Xenopus as a model system to study transcriptional regulatory networks

Abstract

Development is controlled by a complex series of events requiring sequential gene activation. Understanding the logic of gene networks during development is necessary for a complete understanding of how genes contribute to phenotype. Pioneering work initiated in the sea urchin and Drosophila has demonstrated that reasonable transcriptional regulatory network diagrams representing early development in multicellular animals can be generated through use of appropriate genomic, genetic, and biochemical tools. Establishment of similar regulatory network diagrams for vertebrate development is a necessary step. The amphibian Xenopus has long been used as a model for vertebrate early development and has contributed greatly to the elucidation of gene regulation. Because the best and most extensively studied transcriptional regulatory network in Xenopus is that underlying the formation and function of Spemann's organizer, we describe the current status of our understanding of this gene regulatory network and its relationship to mesodermal patterning. Seventy-four transcription factors currently known to be expressed in the mesoendoderm of Xenopus gastrula were characterized according to their modes of action, DNA binding consensus sequences, and target genes. Among them, nineteen transcription factors were characterized sufficiently in detail, allowing us to generate a gene regulatory network diagram. Additionally, we discuss recent amphibian work using a combined DNA microarray and bioinformatics approach that promises to accelerate regulatory network studies.gastrulation ͉ mesoderm ͉ organizer ͉ transcription factor ͉ gene regulation

Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network

“…7) that likely target different subsets of these CRMs. Such feed-forward regulation is a prevalent feature in many developmental networks (Davidson et al 2002;Schroeder et al 2004;Inoue et al 2005;Koide et al 2005;Sandmann et al 2007a).…”

Canalization and symmetry in Boolean models for genetic regulatory networks

“…Organisms with larger numbers of genes have a larger number of potentially realizable cell types. There has been a recent dramatic increase in the amount of experimental information available on the structure of genetic regulatory networks in a range of organisms, including E. coli [7], budding yeast S. cervisiae [8,9], Drosophila species [10], Xenopus [11], and the embryo of the sea urchin S. purpuratus [12]. In the simplest representation, the nodes of the network are genes and the links between genes describe their interactions.…”

The Ars insulator facilitates I‐SceI meganuclease‐mediated transgenesis in the sea urchin embryo

“…Gene regulatory networks (GRNs) that control animal development have been studied in several model organisms (Oliveri and Davidson, 2004;Koide et al, 2005;Imai et al, 2006). In these GRNs, many network genes have been reported to be regulated both temporally and spatially (Fuchikami et al, 2002;Amore et al, 2003).…”