Transcribed genes are localized according to chromosomal position within polarized Drosophila embryonic nuclei

When some genes are silenced, their positions within the nucleus can change dramatically [1] [2]. It is unclear, however, whether genes move to new positions when they are activated [3]. The chromosomes within the polarized nuclei of the fruit fly Drosophila have a well-characterized apical-basal orientation (the Rabl configuration [4]). Using a high-resolution in situ hybridization method [5], we found that each of 15 transcribed genes was localized as predicted by their chromosomal position and by the known polarized organization of the chromosomes. We also found that, within their specific apical-basal plane, most nascent transcript foci could occupy any radial position. There was no correlation between the apical-basal position of the transcribed locus and the final cytoplasmic site of localization of the RNA along the apical-basal axis of the cell. There was also no relationship between the distance of loci from the nuclear periphery and the amount of nascent mRNA decorating the gene. Our results are consistent with the view that effective transcription can occur without major re-localization of the genes themselves.