LITERATURE REVIEW OF EMBRYONIC DEVELOPMENT EPIGENETICS: CHROMATIN MODIFICATION AND CELL PROGRAMMING
DOI:
10.54443/morfai.v5i6.4502Published:
2025-12-10Downloads
Abstract
This study aims to comprehensively examine epigenetic mechanisms in embryonic development, focusing on the role of chromatin modification and cell programming as regulators of gene expression without changes in DNA sequence. The type of study used was qualitative , with a descriptive approach through literature review, which examined scientific literature from reputable international journals such as Nature, Trends in Genetics, and The FEBS Journal published between 2015 and 2025. Data were collected through systematic searches of scientific articles using thematic and inductive analysis techniques, including theme identification, data reduction, and concept categorization. The results of the study show that DNA methylation, acetylation, and histone methylation are key factors in regulating gene expression during the zygotic genome activation (ZGA) phase and the formation of cell lineages. This process demonstrates the complex interaction between epigenetic and transcriptional factors that determine the direction of cell differentiation. In addition, similarities in epigenetic regulation principles between mammals and plants were found, indicating the conservation of biological mechanisms across species. The implications of the study " " include the development of regenerative therapies, increased effectiveness of assisted reproductive technologies, and innovations in agricultural biotechnology. In conclusion, this study confirms that epigenetics is an important layer of regulation in developmental biology that enriches our understanding of the mechanisms of life formation from the earliest stages.
Keywords:
epigenetics, chromatin modification, cell programming, embryonic development, , zygotic genome activation.References
Abraham, D.; P., P. (2024). A Methodological Framework for Descriptive Phenomenological Research. Western Journal of Nursing Research, 47
Alawiyah, K., Anggraini, D., Mubarok, W., & Hardestyariki, D.(2024). Molecular and Epigenetic Impacts of Pesticides on the Female Reproductive System: A Review. BIOVALENTIA: Biological Research Journal,10(1), 1-23.
Alfarisi, H., Sa'diah, S., Juliandi, B., Wresdiyati, T. (2024). Antidiabetic Effect of Acalypha hispida Extract and Nanoextract: Mechanism of Action on Pancreatic β-Cell Function via Histone Acetylation. Advances in Pharmacological and Pharmaceutical Sciences, 2024(048389), 1-16.
Atlasi, Y., & Stunnenberg, H. (2017). The interplay of epigenetic marks during stem cell differentiation and development. Nature Reviews Genetics, 18 , 643–658. https://doi.org/10.1038/nrg.2017.57
Balder, P., Jones, C., Coward, K., & Yeste, M. (2024). Sperm chromatin: Evaluation, epigenetic signatures and relevance for embryo development and assisted reproductive technology outcomes. European Journal of Cell Biology, 103 (3
Bandaranayake, P. (2024). Application of grounded theory methodology in library and information science research: An overview. Sri Lanka Library Review. https://doi.org/10.4038/sllr.v38i2.70
Bingham, A. (2023). From Data Management to Actionable Findings: A Five-Phase Process of Qualitative Data Analysis. International Journal of Qualitative Methods, 22 . https://doi.org/10.1177/16094069231183620
Bozdemir, N., Kablan, T., Biyikli, E., Cinar, O., & Uysal, F. (2025). A comprehensive review of histone modifications during mammalian oogenesis and early embryo development. Histochemistry and Cell Biology, 163
Chen, C., Gao, Y., Liu, W., & Gao, S. (2022). Epigenetic regulation of cell fate transition: Learning from early embryo development and somatic cell reprogramming. Biology of Reproduction, 107
Cusanovich, D., Reddington, J., Garfield, D., Daza, R., Marco-Ferreres, R., Christiansen, L., Qiu, X., Steemers, F., Trapnell, C., Shendure, J., & Furlong, E. (2017). The cis-regulatory dynamics of embryonic development at single cell resolution. Nature, 555
De-La-Peña, C., Nic-Can, G., Galaz-Ávalos, R., Avilez-Montalvo, R., & Loyola-Vargas, V. (2015). The role of chromatin modifications in somatic embryogenesis in plants. Frontiers in Plant Science, 6 . https://doi.org/10.3389/fpls.2015.00635
Doyle, L. ; M., C. ;. Keogh, B. ;. Brady, A. ;. McCann, M. (2019). An overview of the qualitative descriptive design within nursing research. Journal of Research in Nursing, 25 . https://doi.org/10.1177/1744987119880234
Edwards-Lee, C., Jarred, E., & Western, P. (2025). Coordinated regulation of chromatin modifiers reflects organised epigenetic programming in mouse oocytes. Epigenetics & Chromatin, 18 . https://doi.org/10.1186/s13072-025-00583-9
Fife, S. ; G., J. (2024). Deductive Qualitative Analysis: Evaluating, Expanding, and Refining Theory. International Journal of Qualitative Methods, 23 . https://doi.org/10.1177/16094069241244856
Fu, X., Zhang, C., & Zhang, Y. (2020). Epigenetic regulation of mouse preimplantation embryo development. Current Opinion in Genetics & Development, 64
Granikov, V. ; H., Q. ;. Crist, E. ;. Pluye, P. (2020). Mixed methods research in library and information science: A methodological review. Library & Information Science Research, 42 (2). https://doi.org/10.1016/j.lisr.2020.101003
Jimenez, S. ; B., J. ;. De La Torre, R. (2024). How do university libraries contribute to the research process? The Journal of Academic Librarianship. https://doi.org/10.1016/j.acalib.2024.102930
Kalpokaite, N., & Radivojevic, I. (2018). Demystifying Qualitative Data Analysis for Novice Qualitative Researchers. The Qualitative Report. https://doi.org/10.46743/2160-3715/2019.4120
Liu, M., Yue, Y., Chen, X., Xian, K., Dong, C., Shi, M., Xiong, H., Tian, K., Li, Y., Zhang, Q., & He, A. (2025). Genome-coverage single-cell histone modifications for embryo lineage tracing. Nature, 640
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. (2016). Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature, 537
Macrae, T., Fothergill-Robinson, J., & Ramalho-Santos, M. (2022). Regulation, functions and transmission of bivalent chromatin during mammalian development. Nature Reviews Molecular Cell Biology, 24 , 6–26. https://doi.org/10.1038/s41580-022-00518-2
Pladevall-Morera, D., & Żylicz, J. (2022). Chromatin as a sensor of metabolic changes during early development. Frontiers in Cell and Developmental Biology, 10 . https://doi.org/10.3389/fcell.2022.1014498
Pratt, M. (2025). On the Evolution of Qualitative Methods in Organizational Research. Annual Review of Organizational Psychology and Organizational Behavior. https://doi.org/10.1146/annurev-orgpsych-111722-032953
Schüle, K., & Probst, S. (2025). Epigenetic control of cell identities from epiblast to gastrulation. The FEBS Journal. https://doi.org/10.1111/febs.70024
Sotomayor-Lugo, F., Iglesias-Barrameda, N., Castillo-Aleman, Y., Casado-Hernandez, I., Villegas-Valverde, C., Bencomo-Hernandez, A., Ventura-Carmenate, Y., & Rivero-Jiménez, R. (2024). The dynamics of histone modifications during mammalian zygotic genome activation. International Journal of Molecular Sciences, 25 . https://doi.org/10.3390/ijms25031459
Sun, L., Fu, X., & Hutchins, A. (2021). Chromatin and epigenetic rearrangements in embryonic stem cell fate transitions. Frontiers in Cell and Developmental Biology, 9 . https://doi.org/10.3389/fcell.2021.637309
Tao, Z., Shen, L., Gu, X., Wang, Y., Yu, H., & He, Y. (2017). Embryonic epigenetic reprogramming by a pioneer transcription factor in plants. Nature, 551 , 124–128. https://doi.org/10.1038/nature24300
Vila-Henninger, L., Dupuy, C., Van Ingelgom, V., Caprioli, M., Teuber, F., Pennetreau, D., Bussi, M., & Gall, C. (2022). Abductive coding: Theory building and qualitative (re)analysis. Sociological Methods & Research, 53 , 968–1001. https://doi.org/10.1177/00491241211067508
Xia, W., Xu, J., Yu, G., Yao, G., Xu, K., Zhang, N., Liu, B., Li, T., Lin, Z., Chen, X., Li, L., Wang, Q., Shi, D., Shi, S., Zhang, Y., Song, W., Jin, H., Hu, L., Bu, Z., … Science, 365
Xu, R., Li, C., Liu, X., & Gao, S. (2020). Insights into epigenetic patterns in mammalian early embryos. Protein & Cell, 12
Xu, R., Li, Y., Wu, Y., Liu, X., & Gao, S. (2025). Epigenetic regulation in early embryo development: From zygotic genome activation to the first lineage specification. Trends in Genetics: TIG. https://doi.org/10.1016/j.tig.2025.05.005
Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., Wang, H., Bie, X., Jiang, J., Feng, X., Fu, X., Zhang, X., Du, Z., & Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology, 24
License
Copyright (c) 2025 Kamila Alawiyah, Rizki Andini Nawawi, Meillisa Carlen Mainassy, Syarinta Adenina, Hamzah Alfarisi, Sternatami Liberitera

This work is licensed under a Creative Commons Attribution 4.0 International License.




