Table 1 Representation of regulatory logics in DNFs for expression of genes that initiate expression at the 32-cell stage.
Downstream
genes
DNFs*Cells where gene
expression is activated
in normal embryos
Lhx3/4Foxd˄Fgf9/16/20˄β-cateninA6.1/A6.3/B6.1
NeurogeninFoxd˄Fgf9/16/20˄β-cateninA6.1/A6.3/B6.1
DickkopfFoxd˄Fgf9/16/20˄β-cateninA6.1/A6.3/B6.1
SnailCA-Raf˄Macho-1˅B6.4
Tbx6-r.bB6.1/B6.2
Wnt3CA-Raf˄Macho-1˅B6.4
Tbx6-r.bB6.1/B6.2
Wnt5CA-Raf˄Macho-1˅B6.4
Tbx6-r.bB6.1/B6.2
Bmp3Foxa.a˄FoxdA6.1-4/B6.1/B6.2
Hes.bFoxd˄Fgf9/16/20˅A6.1-4/B6.1/B6.2
¬Sox1/2/3˄¬Hes.a
˄Fgf9/16/20
˄¬Efna.d˄¬Prdm1-r
B6.4
Zic-r.bFoxa.a˄Foxd˄Fgf9/16/20
˄¬β-catenin˅
A6.2/A6.4/B6.2
¬β-catenin˄Macho-1˅B6.4
¬Sox1/2/3˄¬Hes.a
˄Fgf9/16/20
˄¬β-catenin˅
B6.4
Foxa.a˄¬Hes.a˄Fgf9/16/20
˄¬β-catenin
None
Dmrt.aSox1/2/3˄Foxa.a
˄¬Foxd˄Fgf9/16/20˄¬Efna.d
˄¬β-catenin
a6.5
Otx¬β-catenin˄Macho-1˅B6.4
Tbx6-r.a˄Fgf9/16/20˅B6.1/B6.2
Tbx6-r.b˄Fgf9/16/20˅B6.1/B6.2
¬Foxd˄Fgf9/16/20˄¬Efna.d˅a6.5/b6.5/B6.4
Fgf9/16/20˄¬Gdf1/3-r˄¬AdmpNone
Dlx.bSox1/2/3˄Foxa.a˄¬Foxd˄¬β-catenin˅a6.5-8
Sox1/2/3˄Efna.d˅a6.6-8/b6.6-8
Sox1/2/3˄¬Foxd˄¬Fgf9/16/20None
NodalFoxa.a˄Fgf9/16/20˄β-catenin˅A6.1/A6.3/B6.1
Tbx6-r.b˄β-catenin˅B6.1
Sox1/2/3˄¬Foxa.a
˄¬Foxd˄Fgf9/16/20˄¬Efna.d
˄¬β-catenin˅
b6.5
Fgf9/16/20˄¬Gdf1/3-r
˄¬Admp˄¬Prdm1-r/¬Foxa.a§
None

*Note that β-catenin acts with Tcf7, which is present in all cells, for activating targets, and that β-catenin represses Gata.a (7, 13). Because Gata.a is present in all cells, ¬β-catenin means that Gata.a becomes active.

†This conjunction was determined by not only knockdown experiments but also overexpression experiments (fig. S2).

These conjunctions represent expression in experimental conditions only.

§We were not able to determine this conjunction uniquely. The expression patterns of Prdm1-r and Foxa.a indicate that either of them or both are involved. However, this conjunction represents expression in experimental conditions only but not expression in normal 32-cell embryos.