To study the cell type specificity of the direction of replication of the human c-myc genes and the relationship of replication polarity to transcriptional activity, we analyzed the directions of replication of the c-myc genes in two Burkitt lymphoma cell lines, CA46 and ST486, and in HeLa cells. On the basis of in vitro runoff replication of forks initiated in intact cells, we found that transcribed c-myc genes in the germ line configuration in HeLa cells were replicated in the direction of transcription from origins in the 5'-flanking DNA, while the repressed, unrearranged c-myc genes of CA46 and ST486 cells were replicated in the antitranscriptional direction. In contrast, the transcribed c-myc genes of CA46 cells were replicated in the transcriptional direction, while the translocated, amplified c-myc genes of ST486 cells showed no preferred polarity of replication. The data also provided evidence for the existence of an endogenous barrier to DNA polymerases in the flanking DNA immediately 5' to the HeLa c-myc genes.The replication of eucaryotic chromosomes is controlled through the selection of sites for the initiation of DNA synthesis (2,6,7,10,12,14,19,21,24,32,39) and through the temporal programming of the activity at these sites (10,12,19,23). Combined with evidence for the existence of proteins which recognize the replication origins of viral minichromosomes (11,17,28,44), these results suggest that chromosome replication can be regulated in trans by DNA sequence-specific protein binding.That the activity of eucaryotic genes is related to the replication of chromatin is supported by several observations that transcribed genes are replicated early in the S phase of the cell cycle (8,9,16,18) and by the demonstration that the efficient transcription of certain transfected genes requires the replication of their chromatin template (13, 42). Moreover, Miller and Nasmyth (31) have demonstrated that passage through the S phase is necessary for repression of the silent mating type loci in Saccharomyces cerevisiae. Smithies (37) has proposed that the processes of replication and transcription are linked such that transcriptionally active genes are replicated from upstream origins, whereas inactive genes are replicated from either upstream or downstream origins. Consistent with this proposal, we have shown that the avian histone H5 genes are replicated in the transcriptional direction in embryonic erythrocytes, where they are expressed, but in the antitranscriptional direction in lymphoblastoid cells and chicken embryo fibroblasts, where they are quiescent (43). In comparison, the avian alpha-pi and alpha-D globin genes are replicated in the transcriptional direction both in cells in which they are active (erythrocytes) and in cells in which they are inactive (lymphoblastoid cells and fibroblasts) (26; Y. I. Lindstrom and M. Leffak, manuscript in preparation).To investigate further the relationship between replication polarity and transcriptional activity, we used the in vitro runoff replication (IVR) assay (2...