Rearrangement of chromatin domains during development in Xenopus

A dynamic change in the organization of different gene domains transcribed by RNA polymerase I, II, or III occurs during the progression from quiescen t [pre-midblastula transition (pre-MBT)] to active (post-MBT) embryos durin g Xenopus development. In the rDNA, c-myc, and somatic 5S gene domains, a t ransition from random to specific anchorage to the nuclear matrix occurs wh en chromatin domains become active. The keratin gene domain was also random ly associated to the nuclear matrix before MBT, whereas a defined attachmen t site was found in keratinocytes. In agreement with this specification, li gation-mediated (LM)-PCR genomic footprinting carried out on the subpopulat ion of 5S domains specifically attached to the matrix reveals the hallmarks of determined chromatin after the midblastula transition. In contrast, the same analysis performed on the total 5S gene population does not reveal sp ecific chromatin organization, validating the use of nuclear matrix fractio nation to unveil active chromatin domains. These data provide a means for t he determination of active chromosomal territories in the embryo and emphas ize the role of nuclear architecture in regulated gene expression during de velopment.