To obtain a better understanding of the relationship between metaphase chromosome banding patterns and genome organization, attention was focused on regions of metaphase chromosomes that were found to contain the genes for a specific cellular enzyme, dihydrofolate reductase (DHFR) . These studies involved the use of highly methotrexateresistant mouse lymphoblastoid cells (L5178YR), which contain approximately 300 times the number of DHFR genes present in parental cells (L5178YS) . Karyotypic analysis revealed the presence of two very large, nonhomologous, marker chromosomes that were absent in the parental line . In situ hybridization of 3H-labeled cloned DHFR cDNA to metaphase chromosomes of L5178YR cells was used to localize the DHFR genes to a very large Giemsa (G)-negative region on each of the two large marker chromosomes. Regional patterns of DNA replication in metaphase chromosomes were studied by autoradiographic visualization of [3H]thymidine incorporation and by fluorescent microscopic visualization of bromodeoxyuridine incorporation . Because the amplified DHFR genes were present within two prominent cytogenetic regions on two easily identifiable chromosomes, it was possible to observe the following. The amplified DHFR genes were located in chromosome regions that replicated at the same time during the first half of a 9-h S-phase . DNA replication began simultaneously and terminated simultaneously at many locations throughout each amplified region . We conclude that transcriptionally active DHFR genes are located within large G-negative regions of metaphase chromosomes and that the DNA within these regions replicates during the first half of S-phase .The genome of animal cells is subdivided into 30,000 replication units, or replicons, ranging in size from 50 to 330 kilobasepairs (kb) (13,22,23) . DNA replication proceeds bidirectionally within each replicon from an origin until reaching replication forks proceeding outward from adjacent origins of replication (24, 28) . Groups of replicons are activated in a defined temporal order that is maintained from one S-phase to the next (1,11,39,40,45,47) . Clusters of replicons initiate replication in synchrony and are similar in size and rate of fork movement (21,27) . This clustering of replicon activity may be responsible for the regional patterns of DNA replication observed in metaphase chromosomes (9,12,15,30,35,38,46) . A number of reports have indicated that the DNA of specific cytogenetic loci replicate at characteristic times within S-phase . THE JOURNAL OF CELL BIOLOGY " VOLUME 92 FEBRUARY 1982 531-539 © The Rockefeller University Press " 0021-9525/82/02/0531/09 $1 .00In particular, it has been observed that heterochromatic chromosomal regions are usually the last to complete replication. These include the inactive X chromosome in females (facultative heterochromatin [8,18,36]) and centromeric regions (constitutive heterochromatin [11,16]). The darkly staining Gpositive bands produced by Giemsa staining procedures contain DNA that replicate...