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.
Abstract
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.
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.
Helicoverpa armigera is one of the most destructive polyphagous pests, yet the transcriptional organization underlying its digestive capacity remains poorly resolved. Here, we compiled 579 publicly available RNA-seq libraries representing 54 independent experiments and quantified transcript abundance across tissues and developmental stages. This complete dataset was used to support broader tissue-level expression profiling. After metadata harmonization and quality filtering, a subset of 130 biologically comparable libraries from five tissue/developmental categories was retained for weighted gene co-expression network analysis. WGCNA identified four biologically informative modules, among which the turquoise module was positively associated with fourth- and fifth-instar larval midgut samples. Independent expression profiling revealed strong midgut-biased expression of several trypsin- and chymotrypsin-like serine proteases, although only a subset of these genes was assigned to the turquoise module. Descriptive functional annotation of this module identified 202 co-expressed loci, including digestive enzymes, nutrient transporters, detoxification-related proteins, epithelial components and putative transcriptional or signaling-associated genes. Phylogenetic analyses and manual inspection of genomic locations further showed that several digestive protease genes occur in local clusters and have closely related counterparts in H. zea, suggesting partial conservation of local genomic organization. Collectively, these results describe a midgut-associated co-expression module containing genes associated with digestive, absorptive and protective functions and provide candidate genes for future functional studies.
Bairon J. Matabanchoy Pejendino, Vicente E. Mallama Cadena, M. C. Rodriguez et al.· BioTech· 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
It is demonstrated 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
Incomplete zygotic genome activation (ZGA) is a major barrier limiting the developmental competence of somatic cell nuclear transfer (SCNT) embryos in pigs. α-Ketoglutarate (α-KG), a key metabolic intermediate and cofactor for α-KG-dependent dioxygenases, has been implicated in epigenetic remodeling during early embryogenesis. In this study, we investigated whether α-KG supplementation could improve developmental potential and ZGA-associated events in porcine SCNT embryos. α-KG treatment improved cleavage progression, increased blastocyst formation rates, increased total blastocyst cell number and ICM cell number, and reduced apoptosis and DNA damage. In addition, α-KG improved microtubule organization and actin distribution during early cleavage stages, contributing to more coordinated cell division. Mechanistically, α-KG increased global 5-hydroxymethylcytosine (5hmC) levels and elevated the abundance of activating histone marks, including H3K4me3 and H3K27ac. Expression of several ZGA-associated genes, including DUXA, ZSCAN4, EIF1A, and KLF17, was significantly increased following α-KG supplementation, accompanied by enhanced nascent RNA synthesis. Notably, inhibition of TET enzymes with Bobcat339 attenuated the effects of α-KG on 5hmC accumulation, transcriptional activity, and embryo development. Collectively, these findings indicate that α-KG improves developmental competence and is associated with enhanced epigenetic remodeling in porcine SCNT embryos, at least in part through TET-associated pathways, providing a potential strategy for improving nuclear reprogramming efficiency in animal cloning.
Baobao Zhao, Jie Wang, Zihan Xu et al.· Reproduction· 0 citations
Sex reversal is an intricate and fascinating process orchestrated by a finely organized network. The orange-spotted grouper (
Epinephelus coioides
) is a protogynous hermaphroditic fish, but the regulatory mechanism of its sex reversal is not yet well understood.
Here, single-cell transcriptome sequencing (scRNA-seq) of the gonads was performed during sex reversal induced by 17α-methyltestosterone (MT). Based on the scRNA-seq data, various gonadal cell types and subtypes, including eight types of germ cells and nine types of somatic cells, were characterized and identified. Moreover, a single-cell atlas of dynamic changes in gene expression during sex reversal in orange-spotted grouper was constructed. We outlined the precise trajectories of germ stem cells (GSCs) and male somatic cells, which revealed that new male germ cells were originated from a subcluster of GSCs with increased levels of spermatogenesis genes. Moreover, we revealed that
piwil1
and
dmrt1
were important for the male-oriented differentiation of GSCs. Additionally, oocytes exhibited abnormal and significant apoptosis and active proliferation during the early stage of sex reversal.
Overall, these results address the questions of how male germ cells are generated and how female germ cells disappear during sex reversal in orange-spotted grouper. These findings profile a comprehensive dynamic map of gonadal cells during sex reversal, which can provide new insights into sex change in lower vertebrates.
Xi Wu, Tong Wang, Leyi Chang et al.· BMC Biology· 0 citations
