Functional analysis of the evolutionarily conserved cis-regulatory elements on the sox17 gene in zebrafish

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2008.11.010 Byline: Tzu-Min Chan (a)(b), Chung-Hao Chao (a)(b), Horng-Dar Wang (b), Yen-Ju Yu (a), Chiou-Hwa Yuh (a)(c)(d) Keywords: Sox17; Sox32; Pou5f1; Transcription regulation; Evolutionarily conserved non-coding region; Zebrafish endoderm development; Gene Regulatory Networks (GRNs) Abstract: The Sox17 is an important transcription factor for endodermal cells (Danio rerio). According to the predictions of the GRNs, based on perturbation experiments and literature search, the sox17 gene is engaged with two other regulatory genes, sox32 and pou5f1. Nodal signaling operated on several endoderm-specific transcription factors to determine the endoderm specification. In addition, endoderm specification requires the Fgf and Bmp signaling pathways to be repressed in the cells which will become endoderm. It is predicted that Nodal activates sox32 and works synergistically with Pou5f1 to activate sox17. Bmp represses the expression of sox17 on the ventral side and Fgf represses it on the dorsal side. The regulatory inputs of sox17 at the genomic sequence level are not known. Here, we have uncovered the relevant sox17 cis-regulatory elements, and examined the specific input predictions of the GRNs. We discovered three conserved modules, A, B, and C, with a synergistic effect among them. We revealed that the Pou5f1-binding element on the B module and the Sox32-binding element on the C module work synergistically. Furthermore, an evolutionarily non-conserved R module exhibits a repressive effect on both the ventral and dorsal side. We have directly demonstrated the structural and functional relationships of the genomic code at this key node of the endoderm GRNs in zebrafish development. This information provides new insight into the complexity of endoderm formation and serves as a valuable resource for the establishment of a complete endoderm gene regulatory network. Author Affiliation: (a) Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC (b) College of Life Science and Institute of Biotechnology, National Tsing-Hua University, Hsin-Chu, Taiwan, ROC (c) College of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsin-Chu, Taiwan, ROC (d) Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan, ROC Article History: Received 30 May 2008; Revised 31 October 2008; Accepted 11 November 2008