ArticleNature2016
The landscape of accessible chromatin in mammalian preimplantation embryos.
Article in Nature, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 431 papers.
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Who cites it
431 citing papers in PubMed, 768 citations in OpenAlex.
- Single-cell TimeLapse-seq reveals MTA is an essential retrotransposon orchestrating mouse zygotic genome activation.Nature communications · 2026Article
- A systematic single-cell analysis of enhancer RNAs across human and mouse.Nucleic acids research · 2026Article
- Dynamic control of cell state transitions during tissue morphogenesis.The EMBO journal · 2026Review
- High-throughput functional characterization of enhancers in totipotent-like cells.Nature communications · 2026Article
- Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq.Cell research · 2026Article
- Epigenetics in development, disease, and therapy: from mechanisms to clinical interventions.Science China. Life sciences · 2026Review
- High-resolution mapping of embryonic genome activation unveils a decoupling of transcription activation from precocious H3K4me3 removal.Science advances · 2026Article
- The Fallopian tube: Biosensor and dynamic regulator of preimplantation development.PNAS nexus · 2026Review
- Overcoming Barriers in Porcine SCNT: A Comprehensive Review of Developmental Challenges and Innovations.International journal of molecular sciences · 2026Review
- Dissecting the expression pattern during embryonic development and unveiling sustained ZGA genes with oncogenic relevance.BMC genomics · 2026Article
- Contribution of cohesins STAG1 and STAG2 to preimplantation development in mice.Communications biology · 2026Article
- Transposable element regulation in mammalian germ cells and other contexts: multilayered repression, fertility, and regulated activation.Epigenomics · 2026Review
- The Landscape and Regulation of Histone Crotonylation in Mammalian Gametes and Early Embryos.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Dynamic regulation of H3K9 dimethylation drives mouse minor zygotic genome activation.Nature structural & molecular biology · 2026Article
- ToxiTaRGET: a multi-omics database for toxicant-responsive molecular targets.Nature communications · 2026Article
- Selective cellular localization of UHRF1 safeguards mammalian zygotic genome activation and early embryonic development.Cell discovery · 2026Article
- Probing RNA-protein interactions in the early mouse embryo.bioRxiv : the preprint server for biology · 2026Article
- TBP regulates transposable element expression in early mouse embryos.The EMBO journal · 2026Article
- Deciphering tRNA repertoires and translation coordination during mouse early embryogenesis by ORACLE-tRNAseq.Nature communications · 2026Article
- ATAC-seq and RNA-seq reveal key genes and pathways regulating lactation in the mammary gland of Yili horses.BMC genomics · 2026Article
371 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
24 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development.
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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.