A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs

Abstract

Germ layer formation is among the earliest differentiation events in metazoan embryos. In triploblasts, three germ layers are formed, among which the endoderm gives rise to the epithelial lining of the gut tube and associated organs including the liver, pancreas and lungs. In frogs (Xenopus), where early germ layer formation has been studied extensively, the process of endoderm specification involves the interplay of dozens of transcription factors. Here, we review the interactions between these factors, summarized in a transcriptional gene regulatory network (GRN). We highlight regulatory connections conserved between frog, fish, mouse, and human endodermal lineages. Especially prominent is the conserved role and regulatory targets of the Nodal signaling pathway and the T-box transcription factors, Vegt and Eomes. Additionally, we highlight network topologies and motifs, and speculate on their possible roles in development.

Keywords: Endoderm; Evolutionary conservation; Gene regulatory network; Network motifs; Transcription factors; Xenopus.

Figure 1. Xenopus mesendoderm gene regulatory network from fertilization through early-gastrula

The network is comprised of 23 transcription factors and 12 growth factors. Maternal proteins are represented as diamonds, and signaling ligands as circles. Connections are drawn from the transcriptional regulator to the cis-regulatory region of the target gene. Direct connections are indicated as solid lines, and putative connections as dashed lines. Activating connections are represented by arrowheads, and repressive connections as a flat line. Connections from secreted ligands pass through a chevron, and are mediated by their respective intracellular transcription factors (e.g. Smad2/3, β-catenin). Approximate spatiotemporal information is provided from top to bottom (egg through early-gastrula) and from right to left (dorsal to ventral), with some exceptions (e.g. xbra/t). The activation time of zygotic sox7 (boxed) is unknown. All direct connections are annotated for TF binding (blue diamond), reporter assay (pink diamond), and TF binding plus functional validation (maroon diamond). For additional connection details, including experimental evidence and references, see Table 1 and Table S2. Zygotic genome activation, ZGA.

Figure 2. Network motifs found in the Xenopus mesendoderm GRN

(A) Autoregulatory loop, for example by nodal signaling (B) Positive feedback loop, for example between ventral genes Nodal and Wnt signaling (C) Coherent and incoherent feedforward loops and their regulatory structure (D) Type I feedforward loop, which appears to be the most common type of feedforward loop, frequently appears in the structure such that X is a maternal factor, Y is an early zygotic gene, and Z is either an early or late zygotic gene.