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

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.

Sox17 and chordin are required for formation of Kupffer's vesicle and left‐right asymmetry determination in zebrafish

“…The reduction in sox17 expression after chd MO injection suggests that Chd may be upstream of sox17 in the regulatory network. This finding is consistent with the previous observations that BMP regulates endoderm formation by inhibiting endoderm markers in the ventral domain (Chan et al 2009). …”

“…Bmp can repress sox17 expression (Chan et al, 2009), suggesting that Chd and Sox17 are part of an epistatic relationship in which Chd is upstream of Sox17, but such a regulatory loop would not explain the observed synergism. Thus it seems more likely that Chd and Sox17 have parallel functions in the DFC that together promote their developmental progression in the formation of the KV.…”

Nestin Is Essential for Zebrafish Brain and Eye Development through Control of Progenitor Cell Apoptosis

“…The protocol of fluorescence in situ hybridization is as described above with some modifications [14]. The RNA probe was labeled by dinitrophenyl (DNP).…”

VEGFD regulates blood vascular development by modulating SOX18 activity

“…We did not knock down Vegfa (a/b), Plc-ϒ, or Sox17 because in these cases early phenotypes have been reported that would be epistatic to specific later vascular defects in double loss-offunction animals. 5,41,42 We examined the overall gross phenotype and the developing vasculature of injected embryos at 48 hours post fertilization (hpf) (Figure 1). At this stage, the dorsal aorta (DA) and posterior cardinal vein (PCV) have formed distinct vessels in control embryos (Figure 1Bi-iii and Table 1) and arteriovenous separation can be clearly visualized in transverse sections through the trunk ( Figure 1C and Di-iii).…”