Research Professor of Biology and Biological Engineering
Genomic control of gut organogenesis in the sea urchin larva
(Jonathan Valencia, Jina Yun and Isabelle Peter)
After demonstrating that gene regulatory networks can be solved experimentally to the extent that a computational model of the network can reproduce the gene expression patterns observed during embryonic development, this project aims at illuminating a next level of complexity: how do the genomically encoded regulatory networks control the development of entire body parts and organs which eventually consist of many different cell types? As an initial assessment, we are currently identifying the different states that the regulatory network for gut organogenesis may assume during the development of Strongylocentrotus purpuratus larvae. Thus a large scale analysis was performed to reveal the spatial and temporal expression of all known regulatory genes encoded in the sea urchin genome at successive developmental stages from pre-gastrula to pluteus larva when a mature gut is formed. This analysis is now almost complete, with data available for >270 regulatory genes, and we are currently identifying the combinatorial regulatory states expressed in each part of the gut during organogenesis. While knowing the different activity states of a network will not reveal directly the architecture of regulatory interactions, it will provide extremely useful predictions of which linkages may operate at given developmental times, and which ones can be excluded. This project thus provides the basis for experimentally solving the network circuitry underlying gut organogenesis.
Regulatory ontology of the sea urchin larva
(Jonathan Valencia and Isabelle Peter)
The dataset generated for the gut organogenesis project revealed the spatial expression of >270 regulatory genes throughout the sea urchin embryo at several developmental stages. We are currently using this dataset to generate a regulatory ontology for the sea urchin larva, which will identify regulatory state expression in different body parts and cell fates during. Although gene regulatory networks have been solved almost completely for the pre-gastrular sea urchin embryo, there was until recently very little molecular information available for later developmental stages. Here we focus on developmental processes from pre-gastrular embryo up to the sea urchin larva, which is an organism capable of swimming and eating. Using comparative analysis of regulatory gene expression, we have identified >70 different spatial domains in the sea urchin larva, indicating the spatial complexity of this relatively simple organism. We have annotated the expression of more than half of all known regulatory genes in each of these spatial domains at five consecutive developmental stages. This information will be used to generate an atlas for the sea urchin larva which reveals both, the spatial organization of the larva as acquired during development, and the changes of regulatory state expression in each spatial domain.
Cis-regulatory control of hox gene expression during hindgut development
(Miao Cui and Isabelle Peter)
Although hox genes are known to be used as a vectorial patterning system for the development of many animals, this system does not operate during the development of the sea urchin larva, and only hox7 and hox11/13b are even expressed. Nevertheless, the posterior hox gene hox11/13b is crucial for the specification of the posterior hindgut. We have screened approximately 150kb of genomic sequence at the hox11/13b locus for cis-regulatory activity, and identified a cis-regulatory module responsible for the earliest expression of this gene during pre-gastrular development. However, no genomic fragment was found driving expression of a reporter gene at later developmental stages, when this gene is specifically expressed in the hindgut. Additional experiments revealed that a second cis-regulatory module, located only 700bp downstream of the early module, is required for expression in hindgut precursor cells. Curiously, neither module is by itself sufficient to drive expression in the hindgut, but the presence of both modules is required for hindgut-specific expression of hox11/13b. We are currently working on identifying the molecular mechanism for this rarely observed AND logic gate of regulatory activity between two cis-regulatory modules.
Evolution of gene regulatory networks controlling endomesodermal patterning during early development in echinoderms
(Eric Erkenbrack, Eric Davidson and Isabelle Peter)
Since the gene regulatory networks controlling the specification of endodermal and mesodermal cell fates in the early sea urchin embryo are almost completely solved, they provide a unique opportunity to investigate how these networks have changed during echinoderm evolution. We have analyzed the spatial and temporal expression of several regulatory genes of the endomesodermal networks of S. purpuratus (Sp) in embryos of the cidaroid pencil urchin Eucidaris tribuloides (Et). In addition, we have experimentally tested whether some of the most important regulatory linkages within Sp networks are also functional in Et embryos. Our results show that while the combinatorial regulatory states expressed in the endomesoderm are mostly conserved, the mechanism of their specification is clearly distinct, as indicated for example by a completely different role of the Delta/Notch signaling pathway within the endodermal and mesodermal of the two species.
Network information and circuit design
(Isabelle Peter and Eric Davidson)
The gene regulatory network controlling specification of endomesoderm in sea urchin embryos is one of the best understood experimentally solved gene regulatory networks. The ability of a computational Boolean model of this network to reconstruct the spatial and temporal expression of regulatory genes during early sea urchin development can be considered as a proof of principle that solving gene regulatory networks can indeed reveal the causality of developmental process. Using the endomesoderm network, we are now analyzing the role of individual regulatory linkages in the function of modular network circuits, and the functional organization of these circuits within the overall network.