Influences of DNA Methylation and Histone Acetylation on Gene Expressions
DOI:
https://doi.org/10.54097/yfgsaq61Keywords:
DNA methylation, Histone Acetylation, Nucleosomes, HATs, HDACs, DNMTs, Imprinting Gene, Neuropathic Pain.Abstract
Epigenetics is the concept of modifying the chromatin to achieve the different levels of transcription. This paper mainly focuses on two well-discovered mechanisms of epigenetics: DNA methylation and histone acetylation. While both affect chromatin assembly, the former acts on cytosine in the DNA strand, while the latter mostly acts on the amino acid lysine in the protein histones. Upon methylation and acetylation, the winding of chromatin is either strengthened or loosened. In addition to their actions, this paper illustrated the chemistry bases of DNA methyltransferases (DNMTs), histone acetylases (HATs), and histone deacetylases (HDACs), including the inhibitors that act against them. The discovery of these factors gives insights into clinical adaptations in analyzing pathologies of complex diseases. DNA methylation is largely being explored in neuropathic pain for diagnostic purposes and intensity detection. This paper also stresses the onerous evaluations taken to draw a conclusion in the perspective of epigenetics and the possible attention to be drawn when contradictive patterns are detected.
Downloads
References
[1] Moore, L. D., Le, T., & Fan, G. (2012). DNA methylation and its basic function. Neuropsychopharmacology, 38 (1), 23 – 38.
[2] Castillo-Aguilera, O., Depreux, P., Halby, L., Arimondo, P. B., & Goossens, L. (2017). DNA methylation targeting: The DNMT/HMT crosstalk challenge. Biomolecules, 7 (1), 3.
[3] Lyko, F. (2018). The DNA methyltransferase family: A versatile toolkit for epigenetic regulation. Nature Reviews Genetics, 19 (2), 81 – 92.
[4] Sharif, J., & Koseki, H. (2018). Hemimethylation: DNA’s lasting odd couple. Science, 359 (6380), 1102 – 1103.
[5] Pecori, R., Di Giorgio, S., Paulo Lorenzo, J., et al. (2022). Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination. Nature Reviews Genetics, 23, 505 – 518.
[6] Wang, G., Zhou, Y., Yi, B., Long, Y., Ma, B., & Zhang, Y. (2023). Comprehensive analysis of the prognostic value and biological function of TDG in hepatocellular carcinoma. Cell Cycle, 22 (12), 1478 – 1495.
[7] Zhang, X., Zhang, Y., Wang, C., et al. (2023). TET (ten-eleven translocation) family proteins: Structure, biological functions and applications. Signaling Transduction and Targeted Therapy, 8, 297.
[8] Linowiecka, K., Guz, J., Dziaman, T., Urbanowska-Domańska, O., Zarakowska, E., Szpila, A., Szpotan, J., Skalska-Bugała, A., Mijewski, P., Siomek-Górecka, A., Różalski, R., Gackowski, D., Oliński, R., & Foksiński, M. (2024). The level of active DNA demethylation compounds in leukocytes and urine samples as potential epigenetic biomarkers in breast cancer patients. Scientific Reports, 14 (1), 6481.
[9] Developmental Biology (6th ed.). (2000). Methylation pattern and the control of transcription. Sinauer Associates, Inc.
[10] Lorch, Y., Kornberg, R. D., & Maier-Davis, B. (2023). Role of the histone tails in histone octamer transfer. Nucleic Acids Research, 51 (8), 3671 – 3678.
[11] Annunziato, A. (2008). DNA packaging: Nucleosomes and chromatin. Nature Education, 1 (1), 26.
[12] Genetic imprinting. (n.d.). Genome.gov. https://www.genome.gov/genetics-glossary/Genetic-Imprinting#:~:text=%E2%80%8BGenetic%20Imprinting&text=Genomic%20imprinting%20is%20the%20process,the%20other%20copy%20is%20suppressed.
[13] Mattei, A. L., Bailly, N., & Meissner, A. (2022). DNA methylation: A historical perspective. Trends in Genetics, 38 (7), 676 – 707.
[14] Elhamamsy, A. R. (2017). Role of DNA methylation in imprinting disorders: An updated review. Journal of Assisted Reproduction and Genetics, 34 (5), 549 – 562.
[15] Fernandes, M. T., Almeida-Lousada, H., & Castelo-Branco, P. (2020). Histone modifications in diseases. Histone Modifications in Therapy, 20, 1 – 15.
[16] Bannister, A., & Kouzarides, T. (2011). Regulation of chromatin by histone modifications. Cell Research, 21, 381 – 395.
[17] Mariño-Ramírez, L., Kann, M. G., Shoemaker, B. A., & Landsman, D. (2005). Histone structure and nucleosome stability. Expert Review of Proteomics, 2 (5), 719 – 729.
[18] Vicent, G. P., Nacht, A. S., Font-Mateu, J., Castellano, G., Gaveglia, L., Ballaré, C., & Beato, M. (2011). Four enzymes cooperate to displace histone H1 during the first minute of hormonal gene activation. Genes & Development, 25 (8), 845 – 862.
[19] Ouellette, R. J., & Rawn, J. D. (2018). Amino acids, peptides, and proteins. In Organic Chemistry (pp. 929 – 971).
[20] Luger, K., Mäder, A., Richmond, R., et al. (1997). Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389, 251 – 260.
[21] Mu, A., Latario, C., Pickrell, L., & Higgs, H. (2020). Lysine acetylation of cytoskeletal proteins: Emergence of an actin code. The Journal of Cell Biology, 219.
[22] Fournier, M., Orpinell, M., Grauffel, C., et al. (2016). KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification. Nature Communications, 7, 13227.
[23] Marmorstein, R., & Zhou, M. M. (2014). Writers and readers of histone acetylation: Structure, mechanism, and inhibition. Cold Spring Harbor Perspectives in Biology, 6 (7), a018762.
[24] Ruiz-García, A. B., Sendra, R., Galiana, M., Pamblanco, M., Pérez-Ortín, J. E., & Tordera, V. (1998). HAT1 and HAT2 proteins are components of a yeast nuclear histone acetyltransferase enzyme specific for free histone H4. Journal of Biological Chemistry, 273 (20), 12599 – 12605.
[25] Wang, Y., Miao, X., Liu, Y., Li, F., Liu, Q., Sun, J., & Cai, L. (2014). Dysregulation of histone acetyltransferases and deacetylases in cardiovascular diseases. Oxidative Medicine and Cellular Longevity.
[26] Herrera, J. E., Bergel, M., Yang, X. J., Nakatani, Y., & Bustin, M. (1997). The histone acetyltransferase activity of human GCN5 and PCAF is stabilized by coenzymes. The Journal of Biological Chemistry, 272 (43), 27253 – 27258.
[27] Wapenaar, H., & Dekker, F. J. (2016). Histone acetyltransferases: Challenges in targeting bi-substrate enzymes. Clinical Epigenetics, 8, 59.
[28] Guo, S.-W. (2012). The epigenetics of endometriosis. In Epigenetics in Human Disease (pp. 443–469).
[29] [29] Grunstein, M. (1997). Histone acetylation in chromatin structure and transcription. Nature, 389, 349 – 352.
[30] Seto, E., & Yoshida, M. (2014). Erasers of histone acetylation: The histone deacetylase enzymes. Cold Spring Harbor Perspectives in Biology, 6 (4), a018713.
[31] Milazzo, G., Mercatelli, D., Di Muzio, G., Triboli, L., De Rosa, P., Perini, G., & Giorgi, F. M. (2020). Histone deacetylases (HDACs): Evolution, specificity, role in transcriptional complexes, and pharmacological actionability. Genes, 11 (5), 556.
[32] Park, S. Y., & Kim, J. S. (2020). A short guide to histone deacetylases including recent progress on class II enzymes. Experimental & Molecular Medicine, 52, 204 – 212.
[33] Ogryzko, V. V., Schiltz, R. L., Russanova, V., Howard, B. H., & Nakatani, Y. (1996). The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell, 87 (5), 953 – 959.
[34] Iyer, N., Özdag, H., & Caldas, C. (2004). p300/CBP and cancer. Oncogene, 23, 4225 – 4231.
[35] Cathcart, P., Lucchesi, W., Ottaviani, S., De Giorgio, A., Krell, J., Stebbing, J., & Castellano, L. (2015). Noncoding RNAs and the control of signalling via nuclear receptor regulation in health and disease. Best Practice & Research Clinical Endocrinology & Metabolism, 29 (4), 529 – 543.
[36] Janknecht, R., & Hunter, T. (1996). A growing coactivator network. Nature, 383, 22 – 23.
[37] Yang, X. J., Ogryzko, V., Nishikawa, J., et al. (1996). A p300/CBP-associated factor that competes with the adenoviral oncoprotein E1A. Nature, 382, 319 – 324.
[38] Xu, W., Parmigiani, R., & Marks, P. (2007). Histone deacetylase inhibitors: Molecular mechanisms of action. Oncogene, 26, 5541 – 5552.
[39] Zhang, S. L., Zhu, H. Y., Zhou, B. Y., Chu, Y., Huo, J. R., Tan, Y. Y., & Liu, D. L. (2019). Histone deacetylase 6 is overexpressed and promotes tumor growth of colon cancer through regulation of the MAPK/ERK signal pathway. OncoTargets and Therapy, 12, 2409 – 2419.
[40] Balliu, M., Guandalini, L., Romanelli, M. N., D'Amico, M., & Paoletti, F. (2015). HDAC-inhibitor (S)-8 disrupts HDAC6-PP1 complex prompting A375 melanoma cell growth arrest and apoptosis. Journal of Cellular and Molecular Medicine, 19 (1), 143 – 154.
[41] He, Y., Sun, M. M., Zhang, G. G., et al. (2021). Targeting PI3K/Akt signal transduction for cancer therapy. Signaling Transduction and Targeted Therapy, 6, 425.
[42] Abbas, T., & Dutta, A. (2009). p21 in cancer: Intricate networks and multiple activities. Nature Reviews Cancer, 9 (6), 400 – 414.
[43] Cole, P. (2008). Chemical probes for histone-modifying enzymes. Nature Chemical Biology, 4, 590 – 597.
[44] Huang, M., Huang, J., Zheng, Y., Sun, Q. (2019). Histone acetyltransferase inhibitors: An overview in synthesis, structure-activity relationship and molecular mechanism. European Journal of Medicinal Chemistry, 178, 259 – 286.
[45] Lys-COA. Bio. (n.d.). https://www.bio-techne.com/p/small-molecules-peptides/lys-coa_5103#product-documents.
[46] Barritt, S. A., DuBois-Coyne, S. E., & Dibble, C. C. (2024). Coenzyme A biosynthesis: Mechanisms of regulation, function and disease. Nature Metabolism, 6, 1008 – 1023.
[47] Costigan, M., Scholz, J., & Woolf, C. J. (2009). Neuropathic pain: A maladaptive response of the nervous system to damage. Annual Review of Neuroscience, 32, 1 – 32.
[48] Jiang, W., Tan, X. Y., Li, J. M., Yu, P., & Dong, M. (2022). DNA methylation: A target in neuropathic pain. Frontiers in Medicine, 9, 879902.
[49] Massart, R., Dymov, S., Millecamps, M., et al. (2016). Overlapping signatures of chronic pain in the DNA methylation landscape of prefrontal cortex and peripheral T cells. Scientific Reports, 6, 19615.
[50] Bielczyk-Maczynska, E., Zhao, M., Zushin, P. J. H., et al. (2022). G protein-coupled receptor 151 regulates glucose metabolism and hepatic gluconeogenesis. Nature Communications, 13, 7408.
[51] Maiarù, M., Acton, R. J., Woźniak, E. L., Mein, C. A., Bell, C. G., Géranton, S. M. (2023). A DNA methylation signature in the stress driver gene Fkbp5 indicates a neuropathic component in chronic pain. Clinical Epigenetics, 15 (1), 155.
[52] Guo, X., Yao, Y., & Tao, Y.-X. (2019). Role of DNA methylation in chronic pain. In Translational Epigenetics (Vol. 7, pp. 99-110). Academic Press.
Downloads
Published
Issue
Section
License
Copyright (c) 2024 Highlights in Science, Engineering and Technology

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







