This repository contains the scripts to reproduce the result of the manuscript Regulatory factors identification for nodal genes in zebrafish by causal inference

Activation of nodal genes is critical for mesoderm and endoderm induction. Our previous study reported that the zebrafish nodal genes ndr1/squint and ndr2/cyclops are coordinately regulated by maternal Eomesa, Hwa-activated β-catenin (Hwa/β-catenin) signaling, and Nodal autoregulation (Nodal/Smad2) signaling. However, the exact contribution and underlying mechanisms are still elusive. Here we applied “causal inference” to evaluate the causal between the independent and dependent variables, and found that Hwa/β-catenin and Smad2 are the cause of ndr1 activation, while Eomesa is the cause of ndr2 activation. Mechanistically, the different cis-regulatory regions of ndr1 and ndr2 bound by Eomesa, β-catenin, and Smad2 were screened out via ChIP-qPCR and verified by the transgene constructs. The marginal GFP expression driven by ndr1 transgenesis could be diminished without both maternal Eomesa and Hwa/β-catenin. While Eomesa, not β-catenin, could bind and activate ndr2 demonstrated by ndr2 transgenesis. Thus, the distinct regulation of ndr1/ndr2 relies on different cis-regulatory regions.

• /data/: the raw data to reproduce the figures
• /result/: the analysis result and figure of the manuscript
• ols and casual inference.ipynb: the raw code to reproduce the ols and casual inference analysis
• ols and plot.ipynb: the raw code to reproduce the ols figure in each time point

• Zehua Zeng (starlitnightly@163.com)