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A bivalent chromatin structure marks key developmental genes in embryonic stem cells

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Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclassesPreprint

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ChromHMM: automating chromatin-state discovery and characterization

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PHF13 epigenetically activates TGFβ driven epithelial to mesenchymal transition

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Genetic mosaics and time-lapse imaging identify functions of histone H3.3 residues in mouse oocytes and embryos

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Transcriptional response of Hoxb genes to retinoid signalling is regionally restricted along the neural tube rostrocaudal axis

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Bivalency in Drosophila embryos is associated with strong inducibility of Polycomb target genes

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H3K27me3 at pericentromeric heterochromatin is a defining feature of the early mouse blastocyst

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Sex affects immunolabeling for histone 3 K27me3 in the trophectoderm of the bovine blastocyst but not labeling for histone 3 K18ac

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TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS)

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The dynamic landscape of enhancer-derived RNA during mouse early embryo development

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Genome-Wide Analysis of H3K27me3 in Porcine Embryonic Muscle Development

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Comparative analysis of histone H3K27me3 modifications between blastocysts and somatic tissues in cattle

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KDM5-mediated redistribution of H3K4me3 is required for oocyte-to-embryonic transition in cattle

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LncRNA affects epigenetic reprogramming of porcine embryo development by regulating global epigenetic modification and the downstream gene SIN3A

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Research advances of polycomb group proteins in regulating mammalian development

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Single-embryo transcriptomic atlas of oxygen response reveals the critical role of HIF-1α in prompting embryonic zygotic genome activation

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Acetylation at lysine 27 on maternal H3.3 regulates minor zygotic genome activation

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Non-canonical imprinting, manifesting as post-fertilization placenta-specific parent-of-origin dependent methylation, is not conserved in humans

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Increase in DNA Damage by MYCN Knockdown Through Regulating Nucleosome Organization and Chromatin State in Neuroblastoma

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Histone Demethylase UTX is an Essential Factor for Zygotic Genome Activation and Regulates Zscan4 Expression in Mouse Embryos

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The potential underlying mechanism of the leukemia caused by MLL‐fusion and potential treatments

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The dynamic chromatin landscape and mechanisms of DNA methylation during mouse germ cell development

Shirane, K. (2022) · Genes & Genetic Systems · doi:10.1266/ggs.21-00069 · Cited by 9

Plant Epigenomics

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Molecular mechanisms underlying totipotency

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Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP

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Integrating High-Throughput Approaches and in vitro Human Trophoblast Models to Decipher Mechanisms Underlying Early Human Placenta Development

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dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo developmentPreprint

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Compressive Forces Induce Epigenetic Activation of Aged Human Dermal Fibroblasts Through ERK Signaling Pathway

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Cellular osmoregulation enhances porcine embryo development by restoring zygotic genome activation via metabolic–epigenetic crosstalk

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The Novel Protease Activities of JMJD5–JMJD6–JMJD7 and Arginine Methylation Activities of Arginine Methyltransferases Are Likely Coupled

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Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress

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Allelic reprogramming of chromatin states in human early embryos

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Epigenetic drug screening for trophoblast syncytialization reveals a novel role for MLL1 in regulating fetoplacental growth

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H2A.Z reinforces maternal H3K4me3 formation and is essential for meiotic progression in mouse oocytes

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Maternal epigenetic inheritance

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Activation of transcription factor circuity in 2i-induced ground state pluripotency is independent of repressive global epigenetic landscapes

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Histone demethylase KDM4A overexpression improved the efficiency of corrected human tripronuclear zygote development

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The role of protein arginine methyltransferase 7 in human developmentally arrested embryos cultured

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MACMIC Reveals a Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes

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Global regulatory transitions at core promoters demarcate the mammalian germline cyclePreprint

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The impact of retrotransposons on zygotic genome activation and the chromatin landscape of early embryos

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Persistent Wnt signaling affects IVF embryo implantation and offspring metabolism

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Epigenetic regulation and mechanobiological adaptation in tenocytes during maturation

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RNA-m5C regulatory atlas of human fetal tissues uncover the activities of Nsun2/Jarid2/Alyref axis

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EZHIP restricts noncanonical PRC2 binding and regulates H3K27me3 intergenerational inheritance and reprogramming

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H3.3 kinetics predicts chromatin compaction status of parental genomes in early embryos

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Optogenetics for sensors: On-demand fluorescent labeling of histone epigenetics

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When Dad’s Stress Gets under Kid’s Skin—Impacts of Stress on Germline Cargo and Embryonic Development

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H3K4me3 Genome-Wide Distribution and Transcriptional Regulation of Transposable Elements by RNA Pol2 Deposition

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Transcriptional and epigenetic control of cell fate decisions in early embryos

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EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences

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Chromatin architecture reorganization during somatic cell reprogramming

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Epigenetic reorganization during early embryonic lineage specification

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Maternal EHMT2 is essential for homologous chromosome segregation by regulating Cyclin B3 transcription in oocyte meiosis

Meng, T., Lei, W., Lu, X., Liu, X., Ma, X., Nie, X.-Q., Zhao, Z., Li, Q., Huang, L., Hou, Y., et al. (2022) · International Journal of Biological Sciences · doi:10.7150/ijbs.75298 · Cited by 7

Current progress in bionanomaterials to modulate the epigenome

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Tumor Environment Promotes Lnc57Rik-Mediated Suppressive Function of Myeloid-Derived Suppressor Cells

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NELFA and BCL2 induce the 2C ‐like state in mouse embryonic stem cells in a chemically defined medium

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The genome-wide molecular regulation of mouse gastrulation embryo

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Analysis of accessible chromatin landscape in the inner cell mass and trophectoderm of human blastocysts

Yang, M., Tao, X., Titus, S., Zhao, T., Scott, R. T. W., & Seli, E. U. (2020) · Molecular Human Reproduction · doi:10.1093/molehr/gaaa048 · Cited by 7

DamID to Map Genome-Protein Interactions in Preimplantation Mouse Embryos

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Chemo-Mechanical Cues Modulate Nano-Scale Chromatin Organization in Healthy and Diseased Connective Tissue CellsPreprint

Heo, S.-J., Thakur, S., Chen, X., Loebel, C., Xia, B., McBeath, R., Burdick, J. A., Shenoy, V. B., Mauck, R. L., & Lakadamyali, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.27.441596 · Cited by 7

RIF1 controls replication timing in early mouse embryos independently of lamina-associated nuclear organization

Nakatani, T., Schauer, T., Pal, M., Ettinger, A. W., Altamirano‐Pacheco, L., Zorn, J., Gilbert, D. M., & Torres‐Padilla, M. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.03.016 · Cited by 6

Methylation patterns of Lys9 and Lys27 on histone H3 correlate with patient outcome and tumor progression in lung cancer

Zhang, Y., Zheng, B., Lou, K., Xu, X., & Xu, Y. (2022) · Annals of Diagnostic Pathology · doi:10.1016/j.anndiagpath.2022.152045 · Cited by 6

Arsenite exposure disturbs maternal-to-zygote transition by attenuating H3K27ac during mouse preimplantation development

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Adenosylhomocysteinase plays multiple roles in maintaining the identity and pluripotency of mouse embryonic stem cells

Jiang, Q., Lan, S., Tan, F., Liang, Y., Guo, Z., Hou, Y., Zhang, H., Wu, G., & Liu, Z. (2023) · Biology of Reproduction · doi:10.1093/biolre/ioad165 · Cited by 7

Impact of high-fat diet on ovarian epigenetics: Insights from altered intestinal butyric acid levels

Qi, J., Xia, C., Zhang, Y., Ding, R., Zhang, Y., Cao, W., Duan, C., Yao, Z., Qin, H., Ye, Y., et al. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e33170 · Cited by 6

Sperm histone modifications may predict success in human assisted reproduction: a pilot study

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KDM2A and KDM2B protect a subset of CpG islands from DNA methylation

Liu, Y., Liu, Y., Zhu, Y., Hu, D., Nie, H., Xie, Y., Sun, R., He, J., Zhang, H., & Lu, F. (2024) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.10.012 · Cited by 6

Epigenetic control of cell identities from epiblast to gastrulation

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Inhibition of RNA synthesis during Scriptaid exposure enhances gene reprogramming in SCNT embryos

Rissi, V. B., Glanzner, W. G., de Macedo, M. P., Mujica, L. K. S., Campagnolo, K., Gutierrez, K., Bridi, A., Baldassarre, H., Gonçalves, P. B. D., & Bordignon, V. (2018) · Reproduction · doi:10.1530/rep-18-0366 · Cited by 6

Deletion of BAF250a affects oocyte epigenetic modifications and embryonic development

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Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq

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Cancer stem/progenitor signatures refine the classification of clear cell renal cell carcinoma with stratified prognosis and decreased immunotherapy efficacy

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Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies

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Transcriptional Regulation of the First Cell Fate Decision.

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Peculiarities of DNA and Histone H3 Methylation in the Hippocampus and Neocortex of Rats Subjected to Pathological Treatments during the Prenatal Period

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The Effect of Increased miR-16-1 Levels in Mouse Embryos on Epigenetic Modification, Target Gene Expression, and Developmental Processes

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Integrated Glycosylation Patterns of Glycoproteins and DNA Methylation Landscapes in Mammalian Oogenesis and Preimplantation Embryo Development

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Melatonin and spermidine protect early mouse embryos from ethylparaben toxicity by restoring histone modifications and subcellular structures

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Integration ATAC ‐Seq and RNA ‐Seq Analysis of Mammary Placodes in Erhualian and Bamaxiang Pigs Identified Candidate Genes Influencing Pig Teat Number Variation

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PLETHORA transcription factors orchestrate epigenetic silencing of bivalent chromatin to promote root meristem development in rice

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Mechanisms of Anti-PD Therapy Resistance in Digestive System Neoplasms

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Bisphenol B restrains rat leydig cell function via H3K27me3/H3K9me3 histone modifications

He, J., Zhang, H., Quan, H., Wang, Q., Wen, C., Wang, Y., Zhu, Y., Ge, R., & Li, X. (2025) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2025.117847 · Cited by 5

SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis

Zhao, D., & Zheng, D. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2577-4 · Cited by 5

Wenshen Shengjing Decoction Improves Early Embryo Development by Maintaining Low H3K27me3 Levels in Sperm and Pronuclear Embryos of Spermatogenesis Impaired Mice

Sun, Y., Gao, F., Xu, D., Lu, L., Chen, Q., Yang, Z., Wang, X., & Pan, X. (2021) · Evidence-based Complementary and Alternative Medicine · doi:10.1155/2021/8035997 · Cited by 5

New Wenshen Shengjing Decoction Improves Early Embryonic Development by Maintaining Low Levels of H3K4me3 in Sperm

Zhang, W., Lu, L., Sun, Y., Dong, Z., Lei, X., Peng, Z., Zhang, B., Cao, S., Wang, X., & Pan, X. (2022) · BioMed Research International · doi:10.1155/2022/9775473 · Cited by 5

Hypoxia-sensitive cells trigger NK cell activation via the KLF4-ASH1L-ICAM-1 axis, contributing to impairment in the rat epididymis

Zeng, J., Gao, W., Tang, Y., Wang, Y., Liu, X., Yin, J., Su, X., Zhang, M., Kang, E., Tian, Y., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113442 · Cited by 5

3-Nitropropionic acid exposure inhibits embryo development by disrupting mitochondrial function and inducing oxidative stress

Zhou, X., Ruan, H., Dong, L., Yu, Y., Sun, Y., Xiang, H., Cao, Y., & Ding, Z. (2025) · Chemico-Biological Interactions · doi:10.1016/j.cbi.2025.111389 · Cited by 5

Maternal transcription factor OTX2 directly induces SETD1A and promotes embryonic genome activation in human pre-implantation embryos

Zhang, T., Peng, Z., Meng, F., Li, Z. Y., Chen, J., Zhou, Q., Leng, L., Bo, H., Lu, G., Deng, Y. L., et al. (2025) · Science China Life Sciences · doi:10.1007/s11427-024-2875-3 · Cited by 5

Histone Modification Analysis of Low-Mappability Regions

Yoshizawa-Sugata, N., & Masai, H. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2433-3_18 · Cited by 5

P14AS upregulates gene expression in the CDKN2A/2B locus through competitive binding to PcG protein CBX7

Li, Z., Qiao, J., Ma, W., Zhou, J., Gu, L., Deng, D., & Zhang, B. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.993525 · Cited by 5

A Tremendous Reorganization Journey for the 3D Chromatin Structure from Gametes to Embryos

Chen, Z., & Chen, X. (2022) · Genes · doi:10.3390/genes13101864 · Cited by 6

Epitranscriptome: m6A and its function in stem cell biology

Park, C., & Hong, K. (2016) · Genes & Genomics · doi:10.1007/s13258-016-0507-2 · Cited by 5

Transgenerational analysis of H3K4me3 and H3K27me3 by ChIP-Seq links epigenetic inheritance to metabolism

An, K., Du, F., Hao, M., Li, G., Zhang, M., Liu, Z. Z., Zhao, Z., Zhang, Z., Yu, D., Wang, D., et al. (2017) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2017.11.004 · Cited by 5

Human embryos arrest in a quiescent-like state characterized by metabolic and zygotic genome activation problemsPreprint

Yang, Y., Shi, L., Fu, X., Ma, G., Yang, Z., Li, Y., Zhou, Y., Yuan, L., Xia, Y., Zhong, X., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.19.473390 · Cited by 5

H3K27me3 dictates atypical genome-nuclear lamina interactions and allelic asymmetry during early embryogenesisPreprint

Guerreiro, I. M., Rang, F. J., Kawamura, Y., Groenveld, F. C., van Beek, R. E., Lochs, S. J. A., Boele, E., Peters, A. H. F. M., & Kind, J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.06.527307 · Cited by 5

Dissecting pre- to post-implantation transition of DNA methylome-transcriptome dynamics in early mammalian development

Zhu, Q., Liu, Y., Hao, X., Yan, S., Ge, J., Zheng, C., Ren, X., & Zhou, F. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115790 · Cited by 4

Remodelling bivalent chromatin is essential for mouse peri-implantation embryogenesis

Li, Y., He, J., Liu, Y., Hui, Y., Liu, S., Zhang, Y., Xiong, Y., Xu, T., Xu, Z., Zhang, Z., et al. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01776-w · Cited by 4

Epigenetic remodeling during early embryonic development

Wan, X., Zhang, S., Li, J., Kong, D., & Chen, M. (2026) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2026.1750381 · Cited by 6

Systematic analysis identifies a connection between spatial and genomic variations of chromatin states

Cao, X. D., Ma, T., Fan, R., & Yuan, G. (2024) · Cell Systems · doi:10.1016/j.cels.2024.10.006 · Cited by 5

Embryonic signatures of intergenerational epigenetic inheritance across paternal environments and genetic backgrounds

Dura, M., Ranjan, B., Serrano, J. B., Paribeni, R., Paribeni, V., Villacorta, L., Beneš, V., Boruc, O., Bošković, A., & Hackett, J. A. (2025) · The EMBO Journal · doi:10.1038/s44318-025-00556-4 · Cited by 7

Epigenetic information in gametes: Gaming from before fertilization

Shi, J., Zhang, X., Liu, Y., & Chen, Q. (2017) · Physics of Life Reviews · doi:10.1016/j.plrev.2017.01.001 · Cited by 4

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

Zhang, B., Zheng, H., Huang, B., Li, W., Xiang, Y., Xu, P., Ming, J., Wu, X., Zhang, Y., Xu, Q., et al. (2016) · Nature · doi:10.1038/nature19361 · Cited by 703

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

Dahl, J. A., Jung, I., Aanes, H., Greggains, G. D., Manaf, A., Lerdrup, M., Li, G., Kuan, S., Li, B., Lee, A. Y., et al. (2016) · Nature · doi:10.1038/nature19360 · Cited by 650

Panoramic views of the early epigenome

Vaquerizas, J. M., & Torres‐Padilla, M. (2016) · Nature · doi:10.1038/nature19468 · Cited by 10

Genome-wide mapping of histone modification H3K4me3 in bovine oocytes and early embryosPreprint

Dang, Y., Luo, L., Shi, Y., Li, S., Wang, S., & Zhang, K. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.22.469629 · Cited by 1

Dynamic patterns of histone H3 lysine 4 methyltransferases and demethylases during mouse preimplantation development

Shao, G., Chen, J., Zhang, L., Huang, P., Lu, H., Jin, J., Gong, A., & Sang, J. (2014) · In Vitro Cellular & Developmental Biology - Animal · doi:10.1007/s11626-014-9741-6 · Cited by 47