Zygotic Genome Research Articles

Sex-specific splicing occurs genome-wide during early Drosophila embryogenesis.

Sex-specific splicing is an essential process that regulates sex determination and drives sexual dimorphism. Yet, how early in development widespread sex-specific transcript diversity occurs was unknown because it had yet to be studied at the genome-wide level. We use the powerful Drosophila model to show that widespread sex-specific transcript diversity occurs early in development, concurrent with zygotic genome activation. We also present a new pipeline called time2Splice to quantify changes in alternative splicing over time. Furthermore, we determine that one of the consequences of losing an essential maternally deposited pioneer factor called CLAMP (chromatin-linked adapter for MSL proteins) is altered sex-specific splicing of genes involved in diverse biological processes that drive development. Overall, we show that sex-specific differences in transcript diversity exist even at the earliest stages of development..

OBOX regulates mouse zygotic genome activation and early development.

Zygotic genome activation (ZGA) activates the quiescent genome to enable thematernal-to-zygotic transition1,2. However, the identity of transcription factors that underlie mammalian ZGA in vivo remains elusive. Here we show that OBOX, a PRD-like homeobox domain transcriptionfactor family (OBOX1-OBOX8)3-5, are key regulators of mouse ZGA. Mice deficient for maternally transcribed Obox1/2/5/7 and zygotically expressed Obox3/4 had a two-cellto four-cellarrest, accompanied by impaired ZGA. TheObox knockout defects could be rescued by restoring either maternal and zygotic OBOX, which suggests that maternal and zygotic OBOX redundantly support embryonic development. Chromatin-binding analysis showed that Obox knockout preferentially affected OBOX-binding targets. Mechanistically, OBOX facilitated the'preconfiguration'of RNA polymerase II,as the polymerase relocated from the initial one-cell binding targets to ZGA gene promoters and distal enhancers. Impaired polymerase II preconfiguration in Obox mutants was accompanied by defective ZGA and chromatin accessibility transition, as well as aberrant activation of one-cell polymerase II targets. Finally, ectopic expression of OBOX activated ZGA genes and MERVL repeats in mouse embryonic stem cells. These data thus demonstrate that OBOX regulates mouse ZGA and early embryogenesis.

Maternal TDP-43 interacts with RNA Pol II and regulates zygotic genome activation

Zygotic genome activation (ZGA) is essential for early embryonic development. However, the regulation of ZGA remains elusive in mammals. Here we report that a maternal factor TDP-43, a nuclear transactive response DNA-binding protein, regulates ZGA through RNA Pol II and is essential for mouse early embryogenesis. Maternal TDP-43 translocates from the cytoplasm into the nucleus at the early two-cell stage when minor to major ZGA transition occurs. Genetic deletion of maternal TDP-43 results in mouse early embryos arrested at the two-cell stage. TDP-43 co-occupies with RNA Pol II as large foci in the nucleus and also at the promoters of ZGA genes at the late two-cell stage. Biochemical evidence indicates that TDP-43 binds Polr2a and Cyclin T1. Depletion of maternal TDP-43 caused the loss of Pol II foci and reduced Pol II binding on chromatin at major ZGA genes, accompanied by defective ZGA. Collectively, our results suggest that maternal TDP-43 is critical for mouse early embryonic development, in part through facilitating the correct RNA Pol II configuration and zygotic genome activation.

Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition

BackgroundThe oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic genome activation. How the transcriptome, translatome, and proteome are coordinated during this critical developmental window remains poorly understood.ResultsUtilizing a highly sensitive and quantitative mass spectrometry approach, we obtain high-quality proteome data spanning seven mouse stages, from full-grown oocyte (FGO) to blastocyst, using 100 oocytes/embryos at each stage. Integrative analyses reveal distinct proteome reprogramming compared to that of the transcriptome or translatome. FGO to 8-cell proteomes are dominated by FGO-stockpiled proteins, while the transcriptome and translatome are more dynamic. FGO-originated proteins frequently persist to blastocyst while corresponding transcripts are already downregulated or decayed. Improved concordance between protein and translation or transcription is observed for genes starting translation upon meiotic resumption, as well as those transcribed and translated only in embryos. Concordance between protein and transcription/translation is also observed for proteins with short half-lives. We built a kinetic model that predicts protein dynamics by incorporating both initial protein abundance in FGOs and translation kinetics across developmental stages.ConclusionsThrough integrative analyses of datasets generated by ultrasensitive methods, our study reveals that the proteome shows distinct dynamics compared to the translatome and transcriptome during mouse OET. We propose that the remarkably stable oocyte-originated proteome may help save resources to accommodate the demanding needs of growing embryos. This study will advance our understanding of mammalian OET and the fundamental principles governing gene expression.

Possible role of translation in unfertilized sea urchin eggs.

Unfertilized eggs of animals contain maternal messenger RNAs (mRNAs) and proteins, which are required for the maintenance of metabolism and regulation of development during the initial stages of embryogenesis. Unfertilized eggs are transcriptionally and translationally quiescent. After fertilization, activated translation of maternal mRNAs is one of the major forces that direct the early stages of embryogenesis before activation of the zygotic genome. However, a low rate and level of protein synthesis have been detected in unfertilized sea urchin eggs indicating that translation is not completely inhibited. Analysis of translatomes of unfertilized eggs and early embryos detected three sets of maternal mRNAs translated either before or after fertilization, or both before and after fertilization. Proteins encoded by maternal mRNAs, which are translated in unfertilized eggs, perform many different functions required for homeostasis, fertilization, egg activation, and early development. This suggests that translation in unfertilized sea urchin eggs may be required to renew the pool of proteins involved in these processes. Thus, translation may be necessary to maintain the fertility and developmental potential of sea urchin eggs during the long-term storage of eggs in ovaries until spawning begins.

Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin.

Nanoscale chromatin organization regulates gene expression. Although chromatin is notably reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. In this work, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed "kiss and kick", in which enhancer-promoter contacts are transient and released by transcriptional elongation. Our results demonstrate that ChromExM is broadly applicable to study nanoscale nuclear organization.

Randomly incorporated genomic N6‐methyldeoxyadenosine delays zygotic transcription initiation in a cnidarian

N6‐methyldeoxyadenosine (6mA) is a chemical alteration of DNA, observed across all realms of life. Although the functions of 6mA are well understood in bacteria and protists, its roles in animal genomes have been controversial. We show that 6mA randomly accumulates in early embryos of the cnidarian Hydractinia symbiolongicarpus, with a peak at the 16‐cell stage followed by clearance to background levels two cell cycles later, at the 64‐cell stage—the embryonic stage at which zygotic genome activation occurs in this animal. Knocking down Alkbh1, a putative initiator of animal 6mA clearance, resulted in higher levels of 6mA at the 64‐cell stage and a delay in the initiation of zygotic transcription. Our data are consistent with 6mA originating from recycled nucleotides of degraded m6A‐marked maternal RNA postfertilization. Therefore, while 6mA does not function as an epigenetic mark in Hydractinia, its random incorporation into the early embryonic genome inhibits transcription. In turn, Alkbh1 functions as a genomic 6mA “cleaner,” facilitating timely zygotic genome activation. Given the random nature of genomic 6mA accumulation and its ability to interfere with gene expression, defects in 6mA clearance may represent a hitherto unknown cause of various pathologies.

Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2

Pioneer transcription factors interact with nucleosomes to scan silent, compact chromatin, enabling cooperative events that modulate gene activity. While at a subset of sites pioneer factors access chromatin by assisted loading with other transcription factors, the nucleosome-binding properties of pioneer factors enable them to initiate zygotic genome activation, embryonic development, and cellular reprogramming. To better understand nucleosome targeting invivo, we assess whether pioneer factors FoxA1 and Sox2 target stable or unstable nucleosomes and find that they target DNase-resistant, stable nucleosomes, whereas HNF4A, a non-nucleosome binding factor, targets open, DNase-sensitive chromatin. Despite FOXA1 and SOX2 targeting similar proportions of DNase-resistant chromatin, using single-molecule tracking, we find that FOXA1 uses lower nucleoplasmic diffusion and longer residence times while SOX2 uses higher nucleoplasmic diffusion and shorter residence times to scan compact chromatin, while HNF4 scans compact chromatin much less efficiently. Thus, pioneer factors target compact chromatin through distinct processes.

Effects of meiotic stage-specific oocyte vitrification on mouse oocyte quality and developmental competence.

Acquisition of germinal vesicle (GV) stage oocytes for fertility preservation (FP) offers several benefits over in vivo matured oocyte cryopreservation following ovarian stimulation, particularly for cancer patients necessitating immediate treatment. Two FP approaches for GV oocytes are available: vitrification before in vitro maturation (IVM) at the GV stage (GV-VI) or post-IVM at the metaphase II (MII) stage (MII-VI). The optimal method remains to be determined. In this study, mouse oocytes were collected without hormonal stimulation and vitrified either at the GV stage or the MII stage following IVM; non-vitrified in vitro matured MII oocytes served as the control (CON). The oocyte quality and developmental competence were assessed to obtain a better method for immediate FP. No significant differences in IVM and survival rates were observed among the three groups. Nevertheless, GV-VI oocytes exhibited inferior quality, including abnormal spindle arrangement, mitochondrial dysfunction, and early apoptosis, compared to MII-VI and CON oocytes. Oocyte vitrification at the GV stage impacted maternal mRNA degradation during IVM. In addition, the GV-VI group demonstrated significantly lower embryonic developmental competence relative to the MII-VI group. RNA sequencing of 2-cell stage embryos revealed abnormal minor zygotic genome activation in the GV-VI group. Vitrification at the GV stage compromised oocyte quality and reduced developmental competence. Consequently, compared to the GV stage, oocyte vitrification at the MII stage after IVM is more suitable for patients who require immediate FP.

P-237 In vitro time to maturation of Metaphase I oocytes: a time-lapse study correlating blastocyst formation and ploidy status

Abstract Study question What is the impact of metaphase I (MI) time to mature period (TTM) regarding blastocyst development and ploidy status? Summary answer A short period of TTM (0.1 to 1.0) is related to an increase number of blastocyst formation when compared to longer TTM (1.1 to 3.0). What is known already To achieve meiotic competence, coordinated nuclear and cytoplasmic changes must occur in the oocyte to support fertilization and DNA replication and to ensure correct ploidy of the zygote and embryonic genome activation. Concomitant with chromosome condensation and migration, oocyte maturation goes by cytoplasm reorganization throughout the transitions of MI, polar body extrusion and MII. Despite the optimization of COH protocols, nearly 20% of the retrieved oocytes remain immature at the GV or MI stages. In vitro maturation of MI could increase the number of available embryos; however, longer culture time may affect oocyte quality, resulting in abnormal fertilization and cleavage. Study design, size, duration Prospective cohort study from 244 patients (n = 277 cycles) that had at least 1 MI oocyte after oocyte retrieval (OPU) following controlled ovarian hyperstimulation (COH) for in vitro fertilization (IVF) treatment according to medical referral in an single private ART center from January/2019 to November/2022. All MI oocytes were placed in a time-lapse incubator (TL, EmbryoScope, Vitrolife, Sweden) to check the exact time of first polar body extrusion (TTM to MII) before intracytoplasmic sperm injection (ICSI). Participants/materials, setting, methods Three hours after OPU, oocytes were denuded and assessed for maturation. Six-hundred and seven MI oocytes were followed in TL and those that reached the MII stage in a maximum of 6 hours post-OPU, were injected by ICSI (at 6h post-OPU) and stratified according to the TTM (0.1-1.0 hours and 1.1-3.0 hours). Fertilization rate, blastocyst formation, and ploidy were assessed. Kruskal-Wallis, chi-squared and Fisher tests were applied for statistical analysis. p < 0,05 was considered significant. Main results and the role of chance Patient mean age (n = 244) was 38,50 ± 3,40 years. From those, 25 patients (10.3%) had 2 cycles and 4 patients (1.6%) had 3 cycles with at least 1 MI oocyte. Age, anti-Müllerian hormone (AMH), #OPU, #MII, %MII (MII/OPU), #MI and MI% (MI/OPU) mean were not statistically different in patients with 1, 2 or 3 cycles in our cohort. One hundred forty-nine patients (61%) in 165 cycles (59.6%) had at least 1 oocyte that reached MII stage. In total, 248 oocytes were injected after 0.1-1.0h (group 1, n = 104, 41.9%) and 1.1-3.0h (group 2, n = 144 oocytes, 58.1%) of in vitro maturation. Age (38,99 ± 3,01 vs 38,85 ± 3,31), AMH (1,27 ± 1,29 vs 1,63 ± 1,87), #OPU (8,98 ± 4,32 vs 8,90 ± 4,34), #MII (4,41 ± 2,74 vs 4,44 ± 2,178), %MII (47.6% ± 18.8% vs 48.4% ± 17.1%) and %MI that followed to ICSI (59.2% ± 28.5% vs 54.8% ± 29.2%) were not different between groups 1 and 2 respectively. The mean number of MI that followed to ICSI were higher in group 1 (1,28 ± 0,48 vs 1,10 ± 0,32, p = 0.0008). Normal fertilization (2PN) and embryo cleavage were similar between groups (54.8% vs 45.1%, p = 0.157, 96.6% vs 93.3%, p = 0.467, respectively). However, blastocyst formation rate (#blastocyst/#fertilized) was higher in group 1 (n = 33, 55.9% vs n = 26, 34.7%, p = 0.015). Euploidy rates were similar between groups (9/28, 32% vs 4/24, 16%, p = 0.336). Limitations, reasons for caution Besides the retrospective nature of this study, male factor and infertility reason were not considered in this analysis. Due to the low number of blastocyst formation and consequentially ploidy assessment and number of embryo transfer, the results regarding euploidy rate may be underestimated and pregnancy rates were not included. Wider implications of the findings Oocytes that reached maturity up to 1 hour after denudation showed higher blastocyst formation rate, thus increasing embryo availability to transfer. In vitro-matured oocytes exhibit increased spindle and chromosomal abnormalities compared with oocytes matured in vivo, which may explain the lower rates of euploid embryos, especially in group 2. Trial registration number Not applicable.

P-276 Telomeres cooperate in zygotic genome activation by affecting DUX4/Dux transcription

Abstract Study question Whether the activation of DUX4, a key inducer in the process of zygotic genome activation (ZGA), is associated with telomere length. Summary answer Telomeres regulate the expression of DUX4/Dux through chromatin remodeling and are thereby involved in ZGA. What is known already In human early embryos, the expression of DUX4 is activated as a key inducer in the initial stage of ZGA, and it, in turn, activates hundreds of genes in the cleavage-stage embryo. Human DUX4 is localized to the subtelomeric region 4q35.2 with a D4Z4 repeat of approximately 10 to 100 units that encodes a homeodomain transcription factor. DUX4 expression is inversely proportional to the telomere length in myoblasts/myotubes derived from FSHD patients Study design, size, duration We characterize the dynamics of telomeres during preimplantation development, and assessed the relationship between the expression of DUX4/Dux and telomere length in preimplantation embryos and human embryonic stem cells. Participants/materials, setting, methods All sperm and immature oocytes were collected after obtaining written informed consent from the donor couples. Telomere length in gametes and early embryos by telomere-specific quantitative fluorescence in situ hybridization (Q-FISH). Main results and the role of chance Zygotic genome activation (ZGA) is initiated once the genome chromatin state is organized in the newly formed zygote. While telomeres are specialized chromatin structures at the ends of chromosomes and are reset during early embryogenesis, the details and significance of telomere changes in preimplantation embryos remain unclear. We demonstrated that the telomere length was shortened in the minor ZGA stage and significantly elongated in the major ZGA stage of human and mouse embryos. Expression of the ZGA pioneer factor DUX4/Dux was negatively correlated with the telomere length. ATAC-sequencing suggested that the chromatin accessibility peaks on the DUX4 promoter region (i.e., the subtelomere of chromosome 4q) were transiently augmented in human minor ZGA. Reduction of telomeric heterochromatin H3K9me3 in the telomeric region also synergistically activated DUX4 expression with p53 in hESCs. We propose herein that telomeres regulate the expression of DUX4/Dux through chromatin remodeling and are thereby involved in ZGA. Limitations, reasons for caution Since the mouse Dux gene is not located at the end of the chromosome, the classical telomere position effect (TPE) pathway may not involve in its activation in early embryos. 3D analysis as presented by Hi-C may be able to make a greater breakthrough in confirming the relationship. Wider implications of the findings We herein provided detailed data on changes in the telomere length during ZGA in human and mouse preimplantation embryos, explored the possibility that the TPE affects regulation of DUX4/Dux gene expression in embryos, and suggest that telomere chromatin remodeling is involved in the ZGA process. Trial registration number not applicable

O-105 Chromatin accessibility of oocytes contributes to PCOS transgenerational inheritance

Abstract Study question What is the underlying mechanism contributing to the transgenerational defects of oocytes and embryos of polycystic ovary syndrome (PCOS)? Summary answer The transgenerational inheritance of abnormal chromatin accessibility in the PCOS oocytes is responsible for the defect of oocytes and embryos in transgeneration. What is known already Studies have provided evidence of compromised oocyte quality and related adverse impacts. Observed PCOS animal-model oocyte defects include meiotic abnormalities, mitochondrial dysfunction, and increased oxidative stress. Elevated androgen levels are associated with reduced fertilization rates and lower cleavage rates during in vitro fertilization (IVF) treatment. PCOS could be transgenerationally transmitted, and unique altered gene expression has been observed in metaphase II (MII) oocytes from all offspring in PCOS mice. Study design, size, duration We profiled the transcriptome and chromatin accessibility of oocytes and preimplantation embryos in F0-F2 offspring of PCOS mice, to explored whether the inheritance of chromatin accessibility defects in PCOS oocytes was responsible for the abnormalities of oocytes and embryos in PCOS offspring. Besides, oocytes from 13 healthy women and 8 women with PCOS, 24 blood samples from 24 women with/without PCOS were analyzed to validate the molecular mechanisms of PCOS inheritance. Duration: 2019.5∼2022.12. Participants/materials, setting, methods PCOS mice models were established by means of DHEA-exposure. Smart-seq2 and DNase-seq were utilized to investigate the transcriptome and chromatin accessibility of oocytes and preimplantation embryos in F0-F2 offspring of PCOS mice. Bioinformatic analysis was applied to explore the differential gene expression and chromatin accessibility of oocytes and embryos in PCOS mice and offspring comparing to controls. Common gene signatures in the tissues of PCOS women and PCOS daughters are analyzed compared to control samples. Main results and the role of chance In PCOS mice, we observed transcriptional alteration in oocytes and 2-cell embryos compared to normal mice. There are 4229 and 1197 differentially expressed genes (DEGs) in PCOS oocytes and 2-cell embryos. The DEGs includes both maternal factors and zygotic genome activation (ZGA) genes. Interestingly, in PCOS 2-cell embryos, we observed hundreds of pre-activated genes which are silence in normal 2-cell embryo but expressed in PCOS 2-cell embryos. Notably, many DEGs in the oocytes of PCOS mice were also differentially expressed in the oocytes of F2 PCOS mice compared to control mice, supporting the transgenerational inheritance of transcriptional alteration in PCOS oocytes. Mechanismly, the changes of chromatin accessibility were associated with the DEGs in PCOS oocytes and embryos. In particular, chromatin accessibility of the pre-activated gene promoters is elevated in PCOS oocytes compared to that in normal oocytes. Furthermore, many of the abnormal chromatin accessibility signals detected in F0 PCOS oocytes were also observed in F2 PCOS oocytes. Finally, our data showed that some DEGs in the oocytes of PCOS mice were also differentially expressed in human PCOS oocytes compared to the control oocytes. Common genes identified in PCOS offspring may be used as potential predictors of PCOS phenotype. Limitations, reasons for caution Which factors contribute to the abnormalities of chromatin accessibility in PCOS oocytes are still unknown. Wider implications of the findings The candidate genes may be used as potential predictors of PCOS phenotype and provide the clues for PCOS offspring . Trial registration number not applicable

Selective binding of retrotransposons by ZFP352 facilitates the timely dissolution of totipotency network

Acquisition of new stem cell fates relies on the dissolution of the prior regulatory network sustaining the existing cell fates. Currently, extensive insights have been revealed for the totipotency regulatory network around the zygotic genome activation (ZGA) period. However, how the dissolution of the totipotency network is triggered to ensure the timely embryonic development following ZGA is largely unknown. In this study, we identify the unexpected role of a highly expressed 2-cell (2C) embryo specific transcription factor, ZFP352, in facilitating the dissolution of the totipotency network. We find that ZFP352 has selective binding towards two different retrotransposon sub-families. ZFP352 coordinates with DUX to bind the 2C specific MT2_Mm sub-family. On the other hand, without DUX, ZFP352 switches affinity to bind extensively onto SINE_B1/Alu sub-family. This leads to the activation of later developmental programs like ubiquitination pathways, to facilitate the dissolution of the 2C state. Correspondingly, depleting ZFP352 in mouse embryos delays the 2C to morula transition process. Thus, through a shift of binding from MT2_Mm to SINE_B1/Alu, ZFP352 can trigger spontaneous dissolution of the totipotency network. Our study highlights the importance of different retrotransposons sub-families in facilitating the timely and programmed cell fates transition during early embryogenesis.

Live-cell imaging reveals redox metabolic reprogramming during zygotic genome activation.

Metabolic programming is deeply intertwined with early embryonic development including zygotic genome activation (ZGA), the polarization of zygotic cells, and cell fate commitment. It is crucial to establish a noninvasive imaging technology that spatiotemporally illuminates the cellular metabolism pathways in embryos to track developmental metabolism in situ. In this study, we used two high-quality genetically encoded fluorescent biosensors, SoNar for NADH/NAD+ and iNap1 for NADPH, to characterize the dynamic regulation of energy metabolism and redox homeostasis during early zygotic cleavage. Our imaging results showed that NADH/NAD+ levels decreased from the early to the late two-cell stage, whereas the levels of the reducing equivalent NADPH increased. Mechanistically, transcriptome profiling suggested that during the two-cell stage, zygotic cells downregulated the expression of genes involved in glucose uptake and glycolysis, andupregulated the expression of genes for pyruvate metabolism in mitochondria and oxidative phosphorylation, with a decline in the expression of two peroxiredoxin genes, Prdx1 and Prdx2. Collectively, with the establishment of in situ metabolic monitoring technology, our study revealed the programming of redox metabolism during ZGA.

In silico characterisation of minor wave genes and LINE-1s transcriptional dynamics at murine zygotic genome activation.

Introduction: In mouse, the zygotic genome activation (ZGA) is coordinated by MERVL elements, a class of LTR retrotransposons. In addition to MERVL, another class of retrotransposons, LINE-1 elements, recently came under the spotlight as key regulators of murine ZGA. In particular, LINE-1 transcripts seem to be required to switch-off the transcriptional program started by MERVL sequences, suggesting an antagonistic interplay between LINE-1 and MERVL pathways. Methods: To better investigate the activities of LINE-1 and MERVL elements at ZGA, we integrated publicly available transcriptomics (RNA-seq), chromatin accessibility (ATAC-seq) and Pol-II binding (Stacc-seq) datasets and characterised the transcriptional and epigenetic dynamics of such elements during murine ZGA. Results: We identified two likely distinct transcriptional activities characterising the murine zygotic genome at ZGA onset. On the one hand, our results confirmed that ZGA minor wave genes are preferentially transcribed from MERVL-rich and gene-dense genomic compartments, such as gene clusters. On the other hand, we identified a set of evolutionary young and likely transcriptionally autonomous LINE-1s located in intergenic and gene-poor regions showing, at the same stage, features such as open chromatin and RNA Pol II binding suggesting them to be, at least, poised for transcription. Discussion: These results suggest that, across evolution, transcription of two different classes of transposable elements, MERVLs and LINE-1s, have likely been confined in genic and intergenic regions respectively in order to maintain and regulate two successive transcriptional programs at ZGA.

PGC7 regulates H3K27me3 modification by inhibiting the interaction of YY1 with PRC2.

Primordial germ cell 7 (PGC7)(Dppa3 or Stella) is a small inherently disordered protein that is mainly expressed in oocytes and plays a vital role in the regulation of DNA methylation reprogramming in imprinted loci through interaction with other proteins. Most of PGC7-deficient zygotes are blocked at two-cell stage with an increased tri-methylation at lysine 27 of histone H3 (H3K27me3) level in the nucleus. Our previous work has indicated that PGC7 interacts with yin-yang1 (YY1) that is essential for the recruitment of enhancer of zeste homolog 2 (EZH2)-containing Polycomb repressive complex 2 (PRC2) to H3K27me3 modification sites. Here, we found that the presence of PGC7 weakened the interaction between YY1 and PRC2 without disrupting the assembly of core subunits of the PRC2 complex. In addition, PGC7 promoted AKT to phosphorylate serine 21 of EZH2, resulting in inhibition of EZH2 activity and the dissociation of EZH2 from YY1, thereby decreasing H3K27me3 level. In zygotes, the PGC7-deficient and AKT inhibitor MK2206 both promoted EZH2 to enter the pronuclei but without disturbing the subcellular localization of YY1 and caused an increase in the level of H3K27me3 in the pronuclei, as well as inhibition of the expression of zygote-activating genes regulated by H3K27me3 in two-cell embryos. In summary, PGC7 could affect zygotic genome activation during early embryonic development by regulating the level of H3K27me3 through regulation of PRC2 recruitment, EZH2 activity, and subcellular localization.NEW & NOTEWORTHY PGC7 and YY1 interaction inhibits recruitment of PRC2 by YY1. PGC7 promotes AKT and EZH2 interaction to increase pEZH2-S21 level, which weakens YY1 and EZH2 interaction, thereby decreasing H3K27me3 level. In zygotes, the PGC7-deficient and AKT inhibitor MK2206 promote EZH2 to enter the pronuclei, and increase H3K27me3 level in the pronuclei, as well as inhibition of the expression of zygote-activating genes regulated by H3K27me3 in two-cell embryos, which ultimately affects early embryo development.

Y-box binding protein 1 influences zygotic genome activation by regulating N6-methyladenosine in porcine embryos.

Y-box binding protein 1 (YBX1) is a member of the family of DNA- and RNA-binding proteins that play crucial roles in multiple aspects, including RNA stabilization, translational repression, and transcriptional regulation; however, its roles in embryo development remain less known. In this study, to investigate the function of YBX1 and its mechanism of action in porcine embryo development, YBX1 was knocked down by microinjecting YBX1 siRNA at the one-cell stage. YBX1 is located in the cytoplasm during embryonic development. The mRNA level of YBX1 was increased from the four-cell stage to the blastocyst stage but was significantly decreased in YBX1 knockdown embryos compared with the control. Moreover, the percentage of blastocysts was decreased following YBX1 knockdown compared with the control. Defecting YBX1 expression increased maternal gene mRNA expression and decreased zygotic genome activation (ZGA) gene mRNA expression and histone modification owing to decreased levels of N6-methyladenosine (m6A) writer N6-adenosine-methyltransferase 70 kDa subunit (METTL3) and reader insulin-like growth factor 2 mRNA-binding protein (IGF2BP1). In addition, IGF2BP1 knockdown showed that YBX1 regulated the ZGA process through m6A modification. In conclusion, YBX1 is essential for early embryo development because it regulates the ZGA process.

Transcription factor ELK1 regulates the expression of histone 3 lysine 9 to affect developmental potential of porcine preimplantation embryos

A series of changes occur in the early embryo that are critical for subsequent development, and the pig is an excellent animal model of human disease, so understanding the regulatory mechanisms of early embryonic development in the pig is of very importance. To find key transcription factors regulating pig early embryonic development, we first profiled the transcriptome of pig early embryos, and confirmed that zygotic gene activation (ZGA) in porcine embryos starts from 4 cell stage. Subsequent enrichment analysis of up-regulated gene motifs during ZGA revealed that the transcription factor ELK1 ranked first. The expression pattern of ELK1 in porcine early embryos was analyzed by immunofluorescence staining and qPCR, and the results showed that the transcript level of ELK1 reached the highest at the 8 cell stage, while the protein level reached the highest at 4 cell stage. To further investigate the effect of ELK1 on early embryo development in pigs, we silenced ELK1 in zygotes and showed that ELK1 silencing significantly reduced cleavage rate, blastocyst rate as well as blastocyst quality. A significant decrease in the expression of the pluripotency gene Oct4 was also observed in blastocysts from the ELK1 silenced group by immunofluorescence staining. Silencing of ELK1 also resulted in decreased H3K9Ac modification and increased H3K9me3 modification at 4 cell stage. To investigate the effect of ELK1 on ZGA, we analyzed transcriptome changes in 4 cell embryos after ELK1 silencing by RNA seq, which revealed that ELK1 silencing resulted in significant differences in the expression of a total of 1953 genes at the 4 cell stage compared with their normal counterparts, including 1106 genes that were significantly upregulated and 847 genes that were significantly downregulated. Through GO and KEGG enrichment, we found that the functions and pathways of down-regulated genes were concentrated in protein synthesis, processing, cell cycle regulation, etc., while the functions of up-regulated genes were focused on aerobic respiration process. In conclusion, this study demonstrates that the transcription factor ELK1 plays an important role in regulation of preimplantation embryo development of pigs and deficiency of ELK1 leads to abnormal epigenetic reprogramming as well as zygotic genome activation, thus adversely affecting embryonic development. This study will provide important reference for the regulation of transcription factors in porcine embryo development.

Ultrasensitive proteomics depicted an in-depth landscape for the very early stage of mouse maternal-to-zygotic transition

Single-cell or low-input multi-omics techniques have revolutionized the study of pre-implantation embryo development. However, the single-cell or low-input proteomic research in this field is relatively underdeveloped because of the higher threshold of the starting material for mammalian embryo samples and the lack of hypersensitive proteome technology. In this study, a comprehensive solution of ultrasensitive proteome technology (CS-UPT) was developed for single-cell or low-input mouse oocyte/embryo samples. The deep coverage and high-throughput routes significantly reduced the starting material and were selected by investigators based on their demands. Using the deep coverage route, we provided the first large-scale snapshot of the very early stage of mouse maternal-to-zygotic transition, including almost 5,500 protein groups from 20 mouse oocytes or zygotes for each sample. Moreover, significant protein regulatory networks centered on transcription factors and kinases between the MII oocyte and 1-cell embryo provided rich insights into minor zygotic genome activation.

Germ cell-specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation.

Translation of maternal mRNAs is detected before transcription of zygotic genes and is essential for mammalian embryo development. How certain maternal mRNAs are selected for translation instead of degradation and how this burst of translation affects zygotic genome activation remain unknown. Using gene-edited mice, we document that the oocyte-specific eukaryotic translation initiation factor 4E family member 1b (eIF4E1b) is the regulator of maternal mRNA expression that ensures subsequent reprogramming of the zygotic genome. In oocytes, eIF4E1b binds to transcripts encoding translation machinery proteins, chromatin remodelers, and reprogramming factors to promote their translation in zygotes and protect them from degradation. The protein products are thought to establish an open chromatin landscape in one-cell zygotes to enable transcription of genes required for cleavage stage development. Our results define a program for rapid resetting of the zygotic epigenome that is regulated by maternal mRNA expression and provide new insights into the mammalian maternal-to-zygotic transition.