Remodeling of chromatin loops does not account for specification of replication origins during Xenopus development

We have investigated the possible relationship between replicons and chromatin loops during Xenopus development. In early embryos, replication of the ribosomal RNA genes (rDNA) can initiate at apparently any sequence. Nevertheless, the need for a regular spacing of replication origins suggests that some periodic chromatin folding might dictate which sites are actually used for initiation. After the midblastula transition, replication initiation is restricted to the rDNA intergenic spacers. A remodeling of chromatin folding could account for this change in origin usage. Here, it is reported that nuclear matrix anchorage of the Xenopus rDNA occurs at multiple, apparently random sequences, throughout embryonic development as well as in adult cells. In vitro matrix rebinding assays confirmed the lack of specific anchoring sequences in the rDNA, before as well as after specific replication origins are established. Thus, no change in loop attachment sites could explain the change in origin usage at this locus. Nonspecific loop anchorage was a special feature of the rDNA locus, since the same nuclear matrices were able selectively to bind the scaffold attachment region (SAR) of the Drosophila histone gene cluster in vitro. Blastula and gastrula nuclear matrices bound a higher amount of SAR sequences than matrices from later stages or adult cells. This developmental change in SAR binding might explain the increase in size of the bulk of genomic DNA loops that occurs after the gastrula stage. However, no change in chromatin loop organization that could explain the midblastula stage transition from small to large replicons was observed.