Aug 2026· Animal Reproduction Science· Vol 293, pp.
108306
· 0 citations· 41 references
Medicine
TL;DR
It is found that CNOT1 was upregulated during mammalian ZGA, and that its knockdown led to developmental arrest and a marked reduction in blastocyst formation, which indicates that CNOT1 is a potential YTHDF2 target that orchestrates maternal mRNA decay and ZGA during goat embryogenesis.
Abstract
Timely and efficient degradation of maternal mRNA is essential for early embryonic development, which occurs from fertilization through the initiation of zygotic genome activation (ZGA). Yet, the regulatory mechanisms governing this process remain poorly characterized. In the present study, we investigated the function of CCR4-NOT transcription complex subunit 1 (CNOT1) during goat embryogenesis. We found that CNOT1 was upregulated during mammalian ZGA, and that its knockdown led to developmental arrest and a marked reduction in blastocyst formation. Moreover, CNOT1 knockdown impaired nascent RNA activity, resulting in 814 upregulated and 1014 downregulated genes, which were enriched for RNA splicing, regulation of chromosome organization, and RNA localization. RNA splicing analysis revealed differential splicing events in 2959 genes, of which 259 were downregulated following CNOT1 knockdown. Notably, CNOT1 was predicted to crosstalk with the m6A reader YTHDF2. Knockdown of YTHDF2 resulted in CNOT1 downregulation at the 8-cell stage in goats and increased transcription levels around polyadenylation sites during ZGA in mice. Together, these findings indicate that CNOT1 is a potential YTHDF2 target that orchestrates maternal mRNA decay and ZGA during goat embryogenesis. Our work provides new insight into the complex regulatory landscape underlying ZGA and may inform strategies to improve the efficiency of goat embryogenesis.
The maternal-to-zygotic transition (MZT) is essential for early embryonic development, comprising zygotic genome activation (ZGA) as well as the degradation of maternal RNAs and proteins, whereas our understanding of repressors' role in this process remains limited in mammals. In our study, we inhibited protein degradation at the 1-cell stage using the proteasome inhibitor MG132 and observed impaired pre-implantation development and defective ZGA. Proteomic analysis of MG132-treated embryos showed that significantly up-regulated proteins in abundance were enriched for RNA-binding proteins (RBPs). Further functional screening highlighted one critical factor, 4E-T (EIF4ENIF1), whose overexpression caused 2-cell stage arrest and failure of ZGA initiation. Moreover, the abnormal accumulation of 4E-T translationally repressed key factors of the 1-cell embryo, including ZBED3 and KDM4A. Mechanistically, the reprsssion is linked to direct interactions of 4E-T with eIF4E and eIF4E1B. These findings suggest that specific maternal RBPs may act as repressors that require precise degradation post-fertilization to relieve translational repression and ensure successful MZT.
Pinhua Wang, Siqi Wang, Haojie Yin et al.· Cellular and Molecular Life...· 0 citations
Programmed establishment of the zygote epitranscriptome orchestrates epitranscriptome fidelity and developmental potency acquisition during mammalian preimplantation embryogenesis. N4-acetylcytidine (ac
4
C) is a conserved RNA modification catalyzed by N-acetyltransferase 10 (NAT10), the currently established mammalian RNA ac
4
C writer, but its maternal function during the maternal-to-zygotic transition remains incompletely understood. In this study, we found that oocyte-specific
Nat10
ablation from primary follicle stage causes female infertility with embryonic developmental arrest predominantly at the 2-cell stage. Notably, the maternal protein NAT10 is essential for ac
4
C deposition on zygotic genome activation (ZGA) transcripts and maternal mRNAs, and the loss of
Nat10
can lead to abnormal accumulation of maternal transcripts and major ZGA inactivation. By interrogating ac
4
C LACE-seq, RNA-seq, and Ribo-lite data, we identify splicing-factor transcripts as prominent NAT10-associated ac
4
C targets whose mRNA abundance and ribosome occupancy are reduced after maternal
Nat10
deletion. These molecular changes are accompanied by impaired nuclear speckle organization and widespread disruption of detectable alternative-splicing events during zygotic splicing activation. Together, our findings demonstrate that the RNA ac
4
C writer NAT10 is essential for the post-transcriptional regulation of mouse zygotic splicing activation and provide valuable view for further exploration of the epigenetic mechanism during maternal-to-zygotic transition.
Wen-Jing Wang, Yu-Ke Wu, Yun-Wen Wu et al.· Cell Death & Disease· 0 citations
The maternal-to-zygotic transition (MZT) is a major developmental event during which inherited transcripts are remodeled and zygotic transcription is established. Although parentally inherited long noncoding RNAs (lncRNAs) are present in early embryos, they have been thought to be dispensable. We have identified more than 2000 inherited lncRNAs in zebrafish embryos, but how these RNAs participate in regulatory programs during early development has remained unexplored. Here, the inheritance of selected zebrafish lncRNAs spanning a broad expression range were confirmed at the pre-MZT stage and full-length sequences were captured by Direct RNA nanopore sequencing. We show that 30% inherited intergenic lncRNAs are preferentially associated with active enhancers, annotated as such in DANIO CODE, whereas non-inherited intergenic lncRNAs rarely overlap with enhancers. Perturbation of five inherited intergenic lncRNAs, individually, using antisense oligonucleotides reduced the expression of their respective neighboring genes at 2.5, 4.3, and/or 6 hours post fertilization, indicating that these RNAs act as positive local regulators during MZT. Together, these findings identify inherited intergenic lncRNAs as enhancer-associated regulators with elncRNA-like properties during early embryogenesis.
Dheeraj Chandra Joshi, Sauranil Guha, Nabeel Ahmed et al.· bioRxiv· 0 citations
N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes and is essential for Arabidopsis embryogenesis. However, how m6A mRNA methylation is coordinated with other regulatory pathways during development including embryogenesis remains largely unknown. Here, we report the SWI/SNF chromatin-remodeling subunit SWI3B as a bona fide interactor of the m6A methyltransferase MTA. Like m6A writer mutants, SWI3B is required for early embryo development. We demonstrate that the interaction between MTA and SWI3B is required for MTA function during embryogenesis. MTA and SWI3B are both required to establish the correct expression pattern of WOX8 and proper auxin maxima during early embryogenesis. Transcriptome analysis of isolated embryos from mta, swi3b, and fip37 mutants identified a shared set of upregulated transcripts, including STM as well as several NAC and ERF transcription factors that are normally absent or expressed at very low levels during early embryogenesis. Embryo-specific overexpression of ANAC087 and ERF114 genes phenocopied early embryonic defects observed in mta and swi3b mutants, indicating that their ectopic expression contributes to the observed developmental phenotype. Moreover, SWI3B and MTA are both required for m6A deposition on specific developmental transcripts. Together, our findings uncover a mechanism by which chromatin remodeling and m6A-mediated RNA regulation cooperate to suppress the precocious stability of key developmental regulators, thereby contributing to the establishment of the transcriptional program required for early embryo patterning in Arabidopsis. Highlights The SWI/SNF subunit SWI3B is a functional interactor of the m6A methyltransferase MTA during Arabidopsis embryogenesis SWI3B and MTA cooperate to establish embryo patterning, WOX8 expression, and auxin maxima MTA and SWI3B suppress precocious expression of STM, ANAC087 and ERF114 transcription factors that disrupt early embryo development SWI3B links chromatin-associated regulation with m6A-mediated control of transcript stability Graphical abstract
Wen Gong, U. Schwartz, L. Fu et al.· bioRxiv· 0 citations
Early embryogenesis is governed by tightly regulated transcriptional programs, including the maternal-to-zygotic transition (MZT), zygotic genome activation (ZGA), and maintenance of pluripotency. While these processes are well studied in model vertebrates, they remain poorly understood in salmonid fishes, whose genomes are shaped by a relatively recent whole genome duplication (WGD) event. Here, we present a temporally resolved transcriptomic analysis of Atlantic salmon (Salmo salar) embryogenesis using bulk RNA-seq across key stages spanning early embryogenesis. Dimensionality reduction and unsupervised clustering of gene expression revealed stage-specific transitions encompassing maternal RNA clearance, cell cycle regulation, and the onset of metabolic activity. We demonstrate that ZGA occurs early and in multiple phases, beginning soon after fertilization, accompanied by chromatin remodelling and the activation of epigenetic regulators. Duplicated gene pairs retained from the salmonid WGD frequently displayed asynchronous expression, indicative of functional divergence and the evolution of additional regulatory complexity of embryonic development. To gain insights into pluripotency, we integrated analyses of gene expression, transcription factor motifs, and chromatin accessibility, to reveal conserved regulators including genes encoding Pou5f3, Nanog, and Sox19b, alongside divergent functions of Klf family members. Our cross-stage profiling allowed us to define a novel panel of stably-expressed reference genes for normalization during quantitative PCR analyses, which were used to validate pluripotency- and differentiation-associated dynamics inferred by RNA-seq. Together, our findings delineate the transcriptional architecture of early embryogenesis in Atlantic salmon, revealing both conserved and lineage-specific features of pluripotency regulation, and providing a foundational resource for future functional genomics and stem cell applications in salmonids.
Prabin Sharma Humagain, Diego Perojil Morata, M. Wessel et al.· bioRxiv· 0 citations
NR5A2 is a key regulator of zygotic genome activation (ZGA), which primarily takes place at the 4-8-cell stage in porcine embryos; however, its associated metabolic programs remain largely uncharacterized. In this study, single-blastomere RNA sequencing was performed using Smart-seq2 in 8-cell-stage porcine embryos derived from in vitro fertilization (IVF) or somatic cell nuclear transfer (SCNT). Based on the bimodal expression pattern of NR5A2, individual blastomeres were categorized into NR5A2-active and NR5A2-inactive groups. Differential expression analysis identified 46 differentially expressed genes (DEGs) in IVF embryos, which were mainly enriched in steroid hormone and lipid metabolism. In SCNT embryos, the top-ranked DEGs were functionally associated with mitochondrial respiration and ribosome biogenesis. A total of 14 NR5A2-associated DEGs were consistently identified in both embryo types and clustered into three core metabolic modules: glycolysis and energy metabolism (represented by HK2), lipid and steroid metabolism (including STAR, LIPG, PLCD1 and DLC1), and inositol metabolism (represented by MIOX). Single-blastomere qRT-PCR in parthenogenetic embryos further validated the bimodal expression of NR5A2, HK2, STAR and MIOX. Collectively, this study reveals an NR5A2-associated metabolic transcriptional signature in blastomeres of both IVF and SCNT embryos. These findings identify candidate metabolic genes that may inform future optimization of in vitro culture media to enhance the developmental competence of porcine embryos and warrant subsequent functional validation.
Zihan Li, Fuheng Xie, Yuqing He et al.· Theriogenology· 0 citations