Cited by 776Epigenetics and DNA MethylationGenomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

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Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

Liu, Xiaoyu, Wang, Chenfei, Liu, Wenqiang, Li, Jingyi, Li, Chong, Kou, Xiaochen, Chen, Jiayu, Zhao, Yanhong, Gao, Haibo, Wang, Hong, Zhang, Yong, Gao, Yawei, Gao, Shaorong·2016·Nature

DOI 10.1038/nature19362

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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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Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Self-citation
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Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
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NCBI GEO: archive for functional genomics data sets—update
Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., Holko, M., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1193 · Cited by 10,418
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Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
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Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclassesPreprint
Cabili, M. N., Trapnell, C., Goff, L. A., Koziol, M. J., Tazón‐Vega, B., Regev, A., & Rinn, J. L. (2011) · Genes & Development · doi:10.1101/gad.17446611 · Cited by 3,551
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Early Xenopus gene regulatory programs, chromatin states, and the role of maternal transcription factors
Paraiso, K. D., Cho, J. S., Yong, J., & Cho, K. W. Y. (2020) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2020.02.009 · Cited by 10

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: Liu, Xiaoyu
Wang, Chenfei
Liu, Wenqiang
Li, Jingyi
Li, Chong
Kou, Xiaochen
Chen, Jiayu
Zhao, Yanhong
Gao, Haibo
Wang, Hong
Zhang, Yong
Gao, Yawei
Gao, Shaorong
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2016-09-14
Volume: 537
Issue: 7621
Pages: 558-562
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature19362
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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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Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

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