Origin recognition complex (ORC), CDC6, and MCM proteins assemble sequentially to form prereplication chromatin. However, their organization remains largely unclear in mammalian cells. Here we show that ORC1 proteins are associated with non-chromatin nuclear structures and assemble in nuclear foci in mammalian cells using an in vivo chemical cross-linking method. CDC6 proteins were also found to assemble in nuclear foci on non-chromatin nuclear structures, although their physical association with ORC1 has been undetectable. In contrast to the situation in yeast cells, CDC6 was found to remain associated with non-chromatin nuclear structures even after cells entered into S phase. Instead, ORC1 proteins were found to be degraded by a proteasome-dependent pathway during S phase. We also found that some ORC2 proteins are associated with non-chromatin nuclear structures like ORC1, although the remainder binds to nuclease-sensitive chromatin. Further analyses indicate that ORC2 physically interacts with ORC1 on non-chromatin nuclear structures. On the other hand, our results suggest that although a small proportion of MCM complexes are loaded onto chromatin regions near ORC foci, most of them are more widely distributed. Possible relations between such organization of prereplication chromatin and complicated origin specification in higher eukaryotic cells are discussed.It has been suggested that nucleic acid metabolism is carried out on spatially organized domain structures in the cell nucleus (reviewed in Ref. 1). Non-chromatin nuclear structures such as the nuclear matrix, the scaffold, and the nucleoskeleton have been suggested as key players in organizing high order chromatin/nuclear structures (reviewed in Refs. 2 and 3). In the case of DNA replication, for example, fluorescence microscopic analyses have revealed discrete granular sites of replication, i.e. replication sites or replication foci (4 -7). Replication foci may be constructed based on non-chromatin nuclear structures, since nascent DNA and many proteins involved in DNA synthesis have been found to attach to these (Refs. 8 and 9; also reviewed in Refs. 2 and 3). In addition, non-chromatin nuclear elements have also been implicated in the initiation step of DNA replication (reviewed in Ref. 10); replication origins are often situated close to matrix/scaffold attachment regions (11)(12)(13)(14). In this regard, it is of interest to ascertain how replication initiation proteins such as the origin recognition complex (ORC), 1 CDC6, and MCM interact with non-chromatin nuclear structures.The ORC, consisting of six subunits ORC1 to -6, was originally identified as binding specifically to definitive origin sequences in budding yeast (15). Subsequent studies with yeast and Xenopus egg extracts suggested stepwise assembly of ORC, CDC6, and MCM, a six-member protein complex, onto chromatin to form prereplication complexes (reviewed in Refs. 16 and 17). An additional protein(s) is also required for the prereplication complex formation (18,19). However, the mode of...