ArticlePLoS biology2024
Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development.
Article in PLoS biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 14 citations in OpenAlex.
- Sperm AluY Epimutations in Male Partners of Couples with Unexplained Recurrent Pregnancy Loss.bioRxiv : the preprint server for biology · 2026Article
- IsoformSwitchAnalyzeR v2: analysis of functional isoform changes in long-read and single-cell sequencing data.NAR genomics and bioinformatics · 2026Article
- Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.Briefings in bioinformatics · 2026Review
- U2AF1 modulates alternative exon selection and guards zygotic splicing activation in mouse preimplantation embryogenesis.Cellular and molecular life sciences : CMLS · 2026Article
- Improving gene isoform quantification with miniQuant.Nature biotechnology · 2026Article
- Blunted Lsm14b activation disrupts maternal mRNA remodeling during the GV-to-MII transition in a mouse model of polycystic ovary syndrome.Frontiers in cell and developmental biology · 2026Article
- Long-read sequencing transcriptome quantification with lr-kallisto.PLoS computational biology · 2025Article
- A father's legacy: the sperm epigenome, preimplantation development, and paternal environment.Epigenomics · 2025Review
- Transposable elements in health and disease: Molecular basis and clinical implications.Chinese medical journal · 2025Review
- Integrated Gene and Isoform-Level Transcriptomic Analysis of Adverse Childhood Experiences in the Human Prefrontal Cortex.The Yale journal of biology and medicine · 2025Article
- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 2025Review
- NLRP7 maintains the genomic stability during early human embryogenesis via mediating alternative splicing.Communications biology · 2025Article
- Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics.Genome research · 2024Review
- Long Story Short: Understanding Isoform-Specific Expression ofAmerican journal of respiratory cell and molecular biology · 2024Article
- Identification of novel cattle (Bos taurus) genes and biological insights of their function in pre-implantation embryo development.BMC genomics · 2024Article
- RNaseH-based ribodepletion of total planarian RNA improves detection of longer and non-polyadenylated transcripts.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Alternative splicing is an essential regulatory mechanism for development and pathogenesis. Through alternative splicing one gene can encode multiple isoforms and be translated into proteins with different functions. Therefore, this diversity is an important dimension to understand the molecular mechanism governing embryo development. Isoform expression in preimplantation embryos has been extensively investigated, leading to the discovery of new isoforms. However, the dynamics of isoform switching of different types of transcripts throughout the development remains unexplored. Here, using single-cell direct isoform sequencing in over 100 single blastomeres from the mouse oocyte to blastocyst stage, we quantified isoform expression and found that 3-prime partial transcripts lacking stop codons are highly accumulated in oocytes and zygotes. These transcripts are not transcription by-products and might play a role in maternal to zygote transition (MZT) process. Long-read sequencing also enabled us to determine the expression of transposable elements (TEs) at specific loci. In this way, we identified 3,894 TE loci that exhibited dynamic changes along the preimplantation development, likely regulating the expression of adjacent genes. Our work provides novel insights into the transcriptional regulation of early embryo development.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.