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Gene regulatory networks controlling functional activities of spatially and temporally distinct endodermal cell populations in the early mouse embryo remain ill defined. The T-box transcription factor Eomes, acting downstream from Nodal/Smad signals, directly activates the LIM domain homeobox transcription factor Lhx1 in the visceral endoderm. Here we demonstrate Smad4/Eomes-dependent Lhx1 expression in the epiblast marks the entire definitive endoderm lineage, the anterior mesendoderm, and midline progenitors. Conditional inactivation of Lhx1 disrupts anterior definitive endoderm development and impedes node and midline morphogenesis in part due to severe disturbances in visceral endoderm displacement. Transcriptional profiling and ChIP-seq (chromatin immunoprecipitation [ChIP] followed by high-throughput sequencing) experiments identified Lhx1 target genes, including numerous anterior definitive endoderm markers and components of the Wnt signaling pathway. Interestingly, Lhx1-binding sites were enriched at enhancers, including the Nodal-proximal epiblast enhancer element and enhancer regions controlling Otx2 and Foxa2 expression. Moreover, in proteomic experiments, we characterized a complex comprised of Lhx1, Otx2, and Foxa2 as well as the chromatin-looping protein Ldb1. These partnerships cooperatively regulate development of the anterior mesendoderm, node, and midline cell populations responsible for establishment of the left-right body axis and head formation.

Original publication




Journal article


Genes Dev

Publication Date





2108 - 2122


Ldb1, Lhx1, definitive endoderm, mesendoderm, midline, node, DNA-Binding Proteins, Embryo, Mammalian, Embryonic Development, Enhancer Elements, Genetic, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Developmental, Germ Layers, Hepatocyte Nuclear Factor 3-beta, LIM Domain Proteins, LIM-Homeodomain Proteins, Multiprotein Complexes, Otx Transcription Factors, Protein Binding, Transcription Factors, Wnt Signaling Pathway