Developmental Gene Regulatory Networks in the Zebrafish Embryo and ZebrafishGRNs website

Tzu-Min Chan^{1, 3}, William Longabaugh², Hamid Bolouri², Hua-Ling Chen¹, Wen-Fang Tseng¹, Chung-Hao Chao¹, Te-Hsuan Jang¹, Yu-I Lin¹, Shao-Chin Hung¹, Karthik Prathapachandran¹, Horng-Dar Wang³ and Chiou-Hwa Yuh^{1,4, 5}

詹子民^{1, 3}，William Longabaugh², Hamid Bolouri², 陳華玲¹，曾文芳¹，趙崇豪¹，讓德選¹, 林佑怡¹，洪紹芹¹，Karthik Prathapachandran¹，汪宏達³，喻秋華^{1, 4, 5}

¹Division of Molecular and Genomic Medicine, National Health Research Institute, ²Institute for Systems Biology, Seattle, USA, ³College of Life Science and Institute of Biotechnology, National Tsing-Hua University, ⁴College of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, ⁵Department of Biological Science & Technology National Chiao Tung University

The genomic developmental program operates mainly through the regulated expression of genes encoding transcription factors and signaling pathways. Complex networks of regulatory genetic interactions control developmental cell specification and fates. Development in the zebrafish, Danio rerio, development has been studied extensively and large amounts of experimental data, including information on spatial and temporal gene expression patterns, are available. A wide variety of maternal and zygotic regulatory factors and signaling pathways have been discovered in zebrafish, and these provide a useful starting point for reconstructing of the gene regulatory networks (GRNs) underlying development. In this review, we describe in detail the genetic regulatory subcircuits responsible for dorsoanterior-ventroposterior patterning and endoderm formation. We describe a number of regulatory motifs, which appear to act as the functional building blocks of the GRNs. Different positive feedback loops drive the ventral and dorsal specification processes. Mutual exclusivity in dorsal-ventral polarity in zebrafish is governed by intracellular cross-inhibiting GRN motifs, including vent/dharma and tll1/chordin. The dorsal-ventral axis seems to be determined by competition between two maternally driven positive-feedback loops (one operating on Dharma, the other on Bmp). This is the first systematic approach aimed at developing an integrated model of the GRNs underlying zebrafish development. Comparison of GRNs organizational motifs between different species will provide insights into developmental specification and its evolution.

The online version of the zebrafish GRNs can be found at http://www.zebrafishGRNs.org . The Website is highly user friendly and designed with simple HTML and JavaScript. So there is no need for downloading any of the activex controls which eat a lot of precious time of the researchers. Mouse HBx-Induced induced HCC Network page is under construction and the Home page is under re-construction to make it friendlier to the viewers.