Transcriptomic view of key events during early embryogenesis in the duplicated Atlantic salmon genome

Histone Modifications in Mammalian Early Embryos.

High-resolution mapping of embryonic genome activation unveils a decoupling of transcription activation from precocious H3K4me3 removal

The lack of temporal resolution in transcriptomic data during mammalian embryonic genome activation (EGA) has precluded the comprehensive understanding of the functional relationships between the various gene regulatory mechanisms governing this process. Here, we finely dissect the transcriptional dynamics of mouse EGA using precision in vitro fertilization (IVF) coupled with single-embryo RNA sequencing. Our highly temporally resolved dataset uncovers an extensive, step-wise remodeling of the embryonic messenger RNA landscape, affecting ∼30% of the total detectable transcripts over a 9-hour time frame. We capture the gradual shift from maternal to embryonic messenger RNAs, successfully identify ribosome biogenesis and translation as hallmarks of EGA, and find previously unidentified gene expression dynamics. We further uncover a set of eight histone demethylating enzymes among the earliest up-regulated EGA genes and leverage our precision-IVF to dissect the transcriptional versus developmental impact of histone H3 lysine-4 trimethylation (H3K4me3) remodeling after fertilization. Our results indicate that precocious removal of H3K4me3 from embryonic chromatin only modestly affects embryonic transcription without perturbing EGA timing, arguing against a major instructive role of precocious remodeling of maternally inherited H3K4me3 after fertilization on genome activation. High-resolution transcriptome mapping coupled with functional perturbations allows us to distinguish direct gene expression effects from general impacts on developmental timing, opening avenues for further quantitative characterization of the impact of epigenome remodeling on embryonic transcription.

Transcriptomics reveals the gene expression dynamics during embryonic development of largemouth bass (Micropterus nigricans) at the endogenous nutrition stage.

The early developmental stages of fish exhibit the highest mortality and greatest environmental sensitivity throughout their life cycle. This period encompasses a series of crucial biological events, including morphogenesis, organ differentiation, and nutritional mode transition from fertilized eggs to newly hatched larvae. Although largemouth bass (Micropterus nigricans) is a commercially important fish species in China, the molecular regulatory mechanisms governing its endogenous nutritional stage remain largely unexplored. To elucidate the molecular basis of this critical period, we performed transcriptomic profiling across six consecutive developmental stages (Multicellular, Blastula, Gastrula, Neurula, Organogenesis, and 5 day post hatching larvae). Our results reveal stage-specific transcriptional programs: the multicellular-to-blastula transition is characterized by stage-specific enrichment of by cell cycle and DNA replication pathways, with MCM complex (mcm2-5) upregulation accelerating proliferation; the blastula-to-gastrula transition features activation of bmp4, fgfr2, and lft1 for germ layer induction; the neurula stage exhibits transcriptional bursts and enrichment of neural tube-related pathways; organogenesis involves simultaneous activation of focal adhesion (col1a1b, col4a5, tnc) and Wnt signaling (wnt1, wnt4, wnt3a) pathway; and 5 dph larvae show visual function maturation, with light transduction genes (gnat1, gnat2, gucy2f, pde6b) identified as hub genes. Mfuzz analysis further reveals sustained upregulation of Cluster 14 (igf2r、napin、vamp7、il1b、aco2) indicating functional maturation, while Cluster 29 (mcm10, espl1, cep152, cep44, cep295) confirms declining cell division activity. Collectively, this study provides a transcriptomic resource for understanding largemouth bass embryonic development and offers molecular insights for improving hatchery practices.

Dissecting the expression pattern during embryonic development and unveiling sustained ZGA genes with oncogenic relevance

Zygotic genome activation (ZGA) represents a pivotal transition in early embryonic development, marking the onset of gene expression following fertilization. Despite its fundamental importance, precisely determining the timing and identifying the key genes involved in ZGA remains a significant challenge. Based on time-course patterns from RNA-seq data spanning all developmental stages, we proposed a computational framework to identify ZGA genes and the onset of ZGA across diverse species. In mice, we identified 690 ZGA-associated genes, 119 of which were previously uncharacterized. Furthermore, we defined a pivotal gene subset termed Sustained ZGA (S-ZGA) genes, which are activated from ZGA and maintain sustained expression throughout subsequent development. Epigenetic analyses revealed that promoter accessibility and H3K4me3 enrichment are primary regulatory mechanisms for S-ZGA genes. Notably, these genes exhibit strong enrichment in tumorigenesis and metastatic processes. This study establishes a computational framework that operates independently of prior knowledge to identify ZGA genes and precisely determine ZGA onset timing across diverse species, and defines a critical subset termed Sustained ZGA (S-ZGA) genes, which are potentially associated with tumorigenesis and metastatic processes. These findings provide a novel perspective on the molecular mechanisms underlying both normal development and cancer.

Comparative single-cell transcriptomics highlights species-biased developmental trajectories and candidate regulatory modules in primate spermatogenesis.

Understanding primate testicular development is essential for elucidating the evolution of male fertility. Here, we integrated publicly available single-cell RNA sequencing datasets from 23 human and 4 macaque testes spanning infant to adult stages. Integrated analysis identified 22 conserved germ cell subtypes, including spermatogonial stem cells, spermatocytes, and spermatids. Notably, a human-enriched late spermatid-like transcriptional state, Sperm.C2, was enriched for genes involved in chromatin condensation, acrosome formation, and fertilization readiness, but was not detected in the macaque dataset analyzed here. Comparative transcriptomic profiling revealed age-related transcriptional dynamics in SSCs, reflecting species-biased developmental strategies between humans and macaques. Moreover, candidate regulators such as CELF4 and CTCF were predicted to be associated with SSC maintenance and spermatid maturation. Together, these findings delineate conserved and species-biased molecular programs governing spermatogenesis and provide a comparative framework for understanding primate germline development.

Enhancer RNA like function of intergenic inherited lncRNAs during maternal to zygotic transition in zebrafish

Findings identify inherited intergenic lncRNAs as enhancer-associated regulators with elncRNA-like properties during early embryogenesis, indicating that these RNAs act as positive local regulators during MZT.