Mammalian skeletal muscles are capable of regeneration after injury. Quiescent satellite cells are activated to reenter the cell cycle and to differentiate for repair, recapitulating features of myogenesis during embryonic development. To understand better the molecular mechanism involved in this process in vivo, we employed high density cDNA microarrays for gene expression profiling in mouse tibialis anterior muscles after a cardiotoxin injection. Among 16,267 gene elements surveyed, 3,532 elements showed at least a 2.5-fold change at one or more time points during a 14-day time course. Hierarchical cluster analysis and semiquantitative reverse transcription-PCR showed induction of genes important for cell cycle control and DNA replication during the early phase of muscle regeneration. Subsequently, genes for myogenic regulatory factors, a group of imprinted genes and genes with functions to inhibit cell cycle progression and promote myogenic differentiation, were induced when myogenic stem cells started to differentiate. Induction of a majority of these genes, including E2f1 and E2f2, was abolished in muscles lacking satellite cell activity after gamma radiation. Regeneration was severely compromised in E2f1 null mice but not affected in E2f2 null mice. This study identifies novel genes potentially important for muscle regeneration and reveals highly coordinated myogenic cell proliferation and differentiation programs in adult skeletal muscle regeneration in vivo.Skeletal muscles are damaged and repaired repeatedly throughout life. Muscle regeneration maintains locomotor function during aging and delays the appearance of clinical symptoms in neuromuscular diseases, such as Duchenne muscular dystrophy (1, 2). This capacity for tissue repair is conferred by satellite cells located between the basal lamina and the sarcolemma of mature myofibers (3, 4). Upon injury, satellite cells reenter the cell cycle, proliferate, and then exit the cell cycle either to renew the quiescent satellite cell pool or to differentiate into mature myofibers (5). Understanding the molecular mechanism by which satellite cell activity is regulated could promote development of novel countermeasures to enhance muscle performance that is compromised by diseases or aging.Both the cell proliferation and differentiation programs are essential for myogenesis. Mammalian cells escape from quiescence (G 0 ) and enter the cell cycle by activating the Cdk 1 /Rb/ E2f signaling pathway (6, 7). In general, mitogen stimulation induces expression and assembly of the G 1 cyclin-dependent kinases (Cdks) (8, 9). Activation of Cdks causes phosphorylation of the retinoblastoma protein (Rb) (10, 11), leading to increased activities of a subset of E2f transcription factors (E2fs) (12) and up-regulation of a variety of E2f-responsive genes encoding proteins directly involved in DNA replication and cell cycle progression (13,14). On the other hand, myogenic differentiation is controlled by interactions of a network of myogenic transcription factors (15). Studies ...