Abstract. According to the current paradigm, replication foci are discrete sites in the interphase nucleus where as- semblies of DNA replication enzymes simultaneously elongate the replication forks of 10–100 adjacent rep- licons (each ~100 kbp). Here we review new results and provide alternative interpretations for old results to show that the current paradigm is in need of further develop- ment. In particular, many replicons are larger than previ- ously thought – so large that their complete replication takes much longer (several hours) than the measured av- erage time to complete replication at individual foci (45–60 min). In addition to this large heterogeneity in replicon size, it is now apparent that there is also a cor- responding heterogeneity in the size and intensity of in- dividual replication foci. An important property of all replication foci is that they are stable structures that per- sist, with constant dimensions, during all cell cycle stag- es including mitosis, and therefore likely represent a fundamental unit of chromatin organization. With this in mind, we present a modified model of replication foci in which many of the foci are composed of clusters of small replicons as previously proposed, but the size and number of replicons per focus is extremely heterogene- ous, and a significant proportion of foci are composed of Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci Ronald Berezney 1 , Dharani D. Dubey 2 , Joel A. Huberman 3 1 Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA 2 Department of Zoology, Kutir Postgraduate College, Chakkey, Jaunpur, U.P. 222146, India 3 Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA Received: 16 August 1999 / Accepted: 17 August 1999 This review is dedicated to the memory of Professor J. Herbert Taylor, whose pioneering studies of chromosomal replication us- ing 3 H-thymidine autoradiography formed the foundation on which the studies described herein were constructed. Correspondence to: J.A. Huberman e-mail: huberman@acsu.buffalo.edu Chromosoma (2000) 108:471–484 Chromosoma Focus © Springer-Verlag 2000 single large replicons. We further speculate that very large replicons may extend over two or more individual foci and that this organization may be important in regu- lating the replication of such large replicons as the cell proceeds through S-phase. Introduction This review article grew out of discussions between two of the authors (R.B. and J.A.H.) regarding interpretation of some of the experiments performed by Ma et al. (1998). These discussions took place in two contexts – during thesis committee meetings for Hong Ma (R.B. was Hong Ma’s thesis advisor, and J.A.H. was a member of her thesis committee) and during meetings of the Buf- falo DNA Replication Group, which sponsors discus- sions among scientists interested in DNA replication who work in Buffalo, N.Y. When D.D. visited the labo- ratory of J.A.H. for 2 months during the spring of 1999, he, too, joined in the discussions. All three of us learned a great deal from our interactions and debates. This re- view article represents our attempt to share some of what we learned with the rest of the world. In addition to acknowledging the stimulating atmo- sphere created by our colleagues in the DNA replication field in Buffalo, we also wish to give credit to the review article by Liapunova (1994), which first brought to our attention the important experiments of Yurov and Liapu- nova (1977), who were the first to demonstrate that mammalian replicons can be very large, in some cases greater than 1 Mbp.