The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output

Abstract

Highlights d The expression domain of the Dorsal target gene sog narrows in the absence of Zelda d Using MS2 reporter transgenes, this can be accurately recapitulated in living embryos d Without Zelda, the onset and degree of reporter activation becomes graded like Dorsal d Zelda promotes accumulation of Dorsal protein at the site of the enhancer

Decoding the Notch signal

“…This "bursty" transcription has been formalized as a two state model of a promoter's activity, which cycles between ON and OFF states with stochastic rate constants (Larson, Singer, & Zenklusen, 2009;Peccoud & Ycart, 1995 The formation of PolII clusters or aggregates is thought to be driven by weak interactions between intrinsically disordered regions/low complexity domains (LCD) in PolII and other proteins (Boehning et al, 2018;Cho et al, 2018;Lu et al, 2018). Similarly, many TFs In agreement with this model, several TFs (Bicoid [Mir et al, 2017[Mir et al, , 2018, Dorsal [Yamada et al, 2019], Zelda [Dufourt et al, 2018;Mir et al, 2018] and Ultrabithorax [Tsai, Alves, & Crocker, 2019;Tsai et al, 2017]) are present in foci or "hubs" in the nucleus. Similarly, many TFs In agreement with this model, several TFs (Bicoid [Mir et al, 2017[Mir et al, , 2018, Dorsal [Yamada et al, 2019], Zelda [Dufourt et al, 2018;Mir et al, 2018] and Ultrabithorax [Tsai, Alves, & Crocker, 2019;Tsai et al, 2017]) are present in foci or "hubs" in the nucleus.…”

Spatiotemporal control of gene expression boundaries using a feedforward loop

“…Zld cooperatively interacts with Dl by enhancing its activity near the cis ‐regulatory modules (CRMs) of DV genes, including that of twi . The cooperative effect of Zld on Dl has been previously modeled as an effective increase in the affinity of Dl for its DNA‐binding site .…”

“…In addition, Zld‐binding sites have been found in large numbers near transcription start sites of several of these genes as well as near their enhancer modules . Zld has also been known to increase the local concentration of patterning transcription factors such as Bcd and Dl, thus effectively increasing its local activity . Considering these known effects of Zld, we decided that Zld was a crucial and well‐founded missing piece of our model.…”

“…However, it is known experimentally that zygotic gene expression begins in nc 10 and observable gene expression for twi is first observed in nc 12, localized to the 20% ventral most nuclei . Therefore, we included in our model the activity of pioneer factor Zelda (Zld), which has been shown to make enhancer regions accessible for transcription factors and to locally increase transcription factor concentration at enhancer sites . A previous model of Zld activity showed that cooperativity between Zld and Dl may help explain Dl‐dependent gene expression patterns .…”

“…[20][21][22][23] Therefore, we included in our model the activity of pioneer factor Zelda (Zld), which has been shown to make enhancer regions accessible for transcription factors and to locally increase transcription factor concentration at enhancer sites. [24][25][26][27][28] A previous model of Zld activity showed that cooperativity between Zld and Dl may help explain Dl-dependent gene expression patterns. 29 We observed that a temporal gradient of Zld stabilizes the gradient of Dl to ensure proper timing of gene expression of its targets.…”