ArticleGenome biology2015
Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape.
Article in Genome biology, 2015. 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 141 papers.
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Who cites it
141 citing papers in PubMed, 239 citations in OpenAlex.
- R-loop homeostasis at transposable elements safeguards transcriptional silencing in replication-quiescent oocytes.Nature communications · 2026Article
- Polycomb shapes active chromatin and promoter bivalency during ovarian reserve formation and activation.bioRxiv : the preprint server for biology · 2026Article
- The superpowers of imprinting control regions.Genome research · 2026Review
- The maternal KRAB-ZFP ZFPOBI1 reveals structural constraints governing ERV transcriptional co-option in mouse oocytes.Frontiers in cell and developmental biology · 2026Article
- Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for Activation.Research square · 2025Article
- Preventing CpG hypermethylation in oocytes safeguards mouse development.Developmental cell · 2025Article
- Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for Activation.bioRxiv : the preprint server for biology · 2025Article
- An Nlrp5-null mutation leads to attenuated de novo methylation in oocytes, accompanied by a significant reduction in DNMT3L.Molecular human reproduction · 2025Article
- H2A.Z is essential for oocyte maturation and fertility in female mouse.Nature structural & molecular biology · 2025Article
- H2A.Z reinforces maternal H3K4me3 formation and is essential for meiotic progression in mouse oocytes.Nature structural & molecular biology · 2025Article
- Epigenome dynamics in early mammalian embryogenesis.Nature reviews. Genetics · 2025Review
- Review
- Genomic imprinting at a porcine ZNF locus via a canonical imprinting mechanism.Animal genetics · 2025Article
- An Epigenomic Roadmap Primes Non-Growing Oocytes for Maturation and Early Embryogenesis.bioRxiv : the preprint server for biology · 2025Article
- Article
- DNA methylation mechanisms in the maturing and ageing oocyte.Epigenetics & chromatin · 2025Review
- Maternal loss of mouse Nlrp2 alters the transcriptome and DNA methylome in GV oocytes and impairs zygotic genome activation in embryos.Clinical epigenetics · 2025Article
- Article
- Maternal PRDM10 activates essential genes for oocyte-to-embryo transition.Nature communications · 2025Article
- Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes.BMC molecular and cell biology · 2025Article
81 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
Abstract
backgroundPreviously, a role was demonstrated for transcription in the acquisition of DNA methylation at imprinted control regions in oocytes. Definition of the oocyte DNA methylome by whole genome approaches revealed that the majority of methylated CpG islands are intragenic and gene bodies are hypermethylated. Yet, the mechanisms by which transcription regulates DNA methylation in oocytes remain unclear. Here, we systematically test the link between transcription and the methylome.
resultsWe perform deep RNA-Seq and de novo transcriptome assembly at different stages of mouse oogenesis. This reveals thousands of novel non-annotated genes, as well as alternative promoters, for approximately 10 % of reference genes expressed in oocytes. In addition, a large fraction of novel promoters coincide with MaLR and ERVK transposable elements. Integration with our transcriptome assembly reveals that transcription correlates accurately with DNA methylation and accounts for approximately 85-90 % of the methylome. We generate a mouse model in which transcription across the Zac1/Plagl1 locus is abrogated in oocytes, resulting in failure of DNA methylation establishment at all CpGs of this locus. ChIP analysis in oocytes reveals H3K4me2 enrichment at the Zac1 imprinted control region when transcription is ablated, establishing a connection between transcription and chromatin remodeling at CpG islands by histone demethylases.
conclusionsBy precisely defining the mouse oocyte transcriptome, this work not only highlights transcription as a cornerstone of DNA methylation establishment in female germ cells, but also provides an important resource for developmental biology research.
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