Functional analysis of the evolutionarily conserved cis-regulatory elements on the sox17 gene in zebrafish.
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.
Chan
Tzu-Min
TM
Division of Molecular and Genomic Medicine, National Health Research Institutes, Taiwan, ROC.
Chao
Chung-Hao
CH
Wang
Horng-Dar
HD
Yu
Yen-Ju
YJ
Yuh
Chiou-Hwa
CH
D000818:Animals; D001483:Base Sequence; D004252:DNA Mutational Analysis; D004707:Endoderm / Q000502:physiology; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D006801:Humans; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D050814:Octamer Transcription Factor-3 / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D055747:SOX Transcription Factors / Q000235:genetics / Q000378:metabolism; D055760:SOXF Transcription Factors / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D015398:Signal Transduction / Q000502:physiology; D015027:Zebrafish / Q000235:genetics / Q000378:metabolism; D029961:Zebrafish Proteins / Q000235:genetics / Q000378:metabolism
D050814:Octamer Transcription Factor-3; C085437:Pou5f3 protein, zebrafish; D011993:Recombinant Fusion Proteins; D055747:SOX Transcription Factors; D055760:SOXF Transcription Factors; D029961:Zebrafish Proteins; C491603:sox17 protein, zebrafish; C438614:sox32 protein, zebrafish