Development of a bioinformatics strategy to search for genes involved in specific metabolic pathways: The case of ESCs

ROHR, CRISTIAN; PARRA, GONZALO; GALIAN, EVANGELINA; YANKILEVICH, PATRICIO; PEREZ CASTRO, CAROLINA

Facultad de Ingeniería de la Universidad Católica de Córdoba (Campus Sur)

Congreso; 2do Congreso Bioinformatica y Biologia Computacional; 2011

Agencia y A2B2C

The study of transcriptional networks involved in various metabolic pathways is fundamental to understand the cellular response. We have developed a strategy based on the use of bioinformatics tools currently available (Biomart, RSATools, DAVID), along with scripts generated by the authors. This strategy was applied to on a systematic search for genes potentially involved in the pluripotent state of embryonic stem cells (ESCSs), determining the possible consensus binding sites for different transcription factors (TFs), Oct4[1], Sox2[2] and Nanog[3], together with complemented analysis of these sites in orthologous genes from different species. Using previously published experimental data (microarray, ChIP on ChIP-and reporter vector) [5], we tested our scripts prediction potential analyzing for the presence of consensus sequences corresponding to these TFs in silico and compared to the real data. Following a comparative analysis between different species, we generated a list of genes including previously reported genes and promise new candidates genes that are potentially regulated by TFs in pluripotent cells. We propose our script is an interesting systematic tool for use in the study of mammalian cell transcriptional networks. 1. N1ichols, J., Zevnik, B., Anastassiadis, K., Niwa, H., Klewe-Nebenius, D.,Chambers, I., Scholer, H., et al.: Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 1998, 95: 379-391. 2. Avilion, A. A., Nicolis, S.K., Pevny, L.H., Perez, L., Vivian, N., Lovell-Badge, R.: Multipotent cell lineages in early mouse development depend on SOX2 function. Genes & Development 2003, 17: 126-140. 3. Mitsui, K., Tokuzawa, Y., Itoh, H., Segawa, K., Murakami, M., Takahashi, K., Maruyama, M., et al.: The Homeoprotein Nanog Is Required for Maintenance of Pluripotency in Mouse Epiblast and ES Cells. Cell 2003, 113: 631-642. 4. Boyer, L. A., Lee, T.I., Cole, M.F., Johnstone, S.E., Levine, S.S., Zucker, J.P., Guenther, M.G., et al.: Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells. Cell 2005, 122: 947-956.