Cell-specific organization of the 5S ribosomal RNA gene cluster DNA loop domains in spermatozoa and somatic cells.

DNA in eucaryotic cells is organized into loop domains, ranging in size from 25 to 100 kb, that are attached at their bases to the structural component of the nucleus termed the nuclear matrix. These DNA loop domains have been shown to be important in the regulation of both DNA replication and RNA transcription. In this study we have compared the structural organization of the DNA loop domains of the 5S rRNA gene cluster in sperm, liver, and brain nuclei in the Syrian golden hamster. The individual loop domains were visualized by fluorescent in situ hybridization to protamine (sperm)- and histone (somatic)-depleted nuclei, termed nuclear matrix halo preparations. We found that in sperm nuclei, the 5S rRNA gene cluster was organized into three small loop domains that were approximately 48 kb each. In both types of somatic cell nuclei examined, the 5S rRNA gene cluster was organized into a single, much larger loop domain that was up to 480 kb in length. The data suggest that at least some of the compaction that sperm DNA undergoes during spermiogenesis is mediated by the nuclear matrix independent of protamine binding. Additionally, this sperm-specific DNA organization may be involved in the specific patterns of DNA replication and transcription of the paternal genome in the embryo.