Spatial organization of transcribing loci during early genome activation in Drosophila

• Published in: Current biology Vol. 31; no. 22; pp. 5102 - 5110.e5
• Main Authors: Huang, Shao-Kuei, Whitney, Peter H., Dutta, Sayantan, Shvartsman, Stanislav Y., Rushlow, Christine A.
• Format: Journal Article
• Language: English
• Published: England Elsevier Inc 22-11-2021
• Subjects: Animals; Drosophila - genetics; Drosophila - metabolism; Drosophila melanogaster - genetics; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; Gene Expression Regulation, Developmental; genome activation; histone locus body; Nuclear Proteins - metabolism; RNA polymerase II; RNA Polymerase II - genetics; speckles; Transcription Factors - metabolism; Transcriptional Activation; Zelda; genome activation; histone locus body; speckles; Zelda; RNA polymerase II
• ISSN: 0960-9822; 1879-0445
• DOI: 10.1016/j.cub.2021.09.027

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 ∼110 discrete “speckles” of 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.
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•RNA polymerase II (RNA Pol II) accumulates into nuclear speckles at genome activation•Without the pioneer factor Zelda, speckle number and size are greatly reduced•RNA Pol II moves instead to the histone locus bodies and histone RNA synthesis increases•Genes in close 3D proximity do not share a RNA Pol II speckle
Genome activation in Drosophila begins at 1 h of development. Huang et al. demonstrate that RNA polymerase II accumulates in discrete foci, or speckles, whose number and size depend on the pioneer factor Zelda. Transcribing genes that come into close 3D proximity (<400 nm) do not share a speckle, suggesting that co-regulated genes do not share RNA polymerase II factories.