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The nuclei actively position themselves throughout muscle development. Extensive data support a direct connection between the regulation of nuclear domains, the maintenance of microtubular architecture in muscle fibers and normal muscle function. The microtubule network is completely restructured during muscle formation. We hypothesized that differences between the microtubule-associated proteome in immature and mature fibers contribute to (1) microtubule reorganization and (2) nucleus localization. We have developed a strategy to isolate and analyze these two proteomes using an original in vitro system that allows the formation of pure “mature” muscle fibers. This strategy led to the selection of nearly 500 candidates that we are currently studying using a siRNA screening approach using primary murine/human muscle cells.