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Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos
Abstract
Histone modifications have critical roles in regulating the expression of developmental genes during embryo development in mammals. However, genome-wide analyses of histone modifications in pre-implantation embryos have been impeded by the scarcity of the required materials. Here, by using a small-scale chromatin immunoprecipitation followed by sequencing (ChIP-seq) method, we map the genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3), which are associated with gene activation and repression, respectively, in mouse pre-implantation embryos. We find that the re-establishment of H3K4me3, especially on promoter regions, occurs much more rapidly than that of H3K27me3 following fertilization, which is consistent with the major wave of zygotic genome activation at the two-cell stage. Furthermore, H3K4me3 and H3K27me3 possess distinct features of sequence preference and dynamics in pre-implantation embryos. Although H3K4me3 modifications occur consistently at transcription start sites, the breadth of the H3K4me3 domain is a highly dynamic feature. Notably, the broad H3K4me3 domain (wider than 5 kb) is associated with higher transcription activity and cell identity not only in pre-implantation development but also in the process of deriving embryonic stem cells from the inner cell mass and trophoblast stem cells from the trophectoderm. Compared to embryonic stem cells, we found that the bivalency (that is, co-occurr…
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“Moreover, bivalent chromatin dynamics accompanies early mESC lineage commitment (Ruthenburg et al., 2007; Schwartz and Pirrotta 2007; Liu et al., 2016).”
From METTL3 uncouples chromatin accessibility from transcription during retinal development (2025) · cites this paper as Liu et al., 2016
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Additional file 2 of Evaluating histone modification analysis of individual preimplantation embryos
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Metadata
- Authors
- Liu, X., Wang, C., Liu, W., Li, J., Li, C., Kou, X., Chen, J., Zhao, Y., Gao, H., Wang, H., Zhang, Y., Gao, Y., & Gao, S.
- Affiliations
- Tongji University (CN)
- Corresponding author
- Zhang, Yong
- Gao, Yawei
- Gao, Shaorong
- ORCID
- Venue
- Nature
- Published
- 2016-09-14
- Volume
- 537
- Issue
- 7621
- Pages
- 558-562
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2519280707
- Cited by
- 746
- References
- 45
- Citations by year
- 2026: 55 · 2025: 82 · 2024: 88 · 2023: 91 · 2022: 81 · 2021: 78 · 2020: 75 · 2019: 67 · 2018: 69 · 2017: 50 · 2016: 8
- FWCI
- 33.62
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- H3K4me3, H3K27me3, histone modifications, preimplantation embryo, mouse embryo development, zygotic genome activation, maternal-to-zygotic transition, DNA methylation, gene silencing, chromatin domains, promoter, fertilisation (biology), epigenetic reprogramming
- MeSH terms
- Animals, Blastocyst, Chromatin, Female, Fertilization, Histones, Lysine, Male, Methylation, Promoter Regions, Genetic, Zygote, Genome, Transcription Initiation Site, Epigenesis, Genetic, Chromatin Immunoprecipitation, Mice, Embryonic Stem Cells
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