A genome-wide approach for understanding of the development of the Ciona embryos Yutaka Satou Department of Zoology, Graduate School of Science, Kyoto University After we determined the genome sequence of Ciona intestinalis, we have taken a genome-based approach to understand mechanisms behind the embryonic development of this animal. First, we comprehensively listed up regulatory genes, i.e. genes encoding sequence-specific transcription factors and signaling molecules, and then determined their expression patterns from the 1-cell stage to the late tailbud stage. We comprehensively knocked-down regulatory genes expressed in the early embryos, and reconstructed the regulatory networks among them. Recently we performed chromatin immunoprecipitation on 11 core transcription factors important for endomesoderm specification. We found that 58 of the 76 interactions are direct. We also identified the tightly interconnected cis-regulatory networks. We experimentally validated the network connections by overexpression of three transcription factors. The regulatory networks we revealed also gave us many implications that remained to be resolved. One of them is the function of ADMP (anti-dorsalizing morphogenetic protein), which belongs to a BMP family. As in the Xenopus embryo, this protein was shown to be involved in the dorsoventral patterning of the embryo, but the detailed mechanism was not necessarily unsolved. We again surveyed the genome for candidate genes involved in the BMP-signaling under a less strict condition. As a result, we identified a novel antagonist specific for ADMP. This antagonist played an essential role in the dorso-ventral patterning of the tailbud embryo. We also found that these two functional related genes, ADMP and its antagonist, were related to each other at the level of transcription.

A genome-wide approach for understanding of the development of the Ciona embryos

Yutaka Satou

Department of Zoology, Graduate School of Science, Kyoto University

After we determined the genome sequence of Ciona intestinalis, we have taken a genome-based approach to understand mechanisms behind the embryonic development of this animal. First, we comprehensively listed up regulatory genes, i.e. genes encoding sequence-specific transcription factors and signaling molecules, and then determined their expression patterns from the 1-cell stage to the late tailbud stage. We comprehensively knocked-down regulatory genes expressed in the early embryos, and reconstructed the regulatory networks among them. Recently we performed chromatin immunoprecipitation on 11 core transcription factors important for endomesoderm specification. We found that 58 of the 76 interactions are direct. We also identified the tightly interconnected cis-regulatory networks. We experimentally validated the network connections by overexpression of three transcription factors.

The regulatory networks we revealed also gave us many implications that remained to be resolved. One of them is the function of ADMP (anti-dorsalizing morphogenetic protein), which belongs to a BMP family. As in the Xenopus embryo, this protein was shown to be involved in the dorsoventral patterning of the embryo, but the detailed mechanism was not necessarily unsolved. We again surveyed the genome for candidate genes involved in the BMP-signaling under a less strict condition. As a result, we identified a novel antagonist specific for ADMP. This antagonist played an essential role in the dorso-ventral patterning of the tailbud embryo. We also found that these two functional related genes, ADMP and its antagonist, were related to each other at the level of transcription.