Figure
Temporal organization of Zygotic Genome Activation and design of published high-throughput experiments used to extract early induced gene clusters.(A) Schematic representation of mRNA concentration evolution during early drosophila embryogenesis. The horizontal axis represents time, in minutes after fertilisation (upper scale) or mitotic cycles (lower scale). Red: maternal mRNAs; light blue: first wave of zygotic transcription; dark blue: second wave of zygotic transcription. (B) Time points sampled in transcriptome microarray experiments performed by Pilot et al. (2006). (C) Respective contribution of maternal and zygotic mRNAs. Arrows represent the action of early expressed TF on secondary targets. (D) Time points of transcriptome microarray experiments published by Lu et al. (2009). D and H denote diploids and haploids; the numbers indicate the mitotic cycle number; E and L stand for early and late. Developmental milestones are indicated for haploid mutant embryos; notice the differences with wild-type timing in (A).
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Background
In all Metazoa, transcription is inactive during the first mitotic cycles after fertilisation. In Drosophila melanogaster, Zygotic Genome Activation (ZGA) occurs in two waves, starting respectively at mitotic cycles 8 (approximately 60 genes) and 14 (over a thousand genes). The regulatory mechanisms underlying these drastic transcription...
Contexts in source publication
Context 1
... as the "maternal-to-zygotic transition" (MZT), this fundamen- tal process is conserved between metazoans [1]. Zygotic Genome Activation (ZGA) occurs in two successive waves: a minor wave involving a few tens of genes, followed by a major wave affecting several hundreds of genes ( Figure 1A). ...Context 2
... order to identify novel factors involved in ZGA, we have used a series of computational analysis tools to revisit three transcriptomic studies: (1) The first study aimed at detecting genes involved in the process of cellularisa- tion: Pilot et al. (2006) [3] extracted mRNAs at five time points corresponding to fertilisation (T0), slow (T1) and fast (T2) phases of cellularisation, early gastrulation (T3) and late gastrulation (T4), respectively ( Figure 1B); (2) De Renzis et al. (2007) [2] compared the expression pro- files of wild-type embryos to those of embryos deleted for half-chromosomes, in order to analyse the respec- tive contributions of maternal and zygotic mRNA during early embryogenesis. They identified five main classes of early expressed genes: (i) maternal and zygotic; (ii) mater- nal degraded and zygotic; (iii) purely zygotic; (iv) early- activated zygotic; (v) secondary targets ( Figure 1C); (3) Lu et al. (2009) [6] compared expression profiles in haploid mutants versus wild type embryos in order to distinguish genes regulated by the NC ratio from those controlled by the maternal clock ( Figure 1D). ...Context 3
... order to identify novel factors involved in ZGA, we have used a series of computational analysis tools to revisit three transcriptomic studies: (1) The first study aimed at detecting genes involved in the process of cellularisa- tion: Pilot et al. (2006) [3] extracted mRNAs at five time points corresponding to fertilisation (T0), slow (T1) and fast (T2) phases of cellularisation, early gastrulation (T3) and late gastrulation (T4), respectively ( Figure 1B); (2) De Renzis et al. (2007) [2] compared the expression pro- files of wild-type embryos to those of embryos deleted for half-chromosomes, in order to analyse the respec- tive contributions of maternal and zygotic mRNA during early embryogenesis. They identified five main classes of early expressed genes: (i) maternal and zygotic; (ii) mater- nal degraded and zygotic; (iii) purely zygotic; (iv) early- activated zygotic; (v) secondary targets ( Figure 1C); (3) Lu et al. (2009) [6] compared expression profiles in haploid mutants versus wild type embryos in order to distinguish genes regulated by the NC ratio from those controlled by the maternal clock ( Figure 1D). ...Context 4
... order to identify novel factors involved in ZGA, we have used a series of computational analysis tools to revisit three transcriptomic studies: (1) The first study aimed at detecting genes involved in the process of cellularisa- tion: Pilot et al. (2006) [3] extracted mRNAs at five time points corresponding to fertilisation (T0), slow (T1) and fast (T2) phases of cellularisation, early gastrulation (T3) and late gastrulation (T4), respectively ( Figure 1B); (2) De Renzis et al. (2007) [2] compared the expression pro- files of wild-type embryos to those of embryos deleted for half-chromosomes, in order to analyse the respec- tive contributions of maternal and zygotic mRNA during early embryogenesis. They identified five main classes of early expressed genes: (i) maternal and zygotic; (ii) mater- nal degraded and zygotic; (iii) purely zygotic; (iv) early- activated zygotic; (v) secondary targets ( Figure 1C); (3) Lu et al. (2009) [6] compared expression profiles in haploid mutants versus wild type embryos in order to distinguish genes regulated by the NC ratio from those controlled by the maternal clock ( Figure 1D). ...Context 5
... main computational analysis tools used in this work are encompassed in the flowchart presented in the Additional file 1: Figure S1 and detailed in the Meth- ods section. We first analysed the clusters of co-expressed genes published by Pilot et al. [3] and clusters that we generated ourselves with classical clustering meth- ods (hierarchical and supervised clustering). ...Context 6
... ROC curves (Additional file 14: Figure S10) high- light a strong enrichment of ZGA predicted CRMs for Zelda (1 h, 2 h, 3 h), TRL (0-8 h), CBP (0-4 h) and H3K4me1 (0-4h) as well as DNAse1 hypersensitive sites (stage 5) that together correspond to signatures of active enhancer. This alone confirms the biological rele- vance of our CRMs defined purely from sequence motifs around ZGA specific genes. ...Context 7
... might reflect the tight regulation of the genes controlled by these CRMs, which are active in few spatially located nuclei, but highly repressed by Polycomb-group proteins in the major part of the embryo, as indicated by a recent study by Negre and co-workers [30]. Moreover these repressive marks remain associated with blastoderm CRMs at later stages (Additional file 15: Figure S11). ...Context 8
... contrast, during the time window corresponding to zygotic genome activation (0-4 h), the predicted CRMs of ZGA genes (red curves on Additional file 14: Figure S10) show a significant enrichment for some marks of transcriptional activity (H3K4me1, CBP) but not for repressive marks (H3K27me3, H3K9me3), where the red curve is intermingled with the negative controls (green, purple and blue curves). This seems consistent with a general activation of many genes in the whole embryo. ...Context 9
... CRM) for a given ChIP-seq annotation track, we interpolated densities between the annotated positions, and sum their values over the whole length of the region, to obtain a total read intensity of the region (I r ). Additional file 16: Figure S12A presents the principle and notations used in following formulas. Let us consider a pair of consecutive annotated positions x i and x i+1 (separated by 100bp for example) with densities d i and d i+1 , respectively. ...Context 10
... computation of ROC curves is based on region rank- ing according to I r as shown in Additional file 16: Figure S12B. Values were then normalized along the x and y axis in order to obtain comparable ROC curves between differ- ent analyses, i.e. different tested regions (predicted CRMs from ZGA or control non-coding sequences, curated CRMs etc) or different genome-wide protein location experiments. ...Similar publications
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Citations
... ZGA is not a singular event but a period during which transcription gradually becomes activated, marked by two distinct transcriptional waves. The first, smaller wave occurs during the early cleavage divisions, while the second, more significant wave coincides with the pause in the first division cycle across diverse species [4,27]. Although the precise timing of these waves and the number of division cycles vary among species [28], the process within a given species is meticulously controlled, exhibiting highly reproducible temporal patterns. ...
Mammalian fertilization initiates the reprogramming of oocytes and sperm, forming a totipotent zygote. During this intricate process, the zygotic genome undergoes a maternal-to-zygotic transition (MZT) and subsequent zygotic genome activation (ZGA), marking the initiation of transcriptional control and gene expression post- fertilization. Histone modifications are pivotal in shaping cellular identity and gene expression in many mammals. Recent advances in chromatin analysis have enabled detailed explorations of histone modifications during ZGA. This review delves into conserved and unique regulatory strategies, providing essential insights into the dynamic changes in histone modifications and their variants during ZGA in mammals. The objective is to explore recent advancements in leading mechanisms related to histone modifications governing this embryonic development phase in depth. These considerations will be useful for informing future therapeutic approaches that target epigenetic regulation in diverse biological contexts. It will also contribute to the extensive areas of evolutionary and developmental biology and possibly lay the foundation for future research and discussion on this seminal topic.
... The experiment indicated that in the case of Zld gene mutation, the important genes for early embryonic development of Drosophila, like genes conducive to sex selection could not be effectively expressed. At the same time, the lack of Zld often directly leads to the death of embryos [2][3][4][5][6]. ...
The genetic regulation mechanism of early Drosophila embryo has been a research hotspot in the past few decades. Understanding the early genetic regulation mechanisms of Drosophila embryos plays an important role in understanding the growth and development of other animals. In previous studies, an important Transcription Activator, Zelda (Zld), was reported. Zld is a global activator of early embryonic transcription. During the early development of embryos, all animals undergo the material-to-zygotic Transition (MZT), where Zld plays an important role in degrading maternal mRNA and mediating the expression of over 120 zygotic genes. The absence or mutation of Zld will directly lead to the inability of the embryo to complete the MZT process and result in lethality. TAGteam is a special sequence upstream of many genes in Drosophila, and Zld plays a role as a binding protein of TAGteam. TAGteam is a highly conserved sequence that generally exists in the form of CAGGTAG. Mutations or lack of TAGteam often result in inability to bind to Zld, resulting in the inability of genes to be expressed normally. The two genes involved in this experiment, CG14014 (2L: 5549709.. 550835 [-]) and CG18269 (2L: 5551838.. 5552756 [+]), are two adjacent genes on the Drosophila chromosome. They are located on two different DNA strands and facing in opposite directions, while their current role is not yet clear. There are typical TAGteam sequences upstream of both genes. This article conducts experiments to verify the relationship between these two genes and the regulation of Zld protein, and explores the possibility of their co-regulation by designing experiments.
... The development of a multicellular organism occurs due to the timely activation of genes in cells of a certain type, which develop in the form of "transcriptional waves" [1,2]. The transcriptional cycle of genes in multicellular organisms is under the control of both temporal and spatial regulators. ...
According to previous studies, during Drosophila embryogenesis, the recruitment of RNA polymerase II precedes active gene transcription. This work is aimed at exploring whether this mechanism is used during Drosophila metamorphosis. In addition, the composition of the RNA polymerase II “paused” complexes associated with promoters at different developmental stages are described in detail. For this purpose, we performed ChIP-Seq analysis using antibodies for various modifications of RNA polymerase II (total, Pol II CTD Ser5P, and Pol II CTD Ser2P) as well as for subunits of the NELF, DSIF, and PAF complexes and Brd4/Fs(1)h that control transcription elongation. We found that during metamorphosis, similar to mid-embryogenesis, the promoters were bound by RNA polymerase II in the “paused” state, preparing for activation at later stages of development. During mid-embryogenesis, RNA polymerase II in a “pause” state was phosphorylated at Ser5 and Ser2 of Pol II CTD and bound the NELF, DSIF, and PAF complexes, but not Brd4/Fs(1)h. During metamorphosis, the “paused” RNA polymerase II complex included Brd4/Fs(1)h in addition to NELF, DSIF, and PAF. The RNA polymerase II in this complex was phosphorylated at Ser5 of Pol II CTD, but not at Ser2. These results indicate that, during mid-embryogenesis, RNA polymerase II stalls in the “post-pause” state, being phosphorylated at Ser2 of Pol II CTD (after the stage of p-TEFb action). During metamorphosis, the “pause” mechanism is closer to classical promoter-proximal pausing and is characterized by a low level of Pol II CTD Ser2P.
... For example, in C. elegans, chromosomes are tethered to the NE through chromosomal regions called pairing centers and not telomeres [20], and the oocyte symmetry is only broken upon fertilization [75]. In Drosophila, chromosomal pairing utilizes centromeres instead of telomeres and intriguingly occurs during the mitotic division preceding meiosis [15,76,77]. Finally, in mice spermatocytes a Bb does not form, and other processes that are not directly involved in chromosomal paring have not been associated with the bouquet configuration. ...
... It has been shown that the regulation of ZGA in Drosophila involves TFs Zelda, Tramtrack, and chromatin remodeling factor Trithorax-like (Trl), which bind the regulatory sites of invertebrate genes activated during ZGA. The involvement of Trl in this process suggests that at least in invertebrates, ZGA probably depends on epigenetic regulation [77]. In the absence of evidence that essential components of this mechanism are evolutionarily conserved, it might be difficult at the moment to see the importance of these findings for vertebrate development. ...
Primordial germ cells (PGCs) are the precursor cells that form during early embryogenesis and later differentiate into oocytes or spermatozoa. Abnormal development of PGCs is frequently a causative factor of infertility and germ cell tumors. However, our understanding of PGC development remains insufficient, and we have few pharmacological tools for manipulating PGC development for biological study or therapy. The zebrafish (Danio rerio) embryos provide an excellent in vivo animal model to study PGCs, because zebrafish embryos are transparent and develop outside the mother. Importantly, the model is also amenable to facile chemical manipulations, including scalable screening to discover novel compounds that alter PGC development. This chapter describes methodologies for manipulating the germline (i.e., PGCs) with small molecules and for monitoring PGC development. Utilizing the 3′UTR of PGC marker genes such as nanos3 and ddx4/vasa is a key component of these methodologies, which consist of expressing fluorescent or luminescent proteins in PGCs, treatment with small molecules, and quantitative observation of PGC development.
... For example, in C. elegans, chromosomes are tethered to the NE through chromosomal regions called pairing centers and not telomeres [20], and the oocyte symmetry is only broken upon fertilization [75]. In Drosophila, chromosomal pairing utilizes centromeres instead of telomeres and intriguingly occurs during the mitotic division preceding meiosis [15,76,77]. Finally, in mice spermatocytes a Bb does not form, and other processes that are not directly involved in chromosomal paring have not been associated with the bouquet configuration. ...
... It has been shown that the regulation of ZGA in Drosophila involves TFs Zelda, Tramtrack, and chromatin remodeling factor Trithorax-like (Trl), which bind the regulatory sites of invertebrate genes activated during ZGA. The involvement of Trl in this process suggests that at least in invertebrates, ZGA probably depends on epigenetic regulation [77]. In the absence of evidence that essential components of this mechanism are evolutionarily conserved, it might be difficult at the moment to see the importance of these findings for vertebrate development. ...
Activation of the embryonic genome during development represents a major developmental transition in all species. The history of its exploration began in the 1950s–1960s, when this idea was put forward and proven experimentally by Alexander Neyfakh. He observed the aberrant development of fish embryos upon X-ray irradiation and noted the different developmental outcomes depending on the stage when fertilized eggs were subjected to irradiation. Neyfakh also discriminated a regional difference of X-irradiation between the nucleus and the cytoplasm. By selecting the X-ray dose causing nuclear damage, he determined the beginning of zygotic transcription, which at that time became known as the morphogenetic function of nuclei. His team defined the link of zygotic transcription with the asynchronization of cell division and cell migration, the two other hallmarks, which along with the morphogenetic function (or the zygotic genome activation), are at the core of the mid-blastula transition during development. Within this framework, current studies using maternal mutants and application of modern methods of whole-embryo and single-cell transcriptomics begin to decipher the molecular mechanisms of the mid-blastula transition (or the maternal-zygotic transition).
... Alternatively, while the Trl/GAF motif was associated with all classes of peaks, it was enriched in Zld-only peaks. Furthermore, Trl/GAF and Dref were shown to be associated with early versus late embryonic expression (stage five and later), respectively (Darbo et al., 2013;Schulz et al., 2015;Hochheimer et al., 2002). These results collectively support the view that Opa, like Dref, is a late-acting factor, and that Trl/GAF may work early with Zelda. ...
Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa’s role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.
... Alternatively, while the Trl/GAF motif was associated with all classes of peaks, it was enriched in Zld-only peaks. Furthermore, Trl/GAF and Dref were shown to be associated with early versus late embryonic expression (stage five and later), respectively (Darbo et al., 2013;Schulz et al., 2015;Hochheimer et al., 2002). These results collectively support the view that Opa, like Dref, is a late-acting factor, and that Trl/GAF may work early with Zelda. ...
Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa’s role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.
... Alternatively, while the Trl/GAF motif was associated with all classes of peaks, it was enriched in Zld-only peaks. Furthermore, Trl/GAF and Dref were shown to be associated with early versus late embryonic expression (stage 5 and later), respectively (Darbo et al. 2013;Schulz et al. 2015;Hochheimer et al. 2002). These results collectively support the view that Opa, like Dref, is a late-acting factor, and that Trl/GAF may work early with Zelda. ...
Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa’s role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.
... The G1-phase is not introduced until cycle 17. Main zygotic genome activation occurs at mitotic cycle 14, which coincides with enrichment of active epigenetic marks, transcription and chromatinremodeling factors (Darbo et al. 2013). Changes in cell cycle and zygotic genome activation represent the main wellstudied events that define the period of MBT during early embryonic development in Drosophila . ...
Su(var) mutations define epigenetic factors controlling heterochromatin formation and gene silencing in Drosophila. Here, we identify SU(VAR)2-1 as a novel chromatin regulator that directs global histone deacetylation during the transition of cleavage chromatin into somatic blastoderm chromatin in early embryogenesis. SU(VAR)2-1 is heterochromatin-associated in blastoderm nuclei but not in later stages of development. In larval polytene chromosomes, SU(VAR)2-1 is a band-specific protein. SU(VAR)2-1 directs global histone deacetylation by recruiting the histone deacetylase RPD3. In Su(var)2-1 mutants H3K9, H3K27, H4K8 and H4K16 acetylation shows elevated levels genome-wide and heterochromatin displays aberrant histone hyper-acetylation. Whereas H3K9me2- and HP1a-binding appears unaltered, the heterochromatin-specific H3K9me2S10ph composite mark is impaired in heterochromatic chromocenters of larval salivary polytene chromosomes. SU(VAR)2-1 contains an NRF1/EWG domain and a C2HC zinc-finger motif. Our study identifies SU(VAR)2-1 as a dosage-dependent, heterochromatin-initiating SU(VAR) factor, where the SU(VAR)2-1-mediated control of genome-wide histone deacetylation after cleavage and before mid-blastula transition (pre-MBT) is required to enable heterochromatin formation.
... Maternal genes also enable the activation of zygotic genes. During this maternal stage, the Zelda pioneer TF has been shown to bind to enhancers of early transcribed developmental genes, favoring their expression (Darbo et al., 2013;Foo et al., 2014;Liang et al., 2008a). This contributes to the first wave of zygotic activation at nc 8 ( Fig. 7, light blue) with the transcription of a small set of genes (mostly segmentation genes) which is then followed by a second massive wave of zygotic transcription (Fig. 7, dark blue) starting at nc 13 and involving thousands of genes (Tadros & Lipshitz, 2009). ...
During development, cell differentiation frequently occurs upon signaling from gradients of molecules, called morphogens. A simple paradigm to study morphogens is the Bicoid gradient, which determines antero-posterior patterning in fruit fly embryos. This transcription factor allows the rapid expression of its major target gene hunchback, in an anterior domain with a sharp boundary. Using the MS2 system to fluorescently tag RNA in living embryos, we were able to show that the ongoing transcription process at the hunchback promoter is bursty Surprisingly, it takes only 3 minutes, from the first hints of transcription at the anterior to reach steady state with the setting of the sharp expression border in the middle of the embryo. To better understand the role of transcription factors other than Bicoid in this process, I used a two-pronged strategy involving synthetic MS2 reporters combined with the analysis of the hunchback MS2 reporter in various mutant backgrounds. The synthetic reporter approach, indicate that Bicoid is able to activate transcription on its own when bound to the promoter but in a stochastic manner. The binding of Hunchback to the Bicoid-dependent promoter reduces this stochasticity while Caudal might act as a posterior repressor gradient. Altogether, this work provide a new light on the mechanisms insuring a precise transcriptional response downstream of Bicoid.
