CLAMP regulates zygotic genome activation in Drosophila embryos

Abstract

Embryonic patterning is critically dependent on zygotic genome activation (ZGA). In Drosophila melanogaster embryos, the pioneer factor Zelda directs ZGA, possibly in conjunction with other factors. Here we have explored novel involvement of Chromatin-Linked Adapter for MSL Proteins (CLAMP) during ZGA. CLAMP binds thousands of sites genome-wide throughout early embryogenesis. Interestingly, CLAMP relocates to target promoter sequences across the genome when ZGA is initiated. Although there is a considerable overlap between CLAMP and Zelda binding sites, the proteins display distinct temporal dynamics. To assess whether CLAMP occupancy affects gene expression, we analyzed transcriptomes of embryos zygotically compromised for either clamp or zelda and found that transcript levels of many zygotically-activated genes are similarly affected. Importantly, compromising either clamp or zelda disrupted the expression of critical segmentation and sex determination genes bound by CLAMP (and Zelda). Furthermore, clamp knockdown embryos recapitulate other phenotypes observed in Zelda-depleted embryos, including nuclear division defects, centrosome aberrations, and a disorganized actomyosin network. Based on these data, we propose that CLAMP acts in concert with Zelda to regulate early zygotic transcription.

Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis

“…Beyond vertebrates, unrelated maternal factors direct genome activation and the induction of stem cells, e.g. Zelda (Liang et al, 2008), CLAMP (Colonnetta et al, 2021; Duan et al, 2021) and GAF (Gaskill et al, 2021) in Drosophila, though they seem to share many functional aspects with vertebrate pluripotency factors, including pioneering roles in opening repressed embryonic chromatin and establishing activating histone modifications (Blythe and Wieschaus, 2016; Gaskill et al, 2021; Hug et al, 2017). This diversity of strategies implies that the gene network regulating pluripotency has been extensively modified over evolutionary time (Endo et al, 2020; Fernandez-Tresguerres et al, 2010), though it is unknown when and under what circumstances major modifications arose.…”

Germline/soma distinction in Drosophila embryos requires regulators of zygotic genome activation

“…In this case, we mated mat-Gal4 (i.e. 67.15 ) virgin females to males carrying UAS-zldi RNAi ( zldi 2z ) or UAS-egfpi as a control ( egfpi z ) ( Colonnetta et al, 2021a ; Duan et al, 2021 ). While the egfpi z embryos had an average of 19.7 PGCs (n=10), the zldi 2z embryos had only 12.9 PGCs on average (n=8; p=0.002 by t-test) ( Table 1 ).…”

“…The global activation of transcription in Drosophila depends on several factors that act genome-wide to coordinate ZGA. The known factors include Zelda (Zld), CLAMP, and GAGA factor (GAF) ( Bhat et al, 1996 ; Colonnetta et al, 2021a ; Duan et al, 2021 ; Gaskill et al, 2021 ; Harrison et al, 2011 ; Liang et al, 2008 ; McDaniel et al, 2019 ; Moshe and Kaplan, 2017 ; Nien et al, 2011 ). Among these, by far the best studied is Zld, a C 2 H 2 zinc-finger transcription factor that binds to target sequences throughout the genome.…”

“…For these reasons, we wondered whether the chromatin factors that set the stage for the major wave of ZGA in NC14 also impact the process of PGC specification in early blastoderm embryos. Making this idea even more plausible is the fact that compromising ZGA regulators adversely influences nuclear division, centrosomes, and cytoskeletal elements ( Bhat et al, 1996 ; Colonnetta et al, 2021a ; Liang et al, 2008 ; Staudt et al, 2006 ), all of which play a critical role in PGC formation and specification. Here, we have examined the role of two different ZGA regulators, Zld and CLAMP, during the establishment of germline/soma distinction in early embryos, and we demonstrate their requirement for proper specification of both soma and PGCs.…”

Dimerization Activity of a Disordered N-Terminal Domain from Drosophila CLAMP Protein

“…CLAMP is an essential transcription factor that binds thousands of sites throughout the genome [ 28 , 29 , 30 ]. Similar to GAF and Zelda proteins, CLAMP is involved in zygotic gene activation (ZGA), a dramatic reprogramming that occurs in the zygotic nucleus to initiate global transcription and prepare the embryo for further development [ 31 , 32 ]. CLAMP and GAF are components of the late boundary complex (LBC), which binds the Fab-7 and Fab-8 boundaries in the bithorax complex and is involved in the regulation of long-distance interactions between enhancers and promoters [ 33 , 34 , 35 , 36 ].…”