ZFIN ID: ZDB-LAB-141211-1
Laboratory of Zebrafish Developmental Genomics
PI/Director: Winata, Cecilia Lanny
Contact Person: Winata, Cecilia Lanny
Email: cwinata@iimcb.gov.pl
URL: http://www.iimcb.gov.pl/research-focus.html
Address: International Institute of Molecular and Cell Biology in Warsaw Ks. J. Trojdena 4 02-109 Warsaw
Country: Poland
Phone: + 48 22 597 07 68
Fax: + 48 22 597 07 15
Line Designation: waw

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Our lab’s research aims to understand the mechanism of gene regulation during embryonic development in vivo by applying genomics methods in combination with experimental embryology, genetics, and biochemistry. We seek to understand the mechanism by which transcription factors (TFs) and the epigenetic landscape interact to regulate the development of an organ. In addition, we investigate the biological consequences of post-transcriptional modifications on maternal mRNAs, which include cytoplasmic polyadenylation and RNA editing.

Niescierowicz, Katarzyna Post-Doc Pawlak, Michal Post-Doc Sulej, Agata Post-Doc
Lapinski, Maciej Graduate Student Migdal, Maciej Graduate Student Nahia, Karim Abu Graduate Student
Parisi, Costantino Graduate Student Tralle, Eugeniusz Graduate Student Pakula, Adrianna Research Staff

Parisi, C., Vashisht, S., Winata, C.L. (2021) Fish-Ing for Enhancers in the Heart. International Journal of Molecular Sciences. 22(8):
Fricke, T., Smalakyte, D., Lapinski, M., Pateria, A., Weige, C., Pastor, M., Kolano, A., Winata, C., Siksnys, V., Tamulaitis, G., Bochtler, M. (2020) Targeted RNA Knockdown by a Type III CRISPR-Cas Complex in Zebrafish. The CRISPR journal. 3:299-313
Winata, C.L., Dodzian, J., Bialek-Wyrzykowska, U. (2019) The zebrafish as a model for developmental and biomedical research in Poland and beyond. Developmental Biology. 457(2):167-168
Minhas, R., Paterek, A., Łapiński, M., Bazała, M., Korzh, V., Winata, C.L. (2019) A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression. Developmental dynamics : an official publication of the American Association of Anatomists. 248(9):837-849
Pawlak, M., Kedzierska, K.Z., Migdal, M., Nahia, K.A., Ramilowski, J.A., Bugajski, L., Hashimoto, K., Marconi, A., Piwocka, K., Carninci, P., Winata, C.L. (2019) Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development. Genome research. 29(3):506-519
Winata, C.L., Korzh, V. (2018) Zebrafish Zic Genes Mediate Developmental Signaling. Advances in experimental medicine and biology. 1046:157-177
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)
Aksoy, I., Utami, K.H., Winata, C.L., Hillmer, A.M., Rouam, S.L., Briault, S., Davila, S., Stanton, L.W., Cacheux, V. (2017) Personalized genome sequencing coupled with iPSC technology identifies GTDC1 as a gene involved in neurodevelopmental disorders. Human molecular genetics. 26:367-382
Tan, H., Onichtchouk, D., Winata, C. (2016) DANIO-CODE: Toward an Encyclopedia of DNA Elements in Zebrafish. Zebrafish. 13(1):54-60
Kraus, P., Winata, C.L., Lufkin, T. (2015) BAC Transgenic Zebrafish for Transcriptional Promoter and Enhancer Studies. Methods in molecular biology (Clifton, N.J.). 1227:245-58
Utami, K.H., Winata, C.L., Hillmer, A.M., Aksoy, I., Long, H.T., Liany, H., Yan, E.C., Mathavan, S., Hong, S.T., Korzh, V., Sarda, P., Davila, S., Cacheux, V. (2014) Impaired Development Of Neural-Crest Cell Derived Organs and Intellectual Disability Caused By MED13L Haploinsufficiency. Human Mutation. 35(11):1311-20
Aanes, H., Winata, C., Moen, L.F., Østrup, O., Mathavan, S., Collas, P., Rognes, T., and Aleström, P. (2014) Normalization of RNA-sequencing data from samples with varying mRNA levels. PLoS One. 9(2):e89158
Winata, C.L., Kondrychyn, I., Kumar, V., Srinivasan, K.G., Orlov, Y., Ravishankar, A., Prabhakar, S., Stanton, L.W., Korzh, V., and Mathavan, S. (2013) Genome wide analysis reveals zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish. PLoS Genetics. 9(10):e1003852
Lindeman, L.C., Andersen, I.S., Reiner, A.H., Li, N., Aanes, H., Ostrup, O., Winata, C., Mathavan, S., Muller, F., Aleström, P., and Collas, P. (2011) Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation. Developmental Cell. 21(6):993-1004
Korzh, S., Winata, C.L., Zheng, W., Yang, S., Yin, A., Ingham, P., Korzh, V., and Gong, Z. (2011) The interaction of epithelial Ihha and mesenchymal Fgf10 in zebrafish esophageal and swimbladder development. Developmental Biology. 359(2):262-76
Aanes, H., Winata, C.L., Lin, C.H., Chen, J.P., Srinivasan, K.G., Lee, S.G., Lim, A.Y., Hajan, H.S., Collas, P., Bourque, G., Gong, Z., Korzh, V., Aleström, P., and Mathavan, S. (2011) Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome research. 21(8):1328-38
Yin, A., Korzh, S., Winata, C.L., Korzh, V., and Gong, Z. (2011) Wnt signaling is required for early development of zebrafish swimbladder. PLoS One. 6(3):e18431
Ung, C.Y., Lam, S.H., Hlaing, M.M., Winata, C.L., Korzh, S., Mathavan, S., and Gong, Z. (2010) Mercury-induced hepatotoxicity in zebrafish: in vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation. BMC Genomics. 11:212
Winata, C.L., Korzh, S., Kondrychyn, I., Korzh, V., and Gong, Z. (2010) The role of vasculature and blood circulation in zebrafish swimbladder development. BMC Developmental Biology. 10:3
Lindeman, L.C., Winata, C.L., Aanes, H., Mathavan, S., Alestrom, P., and Collas, P. (2010) Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos. The International journal of developmental biology. 54(5):803-813
Winata, C.L., Korzh, S., Kondrychyn, I., Zheng, W., Korzh, V., and Gong, Z. (2009) Development of zebrafish swimbladder: the requirement of Hedgehog signaling in specification and organization of the three tissue layers. Developmental Biology. 331(2):222-236
Korzh, S., Pan, X., Garcia-Lecea, M., Winata, C.L., Pan, X., Wohland, T., Korzh, V., and Gong, Z. (2008) Requirement of vasculogenesis and blood circulation in late stages of liver growth in zebrafish. BMC Developmental Biology. 8(1):84
Lam, S.H., Winata, C.L., Tong, Y., Korzh, S., Lim, W.S., Korzh, V., Spitsbergen, J., Mathavan, S., Miller, L.D., Liu, E.T., and Gong, Z. (2006) Transcriptome Kinetics of Arsenic-induced Adaptive Response in Zebrafish Liver. Physiological Genomics. 27(3):351-361