Sudipto ROY

Genes, Development and Disease


Sudipto ROY
Lab Location: #8-12   Email:   Tel: 65869744

Sudipto Roy was educated at some of the most distinguished institutions in India. After schooling from Goethals Memorial in Kurseong, Darjeeling, and La Martiniere for Boys in Calcutta, he graduated with a first class first (honours) in zoology from Presidency College in Calcutta in 1991, and again secured the first position during his M.Sc. studies at the Jawaharlal Nehru University, New Delhi, in 1993. He then moved to the National Centre for Biological Sciences in Bangalore, where he obtained a Ph.D. in developmental genetics, studying the cellular and genetic basis of muscle and neuronal development in the fruit fly, Drosophila, with K. VijayRaghavan. During this period, he travelled to Brandeis University in the US and to Cambridge University, England, as a visiting graduate student. He began post-doctoral studies with Philip Ingham at the Centre for Developmental and Biomedical Genetics at the University of Sheffield, England, in 1998, where he initiated research into vertebrate development using the zebrafish embryo. Dr. Roy has been the recipient of several awards and fellowships from international organizations that include the Company of Biologists (UK), the Wellcome Trust (UK), the Human Frontiers Science Program (HFSP) and the European Molecular Biology Organization (EMBO). In 2002, he was honoured with the prestigious Indian National Science Academy Young Scientist Medal by the President of India, the late Dr. Abdul Kalam. In the same year, he joined the Institute of Molecular and Cell Biology in Singapore as a Young Investigator, and was a Principal Investigator (Assistant Professor) from 2003-2008. Dr. Roy is currently a Senior Principal Investigator, and is an adjunct Associate Professor with the Department of Biological Sciences and the Department of Paediatrics of the National University of Singapore, and was visiting Professor on sabbatical with the National Institute of Biomedical Genomics, Kalyani, India (Jul-Dec, 2017). Over the years, his science has made important contributions to our understanding of many aspects of developmental biology that include how hox genes regulate muscle patterning in flies, the discovery of blimp1 as a selector gene for zebrafish slow-twitch muscle, the genetic pathways regulating vertebrate myoblast fusion, the identification of Kif7 and Dzip1 as ciliary proteins in the vertebrate Hedgehog pathway and elucidation of the master regulatory roles of the FoxJ1, Gmnc and Mcidas transcription factors in programming ciliary differentiation. His current research utilizes the zebrafish and the mouse to study the mechanistic basis of human diseases, notably those arising from dysfunction of cilia and flagella. In 2012, he was awarded the STAR Employee Award from the Agency for Science, Technology and Research of Singapore (A*STAR) for his achievements and services to scientific research in Singapore. Recently, he has developed a liking for communicating science to the general public through writing, and in 2015 won a merit award at the inaugural Asian Scientist Writing Prize competition. In 2016, he was conferred the first distinguished alumnus award on the occasion of the silver jubilee celebrations of the National Centre for Biological Sciences, India.



Cilia and Ciliopathies

Cilia and flagella are hair-like filamentous organelles that have been conserved evolutionarily in the eukaryotes. Our high school lectures have taught us how protozoans, like Paramecium, use beating cilia to swim around in water. We have also learnt that certain tissues in our own bodies have motile cilia. For instance, motile cilia that line the length of our respiratory tract beat to clear mucus that entangles pathogens and pollutants which enter through the nose as we breathe. Cilia also perform sensory functions. Besides locomotion, cilia in the protozoans are used for phototactic and chemotactic behavior. In the metazoans, many sense organs have cilia that have lost the motility apparatus and have become dedicated sensory organelles. Photoreceptors in the eye and olfactory neurons in the nose have such highly specialized sensory cilia. Several decades ago it was discovered that in the vertebrates, not just the sense organs, but almost every cell of the body differentiates a single immotile cilium at the end of cell division or after differentiation. Although regarded as vestigial structures for a long time, it has now become apparent that these so called primary cilia also function as hubs for a large number of signaling pathways that operate during embryonic development and in adult physiology.

Figure 1:  Foxj1 is the master regulator of motile cilia biogenesis. (A) Expression of foxj1 in Kupffer’s vesicle (arrow) of a gastrulating zebrafish embryo. Kupffer’s vesicle functions like the mammalian node in specifying left-right asymmetry. (B) foxj1 expression in the spinal canal (short arrow) and kidney duct (long arrow) of an 18 hour post-fertilization zebrafish embryo. C) Over-expression of Foxj1 can induce ectopic motile cilia. D) A large cohort of known ciliary genes are transcriptionally regulated by Foxj1.

The filamentous part of the cilium that extends out of the cell surface is called the axoneme, and consists of a microtubule scaffold enveloped by an extension of the cell membrane. The axoneme remains anchored to the basal body that is derived from the mother centriole. The ultrastructure of cilia can vary, depending on their function. Sensory or primary cilia typically have 9 radially arranged microtubule doublets (9+0 pattern), whereas the motile cilia, in addition, usually have a central pair of singlet microtubules (9+2 pattern). Furthermore, the motile cilia have dynein arms on the peripheral microtubule doublets that confer motility. A wide spectrum of human diseases arises from defects in cilia formation and function. Abnormalities of the primary cilia result in syndromes like Alstrom, Bardet-Biedl, Joubert, Meckel-Gruber, Senior-Loken as well as other conditions like polycystic kidney disease and nephronophthisis. Symptoms of these diseases range from orofacial deformities, abnormalities in limb development, retinal degeneration, as well as formation of kidney cysts. On the other hand, dysfunctional motile cilia can also instigate pathological consequences, exemplified by disorders such as Primary Ciliary Dyskinesia (PCD) and Kartagener syndrome. Individuals afflicted with PCD have immotile or dyskinetic cilia and flagella, and, consequently, defective mucociliary clearance, chronic pulmonary infections and infertility (in males). Many individuals with PCD show perturbations in left-right asymmetry of internal organs (Kartagener syndrome) that ensue from defective motility of cilia in the embryonic node. Fluid flow over the node, driven by rotary beating of motile cilia, is thought to trigger a signaling cascade that breaks the initial bilateral symmetry of the embryo. Thus, elucidating the developmental basis of ciliary biogenesis will not only further our understanding of key events in embryogenesis , but will also broaden our insights into the etiology of ciliopathies. Such a profound impact of the cilium on human health is indeed the motivation behind the intensive research being carried out world-wide on the biology of this organelle.
We are using genetic and cell biological analysis in the zebrafish embryo and the mouse to understand the regulatory pathways that direct ciliogenesis, the activities of many of the individual proteins that constitute structural and functional components of cilia, and how different developmental and physiological pathways use cilia as platforms for their signaling activity. Over the past few years, we have made important contributions to the field of ciliary biology, some of which are highlighted below. In 2004, through positional cloning in zebrafish, we identified a new zinc finger and coiled-coil containing protein, Dzip1, that we subsequently showed to be associated with the ciliary basal bodies, at the transition zone. In 2017, we discovered that mutations in the paralogous gene DZIP1L cause autosomal recessive polycystic kidney disease (ARPKD), by compromising the transition zone, and thereby the trafficking of ciliary membrane proteins PC1 and PC2. In 2005, we published our work on the identification of Kif7, the first vertebrate orthologue of Costal2, a kinesin-like protein in Drosophila, involved in Hedgehog signaling. Several groups have followed up on our findings and have now shown that Kif7 is a ciliary kinesin that is mutated in fetal hydrolethalus, acrocallosal and Joubert syndromes. In a seminal piece of work published in 2008, our group made the pioneering discovery that the forkhead transcription factor FoxJ1 is the master regulator of motile cilia biogenesis. We found that FoxJ1 is not just necessary for motile cilia to form, but is also sufficient to reprogram cells that normally do not make motile cilia to ectopically differentiate this organelle. Inspired by this striking attribute of FoxJ1, we now have undertaken a genome-wide search for the targets genes that are regulated by this transcription factor. We have found that the expression of more than 600 genes is activated by FoxJ1 during ciliogenesis, giving us the first global view of the vertebrate ciliary transcriptome. Many of these genes encode previously described components of the ciliary apparatus; more importantly, the list is replete with many completely novel genes that have not been implicated in cilia formation or function in previous studies. Our current efforts are directed at understanding the contributions of the proteins encoded by these genes in cilium differentiation and function, and their possible roles in the pathogenesis of ciliopathies. In 2015, we showed that mutation of one such target gene, CCDC11, causes heterotaxy and congenital heart disease in humans, by affecting the motility of cilia within the left-right organizer. In the same year, we showed that another FoxJ1 target gene, gmnc, which encodes a coiled-coil domain containing transcription regulator, programs the differentiation of multiciliated cells.

Figure 2:  Transverse sections of a Dzip1l mutant mouse kidney, false coloured and arranged in a spiral form. Note the presence of cysts in the cortical region. (Courtesy M. C. Rondón Galeano).

Figure 3. Skin of a Xenopus tadpole showing scattered multiciliated cells (upper panel). Skin of a tadpole over-expressing Gmnc, showing a lawn of multiciliated cells (lower panel). Cilia were stained with anti-acetylated tubulin antibodies (green), centrioles/basal bodies with g-tubulin antibodies (red) and DNA with DAPI (blue). (Courtesy F. Zhou, B. Reversade and S. Roy).


Department: Sudipto ROY

Name: Hui Li YEO

Designation: Research Officer


Name: Dale Wallace MAXWELL

Designation: ARAP Student


Name: Rachna NARAYANAN

Designation: Collaborator


Name: Chon U CHAN

Designation: Research Fellow


Name: Rayamajhi DHEERAJ

Designation: SINGA Student


Name: Caroline Lei WEE

Designation: Research Fellow


Name: Hao LU

Designation: Research Fellow


Name: Sunandan DHAR

Designation: SINGA Student


Name: Aidana SHAGIROVA

Designation: SINGA Student


Name: Kuan Han LAI

Designation: Collaborator



Designation: ARAP Student



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.
120, 31-39.

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.

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.
124, 3333-3341.

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.

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

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.

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

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, 469-480.

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

Roy, S., Qiao, T., Wolff, C., and Ingham, P. W. (2001).
Hedgehog signalling pathway is essential for pancreas specification in the zebrafish embryo.
Biology 11, 1358-1363.

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
13, 1169-1181.

Nakano, Y., Kim, R., Kawakami, A., Roy, S., Schier, A., and Ingham, P. W. (2004).
Inactivation of dispatched1 by the chameleon mutation disrupts Hedgehog signalling in the zebrafish embryo.
Developmental Biology 269, 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 fibre identity in response to Hedgehog signalling.
Nature Genetics36, 88-93.

Wolff, C.*, Roy, S.*, Lewis, K.E., Schauerte, H., Joerg-Rauch, G., Kirn, A., Geisler, R., Haffter, P., and 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 and Development 18, 1565-1576.

Roy, S. and Ingham, P. W. (2002).
Hedgehog’s tryst with the cell cycle.
Journal of Cell Science
115, 4393-4397.

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

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 zebrafish embryo.
Development 132, 625-634.

Ng, T., Yu, F., and Roy, S. (2006).
A homologue of the vertebrate SET domain and zinc finger protein Blimp-1 regulates terminal differentiation of the tracheal system in the Drosophila embryo.
Development, Genes and Evolution 216, 243-252.

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, 623-634.

Xu, J., Srinivas, B. P., Tay, S. Y., Mak, A., Yu, X., Lee, S. G. P., Yang, H., Govindarajan, K. R., Leong, B., Bourque, G., Mathavan, S., and Roy, S. (2006).
Genome-wide expression profiling in the zebrafish embryo indentifies target genes regulated by Hedgehog signalling during vertebrate development.
Genetics 174, 735-752.

Roy, S. (2007).
Genetic analysis of the vertebrate Hedgehog signalling pathway using muscle cell fate specification in the zebrafish embryo.
Methods in Molecular Biology 394, 55-66.

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, 781-786.

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, 1445-1453.

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

S. Roy. (2009).
The motile cilium in development and disease: emerging new insights.

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

S. Y. Tay, X. Yu, K. N. Wong, P. Panse, C. P. Ng, S. Roy. (2010)
The Iguana/DZIP1 protein is a novel component of the ciliogenic pathway essential for axonemal biogenesis.
Developmental Dynamics

S. Roy. (2010)
The development and function of vertebrate cilia, in (ed.).
Topical Talks:
The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, (London) 2010
(online at

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

S. Roy. (2012)
Hedgehog and cilia: when and how was their marriage solemnized?
Differentiation (40th anniversary special issue “Cilia in Development and Disease”) 83:S43-8.

S. Roy, K. VijayRaghavan. (2012)
Developmental biology: taking flight.
Current Biology

S. Vij, J. C. Rink, H. K. Ho, D. Babu, M. Eitel, V. Narasimhan, V. Tiku, J. Westbrook, B. Schierwater, S. Roy. (2012)
Evolutionarily ancient association of the FoxJ1 transcription factor with the motile ciliogenic program.
PLoS Genetics 8(11): e1003019.

D. Babu and S. Roy. (2013)
Left-right asymmetry: Cilia stir up new surprises in the node.
Open Biology
3, 130052.

S. P. Choksi, G. Lauter, P.  Swoboda, and S. Roy. (2014)
Switching on cilia: transcriptional networks regulating ciliogenesis.
141, 1427-1441.

S. P. Choksi,  D.  Babu, D. Lau, X. Yu  and S. Roy. (2014)
Systematic discovery of novel ciliary genes through functional genomics in the zebrafish.
141, 3410-3419.

H. Lu, M. T. Toh, V. Narasimhan, S. K. Thamilselvam, S. P. Choksi, S. Roy. (2015)
A function for the Joubert syndrome protein Arl13b in ciliary membrane extension and ciliary length regulation.
Developmental Biology 397, 225-236.

V. Narasimhan, R. Hjeij, S. Vij, N. T. Loges, J. Wallmeier, C. Koerner-Rettberg, C. Werner, S. K. Thamilselvam, A. Boey, S. P. Choksi, P. Pennekamp, S. Roy, H. Omran. (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, 307-318.

V. Narasimhan and  S. Roy. (2015).
Cilia: organelles at heart of heart disease.
Current Biology 25, R559-562.

F. Zhou and S. Roy. (2015).
SnapShot: Motile cilia.
Cell 162, 224.

P. Boyd, V. T. Cunliffe, S. Roy* and J. Wood.* (2015).
Sonic hedgehog functions upstream of disrupted-in-schizophrenia 1 (disc1): Implications for mental illness.
Biology Open 4, 1336-1343.

F. Zhou, V. Narasimhan, M.  Shboul, Y. L. Chong, B. Reversade, and S. Roy. (2015).
Gmnc is a master regulator of the multiciliated cell differentiation program.
Current Biology 25, 3267-3273.

Y. Chen, K. T. Chang, D. W. Lian, H. Lu, S. Roy, N. K. Laksmi, Y. Low, G. Krishnaswamy, A. Pierro, C. C. Ong (2016).
The role of ischemia in necrotizing enterocolitis. 
Journal of Pediatric Surgery 8, 1255-1261.

W. Zhang and S. Roy (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 20, 106-110.

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

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

C. Windpassinger, J. Piard, C. Bonnard, M. Alfadhel, S. Lim, X. Bisteau, S. Blouin, A. B. Ali, A. Y. J. Ng, H. Lu, S. Tohari, S. Z. A. Talib, N. van Hul, M. J. Caldez, L. van Maldergem, S. Youssef, V. Coppola, A. de Bruin, L. Tessarollo, H. Choi, V. Rupp, K. Rötzer, P. Roschger, K. Klaushofer, S. Roy, B. Venkatesh, R. Ganger, F. Grill, F. B. Chehida, U. Altunoglu, A. Al Kaissi, B. Reversade and P. Kaldis, P. (2017).
Mutations in CDK10 in humans and mice cause severe growth retardation, spine malformation, and intellectual disabilities.
American Journal of Human Genetics 101, 391-403.

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

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

Ishita Mukherjee, S. Roy*, and S. Chakrabarti*. (2019). 
Identification of important effector proteins in the FOXJ1 transcriptional network associated with ciliogenesis and ciliary function
Frontiers in Genetics 10, 23.

H. Lu, P. Anujan, F. Zhou, Y. Zhang, Y. L. Chong, C. D. Bingle, and S. Roy. (2019).
Mcidas mutant mice reveal a two-step process for the specification and differentiation of multiciliated cells in mammals. 
Development 146, pii: dev172643.

B. Terré, M. Lewis, G. Gil-Gómez, Z. Han, H. Lu, M. Aguilera, N. Prats, S. Roy, H. Zhao, T. H. Stracker. (2019)
Defects in efferent duct multiciliogenesis underlie male infertility in GEMC1, MCIDAS or CCNO deficient mice. 
Development pii: dev162628.

* = Joint first/senior authors.


Lab get-together

The Developmental Biology Journal Vol. 146 (6)

The Developmental Biology Journal Vol. 146 (8)

The Developmental Biology Journal Vol. 423

The Developmental Biology Journal Vol. 397


Hedgehog Signaling Protocols

Xianwen Yu, Doreen Lau, Chee Peng Ng and Sudipto Roy. Cilia-driven fluid flow as an epigenetic cue for otolith biomineralization on sensory hair cells of the inner ear
Development, 2011.

K. Sampath and S. Roy (editors). Live imaging in zebrafish: Insights into development and disease.
World Scientific Press, 2010.

TheDevelopmental Biology Journal

The EMBO Journal

The Genes & Development Journal

Differentiation Journal

Development Journal