1- Scientific context and project objectives

During the development of a living organism, cell interactions ensure the growth and differentiation of cell coordinates within tissues and organs. Understanding these will eventually improve the diagnosis of developmental diseases, and therefore enable appropriate therapy to be developed. With this in mind, our research team is working on the model organism of drosophila. An organism’s tissue development depends on gene activity and subsequent molecular mechanisms, since the creation of tissue, like muscle, generates reactions between the genes and proteins expressed specifically during muscle development.

Gene expression is regulated by proteins called transcription factors, which bind to DNA sequences and influence the level of gene expression (activation or repression of the activity). The binding of a transcription factor to a cis-regulatory module (CRM), and therefore its involvement in the mechanism studied, can be observed using “ChIP on chip” ChEST technology developed by our team, while gene activity can be quantified by DNA chip technology. Both these types of results are then compared with the phenomena observed using imaging technology (confocal microscopy, IRM). In this way, global data of the activity of genes and their CRMs may be correlated to developmental events, such as the creation of a tendon and growth of muscle fibres around a tendon.

2- Project description

Studying the dynamics of myogenesis in this way will produce images and textual results: biochip data (gene identification), image acquisition data by confocal microscopy, 3D reconstruction parameters and results from ChEST. Since this data is very diverse, it cannot be stored effectively in the same database. A central platform will therefore be necessary to process and query all of the data. The development will take place in two stages, first of all an information system will be constructed, and then several human/machine interaction and data processing services will be developed.

The information system will contain three parts:

• A database storing the transcriptome analysis protocol, 3D reconstruction and acquisition parameters as well as the bioinformatics analysis results.
• A transcriptome matrix and image server with which it will be possible to save large documents securely.
• A data management server for distributing data to the two above components and for retrieving data through complex queries.

Three data processing services will be set up around the information system:
Morphological analysis by microscope imagery. . Using a confocal microscope, series of images of muscle fibre light sections will be acquired at several points during its development. This is in fact a space-time exploration of a muscle fibre’s development. The system will distribute the results of these experiments to the information system. A software chain will then be used to assess the chosen parameters on the images, to carry out a three-dimensional and temporal reconstruction of the development of the muscle fibre, and to develop a three-dimensional parametric model as a basis for future muscle development models.
Transcriptome analysis using DNA chips (GeneArray, Affymetrix). This will involve extracting several types of cells involved in muscle development using GFP markers to sort cells, and quantifying gene expression over time. The aim is to identify those genes whose expression is actively regulated during muscle development and particularly during muscle-tendon interactions.
Analysis of enhancer activity using ChEST technology, based on the combination of in vivo and in silico protocols. Using ChEST, the regulator modules of genes whose expression is regulated by myogenetic factors can be identified. The data gathered by the bioinformatics chaining of this tool is recorded in the database.

3- Public or controlled use

The tool developed will be for public use. That said, the laboratory is entitled not to communicate all of the data obtained through this programme if some of it may be patented.

4- Expected results

The scientific results of the project will provide insight into the mechanisms of muscle development and enable a space-time model of myogenesis to be developed. This knowledge may help to understand myopathies better and, on a different note, to improve the quality of farmed meat. The results of this programme are already of interest to various bodies: the Myores consortium, INVITROGEN, G. Junion (PhD student within the team) project sponsor of a fledgling business (analysis kits based on ChEST).

LifeGrid, the regional information system