McMahon Lab BioTapestry


Introduction

BioTapestry is an interactive tool for building, visualizing and simulating genetic regulatory networks. Here, we have used this as a way of visualizing sonic-hedgehog mediated patterning of the ventral neural tube in the vertebrate embryo. This approach is described in our recent publication ( Vokes et al., 2007) This work is summarized at http://www.people.fas.harvard.edu/~svokes/ and discussed below.

Click here to view the neural tube network model using the BioTapestry interactive network viewer. Information on ways to view and install this information is described below.







Ventral Neural Tube: Time 6
A model for Shh-driven transcriptional network underlying ventral neuronal specification. In this diagram, depicted in standard BioTapestry nomenclature (Longabaugh et al., 2005), neuronal specification is depicted as a sequential series of cell states. All currently expressed genes are in black or colored, while genes not expressed are in gray font. Similarly, active activation or repression is depicted in colored lines, while inactive links (active in previous stages of specification) are depicted in gray. This diagram focuses explicitly on ventral cell specification; thus previous events in general neuronal specification are not shown. Validated Gli targets (all identified or confirmed in our study) are indicated by blue diamonds (ChIP peak), orange diamonds (transgenic validation) or green diamonds (mutation of binding site in transgenic embryos).

Discussion

Our findings together with published reports that have documented the relationship between Gli factors and Shh signaling in specification, and the interactions amongst specific transcriptional regulators downstream of Shh input lead to the model depicted above. This suggests an important dynamic component to ventral patterning where specific neural progenitor populations may change their identity on integrating Hh signaling over time. A partial list of references includes (Briscoe et al., 2000; Ericson et al., 1997; Fogarty et al., 2005; Novitch et al., 2003; Santagati et al., 2003; Sasaki and Hogan, 1996; Vallstedt et al., 2001; Wijgerde et al., 2002).

In this model, Shh signaling within the neural tube is effectively interpreted by region specific combinations of Gli activator and Gli repressor forms. Initially only two cell types are present - one is a V0/V1 bipotential progenitor that depends only indirectly on a loss of Gli-repression, which would in turn result in the loss of an inhibitory dorsal signal (Fogarty et al., 2005; Wijgerde et al., 2002). In the second cell state, there is an initial V2 progenitor, which would then sequentially give rise to V2-FP progenitor domains. Most dorsally, where Shh is never received, Gli-repressors silence all Hh target genes. At the dorsal limits of Hh signaling (at the dorsal-ventral intersect), Gli-repressor would be reduced, thereby relieving the inhibitory action of an unknown factor X on Dbx1 and Dbx2. Dorsal BMP signals have previously been hypothesized to play such a role (Wijgerde et al., 2002); this interaction with Gli-repressor is especially attractive since Gli3 has previously been shown to bind Smad proteins, transcriptional mediators of BMP signaling (Liu et al., 1998). Importantly, the regulation of these domains would not depend on any differential activity of Gli-repressor - only on the attenuation of the dorsal inhibitory input.

In domains that receive a higher Hh input, Gli-repression would be progressively attenuated to the pMN domain and loss of this repressor is sufficient for activation of targets. Within the pV3 and FP domains, however, specification requires varying levels of Gli-activator activity.

There are two ways to explore the neural tube network model. The preferable way is to use the BioTapestry Interactive Network Viewer (developed by William Longabaugh, Eric Davidson, and Hamid Bolouri, and supported by NIH General Medical), which is a Java application. An alternative method, which just displays static images in your web browser, is also available here if you prefer or if you have difficulties with the Java version. See also:

Longabaugh, W. J. R., Davidson, E. H. and Bolouri, H. Computational representation of developmental genetic regulatory networks. Dev. Biol. 283, 1-16, 2005.

Viewing and Installing BioTapestry

The network viewer used here is a simplified version of the full-featured network editor, which is available from BioTapestry.org. The BioTapestry network viewer uses Java Web Start, which is bundled with any recent version of the Java Runtime Environment (JRE). If the above link does not launch the viewer, you will need to install the JRE. The application is known to work with JREs v1.4.1_01 and v1.4.2_02; there are known problems with some other versions v1.4.1_0x. If you need to install a recent JRE on your computer, you can download it from here (click the "Download NOW!" button) or here.

NOTE for Mac users: Although the BioTapestry Viewer runs on MacOS X, there have been reports that launching it from your web browser in 10.3 may fail after the application has been downloaded; you get an incorrect error message saying that the correct version of Java is not present. If this occurs, you can still run BioTapestry from the Java Web Start control panel. Run Applications->Utilities->Java->Java Web Start, select BioTapestry, and click the Start button.

BioTapestry Viewer "Quick Start" User's Guide

Organization of Network Models   Tree View

BioTapestry organizes the network model in the tree view on the left side of the window. You can choose the view you want by clicking on it in this tree view. The different views are:

Full Genome This top level view shows the core network, and contains all the network elements that occur in the different developmental regions at different times.

Ventral Neural Tube Times 1-6 This view shows the summation of every network element that is relevant at some time to each of the developmental regions over the six time periods. If a network element is colored, it is active at some time period in the region. If the element appears in grey, it is relevant to the network, but is never active (e.g. it is repressed at all times).

Time 1, Time2, ... These views each provide a snapshot of all the regions at a single time point. Colored network elements are active at that time point, while gray elements show significant network features for the region that are not currently active.


Running Offline

Java Web Start

After you run BioTapestry the first time, the Java Web Start system caches it locally on your hard drive, so you can run it without being connected to the network, though it will check for newly released updates whenever you are connected to the Internet. When first starting the program, the Web Start system usually asks if you want to make a desktop shortcut. If you choose to do so, the viewer can then be started that way without needing to use your web browser or an active web connection. BioTapestry can also be started by running the Java Web Start Application Manager, which is frequently accessed (on Windows) via the Start->Programs->Java Web Start menu, or else by directly running the program C:\\Program Files\Java Web Start\javaws. From the application manager (see figure at left), you then select the ISB BioTapestry application and click the Start button on the right. You can also create a desktop shortcut from this window by choosing the Application->Create Shortcuts option.


References

Briscoe, J., Pierani, A., Jessell, T. M. and Ericson, J. (2000). A homeodomain protein code specifies progenitor cell identity and neuronal fate in the ventral neural tube. Cell 101, 435-45.

Ericson, J., Rashbass, P., Schedl, A., Brenner-Morton, S., Kawakami, A., van Heyningen, V., Jessell, T. M. and Briscoe, J. (1997). Pax6 controls progenitor cell identity and neuronal fate in response to graded Shh signaling. Cell 90, 169-80.

Fogarty, M., Richardson, W. D. and Kessaris, N. (2005). A subset of oligodendrocytes generated from radial glia in the dorsal spinal cord. Development 132, 1951-9.

Liu, F., Massague, J. and Ruiz i Altaba, A. (1998). Carboxy-terminally truncated Gli3 proteins associate with Smads. Nat Genet 20, 325-6.

Longabaugh, W. J. R., Davidson, E. H. and Bolouri, H. (2005). Computational representation of developmental genetic regulatory networks. Dev Biol 283, 1-16.

Novitch, B. G., Wichterle, H., Jessell, T. M. and Sockanathan, S. (2003). A requirement for retinoic acid-mediated transcriptional activation in ventral neural patterning and motor neuron specification. Neuron 40, 81-95.

Santagati, F., Abe, K., Schmidt, V., Schmitt-John, T., Suzuki, M., Yamamura, K. and Imai, K. (2003). Identification of Cis-regulatory elements in the mouse Pax9/Nkx2-9 genomic region: implication for evolutionary conserved synteny. Genetics 165, 235-42.

Sasaki, H. and Hogan, B. L. (1996). Enhancer analysis of the mouse HNF-3 beta gene: regulatory elements for node/notochord and floor plate are independent and consist of multiple sub-elements. Genes Cells 1, 59-72.

Vallstedt, A., Muhr, J., Pattyn, A., Pierani, A., Mendelsohn, M., Sander, M., Jessell, T. M. and Ericson, J. (2001). Different levels of repressor activity assign redundant and specific roles to Nkx6 genes in motor neuron and interneuron specification. Neuron 31, 743-55.

Vokes, S. A., Ji, H., McCuine, S., Tenzen, T., Giles, S., Zhong, S., Longabaugh, W. J., Davidson, E. H., Wong, W. H. and McMahon, A. P. (2007). Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development 134, 1977-1989.

Wijgerde, M., McMahon, J. A., Rule, M. and McMahon, A. P. (2002). A direct requirement for Hedgehog signaling for normal specification of all ventral progenitor domains in the presumptive mammalian spinal cord. Genes Dev 16, 2849-64.