Firing of DNA replication origins in mammals has been studied in tissue culture, but not in vivo. Here, we subjected mice to partial hepatectomy and examined origin firing in the regenerating liver. In young mice, we observed robust firing of DNA replication origins, whose distribution on the genome was linked to expressed genes. Two replication origins were observed flanking each gene: a primary origin that fired constitutively and a dormant origin that fired when fork progression from the primary origin was blocked. We propose that genes are organized as modular replication-transcription units with their own dedicated replication origins and that this genomic architecture has evolved because it helps maintain genomic stability. In contrast to young mice, origin firing in old mice after partial hepatectomy was significantly compromised and accompanied by induction of a DNA damage response. However, inhibiting ATR, a replication stress checkpoint kinase, fully rescued origin firing in the old mice, suggesting that the initial firing of a small number of origins led to ATR activation, which then suppressed globally new origin firing.