ZFIN ID: ZDB-PERS-960805-487
Sampath, Karuna
Email: K.Sampath@warwick.ac.uk
URL: http://www2.warwick.ac.uk/fac/med/research/biomedical/sampathlab
Affiliation: Sampath Lab
Address: Division of Biomedical Sciences Warwick Medical School University of Warwick Coventry CV4 7AJ United Kingdom
Country: United Kingdom
Phone: (44) 024 765 73412
ORCID ID: 0000-0002-0729-1977

Research Interests:

Maternal Nodal and regulation of Nodal signalling

Functions and regulation of non-coding nodal RNA

RNAs with coding and non-coding roles in development (cncRNAs)

RNA transport, localization, translational control

Polarity, microtubule dynamics

Methods to interrogate functions and dynamics of RNAs and RBPs

Research Summary:
Research in the Sampath laboratory focuses on fundamental mechanisms that control development and differentiation of embryonic progenitors and stem cells, and the molecular mechanisms underlying these processes. We are investigating the roles and regulation of RNAs and RNA-binding proteins (RBPs) in vertebrates using zebrafish embryos and human cells as experimental systems. We use genetic, genomic, imaging, proteomic, and embryological approaches to focus on the following themes: 1) Roles and regulation of maternal nodal RNA as a paradigm for RNAs with both coding and non-coding functions (cncRNAs) 2) Regulation of developmental signaling by RNA elements, RBPs, and RNA regulons, following on our work on translational control of nodal/squint RNA 3) Microtubule based transport and localization of RNAs, and 4) Human fetal and maternal disorders arising from mutations in RNA control elements and RBPs.

Pinto, C.S., Mishima, M., Sampath, K. (2020) Tools of the trade: studying actin in zebrafish. Histochemistry and cell biology. 154(5):481-493
Syed, J., Palani, S., Clarke, S.T., Asad, Z., Bottrill, A.R., Jones, A.M.E., Sampath, K., Balasubramanian, M.K. (2019) Expanding the Zebrafish Genetic Code through Site-Specific Introduction of Azido-lysine, Bicyclononyne-lysine, and Diazirine-lysine. International Journal of Molecular Sciences. 20(10):
Zaucker, A., Kumari, P., Sampath, K. (2019) Zebrafish embryogenesis - A framework to study regulatory RNA elements in development and disease. Developmental Biology. 457(2):172-180
Yi, X., Yu, J., Ma, C., Dong, G., Shi, W., Li, H., Li, L., Luo, L., Sampath, K., Ruan, H., Huang, H. (2019) The effector of Hippo signaling, Taz, is required for formation of the micropyle and fertilization in zebrafish. PLoS Genetics. 15:e1007408
Ng, X.W., Sampath, K., Wohland, T. (2018) Fluorescence Correlation and Cross-Correlation Spectroscopy in Zebrafish. Methods in molecular biology (Clifton, N.J.). 1863:67-105
Winata, C.L., Łapiński, M., Pryszcz, L., Vaz, C., Bin Ismail, M.H., Nama, S., Hajan, H.S., Lee, S.G.P., Korzh, V., Sampath, P., Tanavde, V., Mathavan, S. (2017) Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal to zygotic transition. Development (Cambridge, England). 145(1)
Zaucker, A., Nagorska, A., Kumari, P., Hecker, N., Wang, Y., Huang, S., Cooper, L., Sivashanmugam, L., VijayKumar, S., Brosens, J., Gorodkin, J., Sampath, K. (2017) Translational co-regulation of a ligand and inhibitor by a conserved RNA element. Nucleic acids research. 46(1):104-119
Quach, H.N., Tao, S., Vrljicak, P., Joshi, A., Ruan, H., Sukumaran, R., Varshney, G.K., LaFave, M.C., Screen Team, T.D., Burgess, S.M., Winkler, C., Emelyanov, A., Parinov, S., Sampath, K. (2017) Expression Data for a Multifunctional Mutagenesis System for Analysis of Gene Function in Zebrafish. ZFIN Direct Data Submission.
Wang, Y., Wang, X., Wohland, T., Sampath, K. (2016) Extracellular interactions and ligand degradation shape the nodal morphogen gradient. eLIFE. 5:e13879
Vrljicak, P., Tao, S., Varshney, G.K., Quach, H.N., Joshi, A., LaFave, M.C., Burgess, S.M., Sampath, K. (2016) Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. G3 (Bethesda). 6(4):805-17
Quach, H.N., Tao, S., Vrljicak, P., Joshi, A., Ruan, H., Sukumaran, R., Varshney, G.K., LaFave, M.C., Screen Team, T.D., Burgess, S.M., Winkler, C., Emelyanov, A., Parinov, S., Sampath, K. (2015) A Multifunctional Mutagenesis System for Analysis of Gene Function in Zebrafish. G3 (Bethesda). 5(6):1283-99
Young, T., Poobalan, Y., Tan, E.K., Tao, S., Ong, S., Wehner, P., Schwenty-Lara, J., Lim, C.Y., Sadasivam, A., Lovatt, M., Wang, S.T., Ali, Y., Borchers, A., Sampath, K., Dunn, N.R. (2014) The PDZ domain protein Mcc is a novel effector of non-canonical Wnt signaling during convergence and extension in zebrafish. Development (Cambridge, England). 141:3505-16
Kumari, P., Gilligan, P.C., Lim, S., Tran, L.D., Winkler, S., Philp, R., and Sampath, K. (2013) An essential role for maternal control of Nodal signaling. eLIFE. 2:e00683
Lim, S., Wang, Y., Yu, X., Huang, Y., Featherstone, M.S., and Sampath, K. (2013) A simple strategy for heritable chromosomal deletions in zebrafish via the combinatorial action of targeting nucleases. Genome biology. 14(7):R69
Tran, L.D., Hino, H., Quach, H., Lim, S., Shindo, A., Mimori-Kiyosue, Y., Mione, M., Ueno, N., Winkler, C., Hibi, M., and Sampath, K. (2012) Dynamic microtubules at the vegetal cortex predict the embryonic axis in zebrafish. Development (Cambridge, England). 139(19):3644-3652
Lim, S., Kumari, P., Gilligan, P., Quach, H.N., Mathavan, S., and Sampath, K. (2012) Dorsal activity of maternal squint is mediated by a non-coding function of the RNA. Development (Cambridge, England). 139(16):2903-2915
Gilligan, P.C., Kumari, P., Lim, S., Cheong, A., Chang, A., and Sampath, K. (2011) Conservation defines functional motifs in the squint/nodal-related 1 RNA dorsal localization element. Nucleic acids research. 39(8):3340-9
Tao, S., Cai, Y., and Sampath, K. (2009) The Integrator subunits function in hematopoiesis by modulating Smad/BMP signaling. Development (Cambridge, England). 136(16):2757-2765
Tian, J., Andrée, B., Jones, C.M., and Sampath, K. (2008) The pro-domain of the zebrafish Nodal-related protein Cyclops regulates its signaling activities. Development (Cambridge, England). 135(15):2649-2658
Gore, A.V., Cheong, A., Gilligan, P.C., and Sampath, K. (2007) Gore et al. reply. Nature. 450(7167):E2-E4
Ramasamy, S., Wang, H., Quach, H.N., and Sampath, K. (2006) Zebrafish Staufen1 and Staufen2 are required for the survival and migration of primordial germ cells. Developmental Biology. 292(2):393-406
Gore, A.V., Maegawa, S., Cheong, A., Gilligan, P.C., Weinberg, E.S., and Sampath, K. (2005) The zebrafish dorsal axis is apparent at the four-cell stage. Nature. 438(7070):1030-1035
Tian, J., and Sampath, K. (2004) Formation and Functions of the Floor Plate. In Fish Development and Genetics - the Zebrafish and Medaka Models. Gong, Z. and Korh, V., Eds. Book series of "Molecular Aspects of Fish and Marine Biology". 239(9)
Tian, J., Yam, C., Balasundaram, G., Wang, H., Gore, A., and Sampath, K. (2003) A temperature-sensitive mutation in the nodal-related gene cyclops reveals that the floor plate is induced during gastrulation in zebrafish. Development (Cambridge, England). 130(14):3331-3342
Gore, A.V., and Sampath, K. (2002) Localization of transcripts of the zebrafish morphogen Squint is dependent on egg activation and the microtubule cytoskeleton. Mechanisms of Development. 112(1-2):153-156
Sampath, K., Rubinstein, A.L., Cheng, A.H.S., Liang, J.O., Fekany, K., Solnica-Krezel, L., Korzh, V., Halpern, M.E., and Wright, C.V.E. (1998) Induction of the zebrafish ventral brain and floorplate requires cyclops/nodal signalling. Nature. 395:185-189
Sampath, K. and Stuart, G.W. (1996) Developmental expression of class III and IV POU domain genes in the zebrafish. Biochemical and Biophysical Research Communications. 219:565-571
Sampath, K. (1995) Expression of POU domain genes in zebrafish development. Ph.D. Thesis.

CncRNAs: RNAs with both coding and non-coding roles in development.
Sampath K1, Ephrussi A2. Development. 143(8):1234-41. doi: 10.1242/dev.133298. 2016

Keeping a lid on nodal: transcriptional and translational repression of nodal signalling.
Karuna Sampath, Elizabeth J. Robertson. Open Biol. 2016, 6 150200; DOI: 10.1098/rsob.150200.

P Kumari and K Sampath. cncRNAs: Bi-functional RNAs with protein coding and non-coding functions. Seminars in Cell and Developmental Biology. doi:10.1016/j.semcdb.2015.10.024 (2015).

Gilligan, P, P Kumari, S Lim, A Cheong, A Chang and K Sampath. Conservation defines functional motifs in the squint/nodal-related 1 RNA Dorsal Localization Element. Nucleic Acids Research doi: 10.1093/nar/gkq1185 (2010).

Tao, S and K Sampath. Alternative splicing of Smads in differentiation and tissue homeostasis.
Development, Growth & Differentiation 52: 335-342 (2010).

Sampath, K., Cheng, A.M.S., Frisch, A. and Wright, C.V.E. (1997). Functional differences among Xenopus nodal-related genes in left-right axis determination. Development 124, 3293-3303.

Lowe, L.A., Supp, D.M., Sampath, K., Yokoyama, T., Wright, C.V.E., Potter, S.S., Overbeek, P. and Kuehn, M.R. (1996). Conserved left-right asymmetry of nodal expression and alterations in murine situs inversus. Nature 381, 158-161.

Stuart, G. W., Zhu, Z., Sampath, K. and King, M.W. (1995). POU-domain genes from the flatworm Dugesia tigrina. Gene 161, 299-300.