AUTHOR=Xing Cencan , Zeng Zehua , Li Yaqi , Gong Bo , Shen Weimin , Shah Roshan , Yan Lu , Du Hongwu , Meng Anming 

TITLE=Regulatory factor identification for nodal genes in zebrafish by causal inference

JOURNAL=Frontiers in Cell and Developmental Biology

VOLUME=10

YEAR=2022

URL=https://www.frontiersin.org/journals/cell-and-developmental-biology/articles/10.3389/fcell.2022.1047363

DOI=10.3389/fcell.2022.1047363

ISSN=2296-634X

ABSTRACT=<p>Activation of <italic>nodal</italic> genes is critical for mesoderm and endoderm induction. Our previous study reported that zebrafish <italic>nodal</italic> genes <italic>ndr1</italic>/<italic>squint</italic> and <italic>ndr2</italic>/<italic>cyclops</italic> 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 we found that Hwa/β-catenin and Smad2 are the cause of <italic>ndr1</italic> activation, while Eomesa is the cause of <italic>ndr2</italic> activation. Mechanistically, the different <italic>cis</italic>-regulatory regions of <italic>ndr1</italic> and <italic>ndr2</italic> bound by Eomesa, β-catenin, and Smad2 were screened out <italic>via</italic> ChIP-qPCR and verified by the transgene constructs. The marginal GFP expression driven by <italic>ndr1 transgenesis</italic> could be diminished without both maternal Eomesa and Hwa/β-catenin, while Eomesa, not β-catenin, could bind and activate <italic>ndr2</italic> demonstrated by <italic>ndr2</italic> transgenesis. Thus, the distinct regulation of <italic>ndr1</italic>/<italic>ndr2</italic> relies on different <italic>cis</italic>-regulatory regions.</p>