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Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling.

Martin S, Söllner C, Charoensawan V, Adryan B, Thisse B, Thisse C, Teichmann S, Wright GJ - Mol. Cell Proteomics (2010)

Bottom Line: To try to understand the functional role of these interactions, we determined new expression patterns for 164 genes within our clone library by using whole embryo in situ hybridization at five key stages of zebrafish embryonic development.These expression data were integrated with the binding network to reveal where each interaction was likely to function within the embryo and were used to resolve the static interaction network into dynamic tissue- and stage-specific subnetworks within the developing zebrafish embryo.All these data were organized into a freely accessible on-line database called ARNIE (AVEXIS Receptor Network with Integrated Expression; www.sanger.ac.uk/arnie) and provide a valuable resource of new extracellular signaling interactions for developmental biology.

View Article: PubMed Central - PubMed

Affiliation: Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB101HH, United Kingdom.

ABSTRACT
Extracellular interactions involving both secreted and membrane-tethered receptor proteins are essential to initiate signaling pathways that orchestrate cellular behaviors within biological systems. Because of the biochemical properties of these proteins and their interactions, identifying novel extracellular interactions remains experimentally challenging. To address this, we have recently developed an assay, AVEXIS (avidity-based extracellular interaction screen) to detect low affinity extracellular interactions on a large scale and have begun to construct interaction networks between zebrafish receptors belonging to the immunoglobulin and leucine-rich repeat protein families to identify novel signaling pathways important for early development. Here, we expanded our zebrafish protein library to include other domain families and many more secreted proteins and performed our largest screen to date totaling 16,544 potential unique interactions. We report 111 interactions of which 96 are novel and include the first documented extracellular ligands for 15 proteins. By including 77 interactions from previous screens, we assembled an expanded network of 188 extracellular interactions between 92 proteins and used it to show that secreted proteins have twice as many interaction partners as membrane-tethered receptors and that the connectivity of the extracellular network behaves as a power law. To try to understand the functional role of these interactions, we determined new expression patterns for 164 genes within our clone library by using whole embryo in situ hybridization at five key stages of zebrafish embryonic development. These expression data were integrated with the binding network to reveal where each interaction was likely to function within the embryo and were used to resolve the static interaction network into dynamic tissue- and stage-specific subnetworks within the developing zebrafish embryo. All these data were organized into a freely accessible on-line database called ARNIE (AVEXIS Receptor Network with Integrated Expression; www.sanger.ac.uk/arnie) and provide a valuable resource of new extracellular signaling interactions for developmental biology.

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Genes encoding proteins within extracellular interaction network are expressed in tissue-restricted manner during early development. A, the development of the zebrafish embryo. Drawings of representative stages within each of the five main periods of zebrafish development are shown above a brief description of the main morphogenetic landmarks within each period. Drawings are taken with permission from Kimmel et al. (45). B, a summary of the tissue expression patterns of the genes encoding proteins from the interaction network. The expression patterns were annotated and placed into all the appropriate non-exclusive tissue categories. C, a summary of the temporal expression patterns of the genes encoding proteins from the interaction network. The number of genes expressed at each period of development is plotted, indicating those genes whose expression was ubiquitous (green) or restricted to particular tissues (blue).
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Figure 3: Genes encoding proteins within extracellular interaction network are expressed in tissue-restricted manner during early development. A, the development of the zebrafish embryo. Drawings of representative stages within each of the five main periods of zebrafish development are shown above a brief description of the main morphogenetic landmarks within each period. Drawings are taken with permission from Kimmel et al. (45). B, a summary of the tissue expression patterns of the genes encoding proteins from the interaction network. The expression patterns were annotated and placed into all the appropriate non-exclusive tissue categories. C, a summary of the temporal expression patterns of the genes encoding proteins from the interaction network. The number of genes expressed at each period of development is plotted, indicating those genes whose expression was ubiquitous (green) or restricted to particular tissues (blue).

Mentions: To obtain functional information for the interactions within the network, we determined the expression profiles of all the genes within our protein library, for which no expression pattern had been previously determined, using whole-mount in situ hybridization from gastrula to larval periods of zebrafish embryonic development. In total, we determined 164 new expression patterns, which have been deposited in the publically accessible ZFIN database (44). A complete description of the principal events within these developmental periods is detailed in Kimmel et al. (45): they cover the initiation and completion of primary organogenesis (segmentation to hatching) and the development of circulation (pharyngula) and simple behaviors (larval) (Fig. 3A). To enable a summarized, systematic analysis of the expression data, the gene expression patterns were annotated using a restricted vocabulary and subsequently categorized into 10 general biological systems using the zebrafish anatomical ontology.


Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling.

Martin S, Söllner C, Charoensawan V, Adryan B, Thisse B, Thisse C, Teichmann S, Wright GJ - Mol. Cell Proteomics (2010)

Genes encoding proteins within extracellular interaction network are expressed in tissue-restricted manner during early development. A, the development of the zebrafish embryo. Drawings of representative stages within each of the five main periods of zebrafish development are shown above a brief description of the main morphogenetic landmarks within each period. Drawings are taken with permission from Kimmel et al. (45). B, a summary of the tissue expression patterns of the genes encoding proteins from the interaction network. The expression patterns were annotated and placed into all the appropriate non-exclusive tissue categories. C, a summary of the temporal expression patterns of the genes encoding proteins from the interaction network. The number of genes expressed at each period of development is plotted, indicating those genes whose expression was ubiquitous (green) or restricted to particular tissues (blue).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3101854&req=5

Figure 3: Genes encoding proteins within extracellular interaction network are expressed in tissue-restricted manner during early development. A, the development of the zebrafish embryo. Drawings of representative stages within each of the five main periods of zebrafish development are shown above a brief description of the main morphogenetic landmarks within each period. Drawings are taken with permission from Kimmel et al. (45). B, a summary of the tissue expression patterns of the genes encoding proteins from the interaction network. The expression patterns were annotated and placed into all the appropriate non-exclusive tissue categories. C, a summary of the temporal expression patterns of the genes encoding proteins from the interaction network. The number of genes expressed at each period of development is plotted, indicating those genes whose expression was ubiquitous (green) or restricted to particular tissues (blue).
Mentions: To obtain functional information for the interactions within the network, we determined the expression profiles of all the genes within our protein library, for which no expression pattern had been previously determined, using whole-mount in situ hybridization from gastrula to larval periods of zebrafish embryonic development. In total, we determined 164 new expression patterns, which have been deposited in the publically accessible ZFIN database (44). A complete description of the principal events within these developmental periods is detailed in Kimmel et al. (45): they cover the initiation and completion of primary organogenesis (segmentation to hatching) and the development of circulation (pharyngula) and simple behaviors (larval) (Fig. 3A). To enable a summarized, systematic analysis of the expression data, the gene expression patterns were annotated using a restricted vocabulary and subsequently categorized into 10 general biological systems using the zebrafish anatomical ontology.

Bottom Line: To try to understand the functional role of these interactions, we determined new expression patterns for 164 genes within our clone library by using whole embryo in situ hybridization at five key stages of zebrafish embryonic development.These expression data were integrated with the binding network to reveal where each interaction was likely to function within the embryo and were used to resolve the static interaction network into dynamic tissue- and stage-specific subnetworks within the developing zebrafish embryo.All these data were organized into a freely accessible on-line database called ARNIE (AVEXIS Receptor Network with Integrated Expression; www.sanger.ac.uk/arnie) and provide a valuable resource of new extracellular signaling interactions for developmental biology.

View Article: PubMed Central - PubMed

Affiliation: Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB101HH, United Kingdom.

ABSTRACT
Extracellular interactions involving both secreted and membrane-tethered receptor proteins are essential to initiate signaling pathways that orchestrate cellular behaviors within biological systems. Because of the biochemical properties of these proteins and their interactions, identifying novel extracellular interactions remains experimentally challenging. To address this, we have recently developed an assay, AVEXIS (avidity-based extracellular interaction screen) to detect low affinity extracellular interactions on a large scale and have begun to construct interaction networks between zebrafish receptors belonging to the immunoglobulin and leucine-rich repeat protein families to identify novel signaling pathways important for early development. Here, we expanded our zebrafish protein library to include other domain families and many more secreted proteins and performed our largest screen to date totaling 16,544 potential unique interactions. We report 111 interactions of which 96 are novel and include the first documented extracellular ligands for 15 proteins. By including 77 interactions from previous screens, we assembled an expanded network of 188 extracellular interactions between 92 proteins and used it to show that secreted proteins have twice as many interaction partners as membrane-tethered receptors and that the connectivity of the extracellular network behaves as a power law. To try to understand the functional role of these interactions, we determined new expression patterns for 164 genes within our clone library by using whole embryo in situ hybridization at five key stages of zebrafish embryonic development. These expression data were integrated with the binding network to reveal where each interaction was likely to function within the embryo and were used to resolve the static interaction network into dynamic tissue- and stage-specific subnetworks within the developing zebrafish embryo. All these data were organized into a freely accessible on-line database called ARNIE (AVEXIS Receptor Network with Integrated Expression; www.sanger.ac.uk/arnie) and provide a valuable resource of new extracellular signaling interactions for developmental biology.

Show MeSH