p94/calpain 3 is a Ca2؉ -binding intracellular protease predominantly expressed in skeletal muscles. p94 binds to the N2A and M-line regions of connectin/titin and localizes in the Z-bands. Genetic evidence showing that compromised p94 proteolytic activity leads to muscular dystrophy (limb-girdle muscular dystrophy type 2A) indicates the importance of p94 function in myofibrils. Here we show that a series of p94 splice variants is expressed immediately after muscle differentiation and differentially change localization during myofibrillogenesis. We found that the endogenous N-terminal (but not C-terminal) domain of p94 was not only localized in the Z-bands but also directly bound to sarcomeric ␣-actinin. These data suggest the incorporation of proteolytic N-terminal fragments of p94 into the Z-bands. In myofibrils localization of exogenously expressed p94 shifted from the M-line to N2A as the sarcomere lengthens beyond ϳ2.6 and 2.8 m for wild-type and proteaseinactive p94, respectively. These data demonstrate for the first time that p94 proteolytic activity is involved in responses to muscle conditions, which may explain why p94 inactivation causes limb-girdle muscular dystrophy. p94/calpain 3 is a member of the calpain family of intracellular Ca 2ϩ -requiring Cys proteases, which cleave substrates at specific and limited sites to modulate their structure and function. In contrast to the conventional -and m-calpains, which are ubiquitously expressed in almost all cells (1, 2), p94 is predominantly expressed in skeletal muscle with lesser amounts of several differentially spliced variants in skeletal muscle and nonmuscle cells (3). The human p94 gene, CAPN3, was identified as responsible for limb-girdle muscular dystrophy type 2A (or "calpainopathy") (4). In mice transgenic overexpression of a protease-inactive form of p94, p94:C129S, and p94 gene knockout caused a mild myopathy and muscular dystrophy, respectively (5-7). Furthermore, a defect in the proper proteolytic activity of p94 is a common feature of limb-girdle muscular dystrophy type 2A pathogenic mutations (8). These findings indicate that p94 protease activity is essential to maintain healthy condition of skeletal muscle. However, the specific physiological functions of p94 as a protease in skeletal muscle remain largely unknown.Skeletal muscles contain highly organized sarcomere structures that consist of systematically expressed myofibrillar proteins. One of the earliest myofibrillar proteins expressed in vertebrate myogenic cells is connectin/titin (9), which is the largest protein molecule known and is abundantly expressed in striated muscles where it constitutes an intrasarcomeric filament (10, 11). During sarcomere assembly, connectin is considered a key molecule for integration of thin filament/Z-band precursors (I-Z-I bodies) and the thick filaments, which are independently assembled in growth tips of elongating myotubes. The N terminus of connectin is located in both I-Z-I body and mature Z, and the C terminus is in the M-line of the thick fil...