As discussed in Chapter 1, the processes that control gene expression during cellular differentiation cannot be irreversible since it is possible for the DNA genome of a differentiated cell to give rise to an entire organism containing a wide variety of different cell types. This can occur for example, when differentiated plant cells are cultured under certain conditions or when the nucleus of differentiated animal cells is transplanted into an oocyte (see Chapter 1, Section 1.3).
Multiple-choice questions
Questions for Discussion
- Describe the role of epigenetic mechanisms in establishing social hierarchy in social insects such as honeybees. Ensure that you discuss how the knowledge of these mechanism can be applied in human society.
- Discuss the potential impact of epigenetic modifiers, chemicals used in food production, and other environmental toxins on sex chromosomes and on human endocrine system.
- Discuss molecular pathways by which diet triggers DNA and histone modification.
- Compare and contrast cis vs trans epigenetic mechanism(s) that maintain the epigenetic status within a cell.
- Epigenetic modifications are programmed during development and are affected by the environment. Make a list of the specific epigenetic examples described in this chapter and classify them as developmentally programmed or environmentally modulated.
Further Reading
5.1 Changes in chromatin structure in active or potentially active genes
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Weintraub, H., & Groudine, M. (1976). Chromosomal subunits in active genes have an altered conformation. Science (New York, N.Y.), 193(4256), 848–856. https://doi.org/10.1126/science.948749
5.2 Alterations in DNA methylation in active or potentially active genes
Angeloni, A., & Bogdanovic, O. (2021). Sequence determinants, function, and evolution of CpG islands. Biochemical Society Transactions, 49(3), 1109–1119. https://doi.org/10.1042/BST20200695
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Lee, J., Hyeon, D. Y., & Hwang, D. (2020). Single-cell multiomics: Technologies and data analysis methods. Experimental & Molecular Medicine, 52(9), 1428–1442. https://doi.org/10.1038/s12276-020-0420-2
Liu, W., Wu, G., Xiong, F., & Chen, Y. (2021). Advances in the DNA methylation hydroxylase TET1. Biomarker Research, 9(1), 76. https://doi.org/10.1186/s40364-021-00331-7
Mattei, A. L., Bailly, N., & Meissner, A. (2022). DNA methylation: A historical perspective. Trends in Genetics: TIG, 38(7), 676–707. https://doi.org/10.1016/j.tig.2022.03.010
Papin, C., Le Gras, S., Ibrahim, A., Salem, H., Karimi, M. M., Stoll, I., … Hamiche, A. (2021). CpG Islands Shape the Epigenome Landscape. Journal of Molecular Biology, 433(6), 166659. https://doi.org/10.1016/j.jmb.2020.09.018
Ross, S. E., & Bogdanovic, O. (2019). TET enzymes, DNA demethylation and pluripotency. Biochemical Society Transactions, 47(3), 875–885. https://doi.org/10.1042/BST20180606
Stewart-Morgan, K. R., Petryk, N., & Groth, A. (2020). Chromatin replication and epigenetic cell memory. Nature Cell Biology, 22(4), 361–371. https://doi.org/10.1038/s41556-020-0487-y
Zhang, H., Lang, Z., & Zhu, J.-K. (2018). Dynamics and function of DNA methylation in plants. Nature Reviews. Molecular Cell Biology, 19(8), 489–506. https://doi.org/10.1038/s41580-018-0016-z5.3
5.3 Modification of histones in the chromatin of active or potentially active genes
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de Mendoza, A. (2023). A mammalian DNA methylation landscape. Science (New York, N.Y.), 381(6658), 602–603. https://doi.org/10.1126/science.adj4904
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Kuroda, M. I., Kang, H., De, S., & Kassis, J. A. (2020). Dynamic Competition of Polycomb and Trithorax in Transcriptional Programming. Annual Review of Biochemistry, 89, 235–253. https://doi.org/10.1146/annurev-biochem-120219-103641
Schoelz, J. M., & Riddle, N. C. (2022). Functions of HP1 proteins in transcriptional regulation. Epigenetics & Chromatin, 15(1), 14. https://doi.org/10.1186/s13072-022-00453-8
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5.4 Interaction of different histone modifications, DNA methylation, and regulatory RNAs
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5.5 Changes in chromatin structure in the regulatory regions of active or potentially active genes
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5.6 Other situations in which chromatin structure is regulated
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