Spatial organization of transcribing loci early activation in Drosophila

The early Drosophila embryo provides unique experimental advantages for addressing fundamental questions of gene regulation at multiple levels of organization, from individual gene loci to the entire genome. Using 1.5-h-old Drosophila embryos undergoing the first wave of genome activation,(1) we detected similar to 110 discrete specklesof RNA polymerase II (RNA Pol II) per nucleus, two of which were larger and localized to the histone locus bodies (HLBs).(2,3) In the absence of the primary driver of Drosophila genome activation, the pioneer factor Zelda (Zld),(1,4,5) 70% fewer speckles were present; however, the HLBs tended to be larger than wild-type (WT) HLBs, indicating that RNA Pol II accumulates at the HLBs in the absence of robust early-gene transcription. We observed a uniform distribution of distances between active genes in the nuclei of both WT and zld mutant embryos, indicating that early co-regulated genes do not cluster into nuclear sub-domains. However, in instances whereby transcribing genes did come into close 3D proximity (within 400 nm), they were found to have distinct RNA Pol II speckles. In contrast to the emerging model whereby active genes are clustered to facilitate co-regulation and sharing of transcriptional resources, our data support an individualist model of gene control at early genome activation in Drosophila. This model is in contrast to a collectivist model, where active genes are spatially clustered and share transcriptional resources, motivating rigorous tests of both models in other experimental systems.

Automated summary

Studying early Drosophila embryos revealed that RNA polymerase II accumulates at histone locus bodies during early genome activation. Co-regulated genes do not cluster into nuclear sub-domains, but transcribing genes in close 3D proximity have distinct RNA polymerase II speckles. This challenges the emerging model of clustered active genes in gene regulation.