The molecular mechanisms for the transcriptional regulation underlying embryogenesis in the sea urchin Hemicentrotus pulcherrimus have been well studied, but little is known about nuclear organisation and its correlation with gene expression in this organism. In their Research Article on page 4097, Naoaki Sakamoto and colleagues perform three-dimensional fluorescence in situ hybridisation analysis to report on the nuclear dynamics of intranuclear positioning of the loci encoding the early histones (one of the types of histone in H. pulcherrimus). The authors find that there are two non-allelic early histone gene loci per sea urchin genome, and that interchromosomal interactions are often formed between these loci on separate chromosomes during the morula stage, when expression of the early histone genes are at their highest. Moreover, these interchromosomal interactions between the early histone gene loci may be correlated with active expression at the loci. This article is the first to give insight into the nuclear dynamics of intranuclear positioning of gene loci in a species of sea urchin, and provides an important step in the understanding of the molecular mechanism of sea urchin development.