ArticleNature communications2020
High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 44 citations in OpenAlex.
- Single-oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability.Nature communications · 2026Article
- Transposable element-gene chimera cartography, origination and role in enhancing transcriptome plasticity.Nature structural & molecular biology · 2026Article
- scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase.Nature communications · 2025Article
- Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos.Nucleic acids research · 2025Article
- A comprehensive review of histone modifications during mammalian oogenesis and early embryo development.Histochemistry and cell biology · 2025Review
- Zinc eluted from glassware is a risk factor for embryo development in human and animal assisted reproduction†.Biology of reproduction · 2025Article
- SHMT2 is essential for mammalian preimplantation embryonic development throughMolecular therapy. Nucleic acids · 2025Article
- Self-organization of mouse embryonic stem cells into reproducible pre-gastrulation embryo models via CRISPRa programming.Cell stem cell · 2025Article
- High resolution of full-length RNA sequencing deciphers massive transcriptome complexity during zebrafish embryogenesis.BMC biology · 2025Article
- Zygotic activation of transposable elements during zebrafish early embryogenesis.Nature communications · 2025Article
- Serotonin Signaling in Mouse Preimplantation Development: Insights from Transcriptomic and Structural-Functional Analyses.International journal of molecular sciences · 2024Article
- JmjC catalysed histone H2a N-methyl arginine demethylation and C4-arginine hydroxylation reveals importance of sequence-reactivity relationships.Communications biology · 2024Article
- Kdm4d mutant mice show impaired sperm motility and subfertility.The Journal of reproduction and development · 2024Article
- Alternative splicing of CARM1 regulated by LincGET-guided paraspeckles biases the first cell fate in mammalian early embryos.Nature structural & molecular biology · 2024Article
- Enhancing recognition and interpretation of functional phenotypic sequences through fine-tuning pre-trained genomic models.Journal of translational medicine · 2024Article
- Characterization of alternative splicing during mammalian brain development reveals the extent of isoform diversity and potential effects on protein structural changes.Biology open · 2024Article
- Self-organization of embryonic stem cells into a reproducible embryo model through epigenome editing.bioRxiv : the preprint server for biology · 2024Article
- Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development.PLoS biology · 2024Article
- Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation.Molecular cell · 2023Article
- Relationship of quantitative reverse transcription polymerase chain reaction (RT-PCR) to RNA Sequencing (RNAseq) transcriptome identifies mouse preimplantation embryo reference genes†.Biology of reproduction · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
14 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The transcriptome of the preimplantation mouse embryo has been previously annotated by short-read sequencing, with limited coverage and accuracy. Here we utilize a low-cell number transcriptome based on the Smart-seq2 method to perform long-read sequencing. Our analysis describes additional novel transcripts and complexity of the preimplantation transcriptome, identifying 2280 potential novel transcripts from previously unannotated loci and 6289 novel splicing isoforms from previously annotated genes. Notably, these novel transcripts and isoforms with transcription start sites are enriched for an active promoter modification, H3K4me3. Moreover, we generate a more complete and precise transcriptome by combining long-read and short-read data during early embryogenesis. Based on this approach, we identify a previously undescribed isoform of Kdm4dl with a modified mRNA reading frame and a novel noncoding gene designated XLOC_004958. Depletion of Kdm4dl or XLOC_004958 led to abnormal blastocyst development. Thus, our data provide a high-resolution and more precise transcriptome during preimplantation mouse embryogenesis.
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