Half a century ago the elucidation of the DNA double helix structure was quickly followed by the visualization of replicons in DNA fibers. To connect 1D DNA replication/repair information with whole cell 3D data in mammalian cells, we combined super resolution microscopy and time-lapse analysis of S-phase dynamics with genome size and DNA replication fiber analysis. We found that the subnuclear replication structures can be optically resolved down to single replicons during all S-phase stages. This sets aside the conventional interpretation of nuclear replication foci as replication factories, i.e., the complex entities that process multiple clustered replicons. Further, our data suggest that S-phase dynamics is primarily dictated by chromatin folding and synthetic replisome complexes assemble on template DNA. Accordingly, individual replicons within the chromatin context represent the elementary units of 3D genome duplication and organization. A similar analysis of DNA damage response after ionizing radiation labeled by phosphorylated H2AX, a widely used DNA double strand break signaling marker, yielded (nano)foci of the same order of magnitude. These data raise the hypothesis that both repair and replication structures reflect the same elementary unit of chromatin organization. Finally, we manipulated nuclear chromatin (com)position and found that it affected DNA replication dynamics and it ultimately lead to changes in chromatin composition. Löb, D., Lengert, N., Chagin, V. O, Reinhart, M., Casas-Delucchi, C. S., Cardoso, M. C. and Drossel, B. (2016). 3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression. Nat. Commun. 7: 11207. Chagin, V. O., Casas-Delucchi, C. S., Reinhart, M., Schermelleh, L., Markaki, Y., Maiser, A., Bolius, J. J., Bensimon, A., Fillies, M., Domaing, P., Rozanov, Y. M., Leonhardt, H. and Cardoso, M. C. (2016). 4D visualization of replication foci in mammalian cells corresponding to individual replicons. Nat. Commun. 7: 11231. Natale, F., Rapp, A., Yu, W., Maiser, A., Harz, H., Scholl, A., Grulich, S., Anton, T., Hörl, D., Chen, W., Durante, M., Taucher-Scholz, G., Leonhardt, H. and Cardoso, M. C. (2017). Identification of the elementary structural units of the DNA damage response. Nat. Commun. 8: 15760. Heinz, K. S., Casas-Delucchi, C. S., Török, T., Cmarko, D., Rapp, A., Raska, I. and Cardoso, M. C. (2018). Peripheral re-localization of constitutive heterochromatin advances its replication timing and impairs maintenance of silencing marks. Nucleic Acids Res. 45: 6112-6128. Heinz, K. S., Rapp, A., Casas-Delucchi, C. S., Lehmkuhl, A., Romero-Fernández, I., Sánchez, A., Krämer, O. H., Marchal, J. A. and Cardoso, M. C. (2019). DNA replication dynamics of vole genome and its epigenetic regulation. Epigenetics Chromatin In Press.