaing, A.M., Goh, W.X., Chong, Y.L., Beckers, A., Kannesan, D., Louvel, G., Anujan, P., Ravi, V., Bonnard, C., Moutton, S., Schoen, P., Fradin, M., Colin, E., Megarbane, A., Daou, L., Chehab, G., Di Filippo, S., Rooryck, C., Deleuze, J.F., Boland, A., Arribard, N., Eker, R., Tohari, S., Ng, A.Y., Rio, M., Lim, C.T., Eisenhaber, B., Eisenhaber, F., Venkatesh, B., Amiel, J., Crollius, H.R., Gordon, C.T., Gossler, A., Roy, S., Attie-Bitach, T., Blum, M., Bouvagnet, P., Reversade, B. (2021) Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates. Nature Genetics. 54(1):62-72

Gui, M., Farley, H., Anujan, P., Anderson, J.R., Maxwell, D.W., Whitchurch, J.B., Botsch, J.J., Qiu, T., Meleppattu, S., Singh, S.K., Zhang, Q., Thompson, J., Lucas, J.S., Bingle, C.D., Norris, D.P., Roy, S., Brown, A. (2021) De novo identification of mammalian ciliary motility proteins using cryo-EM. Cell. 184(23):5791-5806.e19

D'Gama, P.P., Qiu, T., Cosacak, M.I., Rayamajhi, D., Konac, A., Hansen, J.N., Ringers, C., Acuña-Hinrichsen, F., Hui, S.P., Olstad, E.W., Chong, Y.L., Lim, C.K.A., Gupta, A., Ng, C.P., Nilges, B.S., Kashikar, N.D., Wachten, D., Liebl, D., Kikuchi, K., Kizil, C., Yaksi, E., Roy, S., Jurisch-Yaksi, N. (2021) Diversity and function of motile ciliated cell types within ependymal lineages of the zebrafish brain. Cell Reports. 37:109775

Ma, J., Scott, C.A., Ho, Y.N., Mahabaleshwar, H., Marsay, K.S., Zhang, C., Teow, C.K., Ng, S.S., Zhang, W., Tergaonkar, V., Partridge, L.J., Roy, S., Amaya, E., Carney, T.J. (2021) Matriptase activation of Gq drives epithelial disruption and inflammation via RSK and DUOX. eLIFE. 10:

Zhou, F., Rayamajhi, D., Ravi, V., Narasimhan, V., Chong, Y.L., Lu, H., Venkatesh, B., Roy, S. (2020) Conservation as well as divergence in Mcidas function underlies the differentiation of multiciliated cells in vertebrates. Developmental Biology. 465(2):168-177

Lu, H., Shagirova, A., Goggi, J.L., Yeo, H.L., Roy, S. (2020) Reissner fibre-induced urotensin signalling from cerebrospinal fluid-contacting neurons prevents scoliosis of the vertebrate spine. Biology Open. 9(5):

Xie, H., Kang, Y., Wang, S., Zheng, P., Chen, Z., Roy, S., Zhao, C. (2020) E2f5 is a versatile transcriptional activator required for spermatogenesis and multiciliated cell differentiation in zebrafish. PLoS Genetics. 16:e1008655

Lu, H., Anujan, P., Zhou, F., Zhang, Y., Chong, Y.L., Bingle, C.D., Roy, S. (2019) Mcidas mutant mice reveal a two-step process for the specification and differentiation of multiciliated cells in mammals. Development (Cambridge, England). 146(6):

Zhang, X., Jia, S., Chen, Z., Chong, Y.L., Xie, H., Feng, D., Wu, X., Song, D.Z., Roy, S., Zhao, C. (2018) Cilia-driven cerebrospinal fluid flow directs expression of urotensin neuropeptides to straighten the vertebrate body axis. Nature Genetics. 50(12):1666-1673

Chong, Y.L., Zhang, Y., Zhou, F., Roy, S. (2018) Distinct requirements of E2f4 versus E2f5 activity for multiciliated cell development in the zebrafish embryo. Developmental Biology. 443(2):165-172

Lu, H., Galeano, M.C.R., Ott, E., Kaeslin, G., Kausalya, P.J., Kramer, C., Ortiz-Brüchle, N., Hilger, N., Metzis, V., Hiersche, M., Tay, S.Y., Tunningley, R., Vij, S., Courtney, A.D., Whittle, B., Wühl, E., Vester, U., Hartleben, B., Neuber, S., Frank, V., Little, M.H., Epting, D., Papathanasiou, P., Perkins, A.C., Wright, G.D., Hunziker, W., Gee, H.Y., Otto, E.A., Zerres, K., Hildebrandt, F., Roy, S., Wicking, C., Bergmann, C. (2017) Mutations in DZIP1L, which encodes a ciliary-transition-zone protein, cause autosomal recessive polycystic kidney disease. Nature Genetics. 49:1025–1034

Zhang, W., Roy, S. (2017) Myomaker is required for the fusion of fast-twitch myocytes in the zebrafish embryo. Developmental Biology. 423(1):24-33

Zhang, W., Roy, S. (2016) The zebrafish fast myosin light chain mylpfa:H2B-GFP transgene is a useful tool for in vivo imaging of myocyte fusion in the vertebrate embryo. Gene expression patterns : GEP. 20(2):106-10

Zhou, F., Narasimhan, V., Shboul, M., Chong, Y.L., Reversade, B., Roy, S. (2015) Gmnc Is a Master Regulator of the Multiciliated Cell Differentiation Program. Current biology : CB. 25(24):3267-73

Boyd, P.J., Cunliffe, V.T., Roy, S., Wood, J.D. (2015) Sonic hedgehog functions upstream of disrupted-in-schizophrenia 1 (disc1): implications for mental illness. Biology Open. 4(10):1336-43

Narasimhan, V., Hjeij, R., Vij, S., Loges, N.T., Wallmeier, J., Koerner-Rettberg, C., Werner, C., Thamilselvam, S.K., Boey, A., Choksi, S., Pennekamp, P., Roy, S., Omran, H. (2015) Mutations in CCDC11, Which Encodes a Coiled-coil Containing Ciliary Protein, Causes situs inversus Due to Dysmotility of Monocilia in the Left-Right Organizer. Human Mutation. 36(3):307-18

Lu, H., Toh, M.T., Narasimhan, V., Thamilselvam, S.K., Choksi, S.P., Roy, S. (2015) A function for the Joubert syndrome protein Arl13b in ciliary membrane extension and ciliary length regulation. Developmental Biology. 397(2):225-36

Choksi, S.P., Babu, D., Lau, D., Yu, X., Roy, S. (2014) Systematic discovery of novel ciliary genes through functional genomics in the zebrafish. Development (Cambridge, England). 141:3410-9

Irimia, M., Tena, J.J., Alexis, M., Fernandez-Miñan, A., Maeso, I., Bogdanovic, O., de la Calle-Mustienes, E., Roy, S.W., Gómez-Skarmeta, J.L., and Fraser, H.B. (2012) Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome research. 22(12):2356-2367

Vij, S., Rink, J.C., Ho, H.K., Babu, D., Eitel, M., Narasimhan, V., Tiku, V., Westbrook, J., Schierwater, B., and Roy, S. (2012) Evolutionarily Ancient Association of the FoxJ1 Transcription Factor with the Motile Ciliogenic Program. PLoS Genetics. 8(11):e1003019

Yu, X., Lau, D., Ng, C.P., and Roy, S. (2011) Cilia-driven fluid flow as an epigenetic cue for otolith biomineralization on sensory hair cells of the inner ear. Development (Cambridge, England). 138(3):487-494

Rochlin, K., Yu, S., Roy, S., and Baylies, M.K. (2010) Myoblast fusion: When it takes more to make one. Developmental Biology. 341(1):66-83

Tay, S.Y., Yu, X., Wong, K.N., Panse, P., Ng, C.P., and Roy, S. (2010) The iguana/DZIP1 protein is a novel component of the ciliogenic pathway essential for axonemal biogenesis. Developmental Dynamics : an official publication of the American Association of Anatomists. 239(2):527-534

Liew, H.P., Choksi, S.P., Wong, K.N., and Roy, S. (2008) Specification of vertebrate slow-twitch muscle fiber fate by the transcriptional regulator Blimp1. Developmental Biology. 324(2):226-235

Yu, X., Ng, C.P., Habacher, H., and Roy, S. (2008) Foxj1 transcription factors are master regulators of the motile ciliogenic program. Nature Genetics. 40(12):1445-1453

Srinivas, B.P., Woo, J., Leong, W.Y., and Roy, S. (2007) A conserved molecular pathway mediates myoblast fusion in insects and vertebrates. Nature Genetics. 39(6):781-786

Roy, S. (2007) Genetic analysis of the vertebrate hedgehog-signaling pathway using muscle cell fate specification in the zebrafish embryo. Methods in molecular biology (Clifton, N.J.). 397(1):55-66

Lee, B.C., and Roy, S. (2006) Blimp-1 is an essential component of the genetic program controlling development of the pectoral limb bud. Developmental Biology. 300(2):623-634

Xu, J., Srinivas, B.P., Tay, S.Y., Mak, A., Yu, X., Lee, S.G., Yang, H., Govindarajan, K.R., Leong, B., Bourque, G., Mathavan, S., and Roy, S. (2006) Genome-wide Expression Profiling in the Zebrafish Embryo Identifies Target Genes Regulated by Hedgehog Signaling During Vertebrate Development. Genetics. 174(2):735-752

Tay, S.Y., Ingham, P.W., and Roy, S. (2005) A homologue of the Drosophila kinesin-like protein Costal2 regulates Hedgehog signal transduction in the vertebrate embryo. Development (Cambridge, England). 132(4):625-634

Roy, S., and Ng, T. (2004) Blimp-1 specifies neural crest and sensory neuron progenitors in the zebrafish embryo. Current biology : CB. 14(19):1772-1777

Wolff, C., Roy, S., Lewis, K.E., Schauerte, H., Joerg-Rauch, G., Kirn, A., Weiler, C., Geisler, R., Haffter, P., Ingham, P.W. (2004) iguana encodes a novel zinc-finger protein with coiled-coil domains essential for Hedgehog signal transduction in the zebrafish embryo. Genes & Development. 18(13):1565-1576

Nakano, Y., Kim, H.R., Kawakami, A., Roy, S., Schier, A.F., and Ingham, P.W. (2004) Inactivation of dispatched 1 by the chameleon mutation disrupts Hedgehog signalling in the zebrafish embryo. Developmental Biology. 269(2):381-392

Baxendale, S., Davison, C., Muxworthy, C., Wolff, C., Ingham, P.W., and Roy, S. (2004) The B-cell maturation factor Blimp-1 specifies vertebrate slow-twitch muscle fiber identity in response to Hedgehog signaling. Nature Genetics. 36(1):88-93

Wolff, C., Roy, S., and Ingham, P.W. (2003) Multiple muscle cell identities induced by distinct levels and timing of hedgehog activity in the zebrafish embryo. Current biology : CB. 13(14):1169-1181

Roy, S., Qiao, T., Wolff, C., and Ingham, P.W. (2001) Hedgehog signaling pathway is essential for pancreas specification in the zebrafish embryo. Current biology : CB. 11(17):1358-1363

Roy, S., Wolff, C., and Ingham, P.W. (2001) The u-boot mutation identifies a Hedgehog-regulated myogenic switch for fiber-type diversification in the zebrafish embryo. Genes & Development. 15(12):1563-1576

Lewis, K.E., Currie, P.D., Roy, S., Schauerte, H., Haffter, P., and Ingham, P.W. (1999) Control of muscle cell-type specification in the zebrafish embryo by hedgehog signalling. Developmental Biology. 216(2):469-480

Roy, S. (1994) Development of the zebrafish nervous system: Mechanisms of cellfate specification and axonal pathfinding in the central nervous system and periphery. Curr. Sci. Bangalore. 66(9):629-633

NON-ZEBRAFISH PUBLICATIONS
(i) DeSimone, S., Coelho, C., Roy, S., VijayRaghavan, K., and White, K. (1996). ERECT WING, the Drosophila member of a family of DNA binding proteins is required in imaginal myoblasts for flight muscle development. Development 120, 31-39.

(ii) Roy, S., Shashidhara, L. S., and VijayRaghavan, K. (1997). Muscles in the Drosophila second thoracic segment are patterned independently of autonomous homeotic gene function. Current Biology 7, 222-227.

(iii) Roy, S. and VijayRaghavan, K. (1997). Homeotic genes and the regulation of myoblast migration, fusion, and fibre-specific gene expression during adult myogenesis in Drosophila . Development 124, 3333-3341.

(iv) Roy, S. and VijayRaghavan, K. (1998). Patterning muscles using organisers: Larval muscles and imaginal myoblasts actively interact to pattern the dorsal longitudinal flight muscles of Drosophila. Journal of Cell Biology 141, 1135-1145.

(v) Anant, S., Roy, S., and VijayRaghavan, K. (1998). Twist and Notch negatively regulate adult muscle differentiation in Drosophila. Development 125, 1361-1369.

(vi) Roy, S., and VijayRaghavan, K. (1999). Muscle pattern diversification in Drosophila: The story of imaginal myogenesis. BioEssays 21, 486-498.

(vii) Landgraf, M., Roy, S., Prokop, A., VijayRaghavan, K., and Bate, M. (1999). even skipped determines the dorsal outgrowth of motor axons in Drosophila. Neuron 22, 43-52.

(viii) Roy, S. and Ingham, P. W. (2002). Hedgehogs tryst with the cell cycle. J. Cell Sci. 115, 4393-4397.