Rushlow, C. | bioRxiv Science

bioRxiv2025

The pioneer factor Zelda induces male-to-female somatic sex reversal in adult tissues

Somatic sex identity must be maintained throughout adulthood for tissue function. Adult somatic stem cells in the Drosophila testis (i.e., CySCs) lacking the transcription factor Chinmo are reprogrammed to their ovarian counterparts by induction of female-specific TraF, but this is not mechanistically understood. Pioneer factors play central roles in direct reprogramming, and many upregulated genes in chinmo-/- CySCs contain binding sites for the pioneer factor Zelda (Zld). microRNAs repress zld mRNA in wild type CySCs, but they are downregulated after Chinmo loss, allowing for zld mRNA translation. Zld depletion from chinmo-/- CySCs suppresses feminization, and ectopic Zld induces TraF and feminizes wild-type CySCs. qkr58E-2 and ecdysone receptor (EcR), direct Zld targets in the embryo, are female-biased in adult gonads and upregulated in chinmo-/- CySCs. The RNA-binding protein Qkr58E-2 produces TraF, while EcR promotes female-biased gene expression. Ectopic Zld feminizes adult male adipose tissue, demonstrating that Zld can instruct female and override male identity in adult XY tissues. HighlightsO_LIzld mRNA is repressed by microRNAs in XY somatic gonadal cells C_LIO_LIZld is upregulated in and required for sex reversal of XY chinmo-/- cells C_LIO_LIZld induces Qkr58E-2 and EcR, which cause TraF and female-biased transcription C_LIO_LIZld feminizes XY adipose cells by inducing TraF and downregulating Chinmo C_LI

developmental biology↗

bioRxiv2021

An "individualist" model of an active genome in a developing embryo

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 whole genome. Using Drosophila embryos undergoing the first wave of genome activation, we detected discrete "speckles" of RNA Polymerase II (Pol II), and showed that they overlap with transcribing loci. We characterized the spatial distribution of Pol II speckles and quantified how this distribution changes in the absence of the primary driver of Drosophila genome activation, the pioneer factor Zelda. Although the number and size of Pol II speckles were reduced, indicating that Zelda promotes Pol II speckle formation, we observed a uniform distribution of distances between active genes in the nuclei of both wildtype and zelda mutant embryos. This suggests that the topologically associated domains identified by Hi-C studies do little to spatially constrain groups of transcribed genes at this time. We provide evidence that linear genomic distance between transcribed genes is the primary determinant of measured physical distance between the active loci. Furthermore, we show active genes can have distinct Pol II pools even if the active loci are in close proximity. 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.

developmental biology↗