Harnessing CRISPR-Cas for Targeted Epigenetic Manipulations: a physiological study of Gene Regulation

Qammar Shaker Hmood

doi:10.61796/jmgcb.v1i5.453

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Qammar Shaker Hmood
qammar.shaker@sci.utq.edu.iq
Department of Biology, College of Science, University of Thi-Qar

Vol. 1 No. 5 (2024): Journal of Medical Genetics and Clinical Biology

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May 10, 2024

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Genome engineering, epigenome editing, as one of the prominent research techniques, has also become instrumental in discovering the gene expression regulation mechanisms and exploring their physiological correlates in health and pathology. This review summarizes the state-of-the-art CRISPR-Cas strategies that focus on epigenetics modification and projects its utility in molecular physiology of gene regulation. In this course we will delve into how CRISPR-Cas systems interact with epigenetic signals through DNA methylation, histone modifications and accessibility to chromatin. Then we look at the physiological effects of epigenetic modulations in cellular differentiation and development, cellular signal and homeostasis, disease pathogenesis, and therapeutic for application. Issues and perspectives on how epigenome manipulations can revolutionize therapeutics are also emphasized exploring the potential of precision medicine and individualized therapies. Overall, the review stresses the pivotal role of epigenetic modulation in the development of our understanding of gene expressions/mediation and cellular physiology. It also provides some inputs on the potential directions that the field of genetic engineering might take in the future.

Hmood, Q. S. (2024). Harnessing CRISPR-Cas for Targeted Epigenetic Manipulations: a physiological study of Gene Regulation. Journal of Medical Genetics and Clinical Biology, 1(5), 115–129. https://doi.org/10.61796/jmgcb.v1i5.453

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Statello, L., Guo, C. J., Chen, L. L., & Huarte, M. (2021). Gene regulation by long non-coding RNAs and its biological functions. Nature reviews Molecular cell biology, 22(2), 96-118.

Muhar, M., Ebert, A., Neumann, T., Umkehrer, C., Jude, J., Wieshofer, C., ... & Zuber, J. (2018). SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science, 360(6390), 800-805.

Castelán-Muñoz, N., Herrera, J., Cajero-Sánchez, W., Arrizubieta, M., Trejo, C., García-Ponce, B., ... & Garay-Arroyo, A. (2019). MADS-box genes are key components of genetic regulatory networks involved in abiotic stress and plastic developmental responses in plants. Frontiers in plant science, 10, 853.

Santos-Zavaleta, A., Salgado, H., Gama-Castro, S., Sánchez-Pérez, M., Gómez-Romero, L., Ledezma-Tejeida, D., ... & Collado-Vides, J. (2019). RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. Nucleic acids research, 47(D1), D212-D220.

Koonin, E. V., & Makarova, K. S. (2019). Origins and evolution of CRISPR-Cas systems. Philosophical Transactions of the Royal Society B, 374(1772), 20180087.

McGinn, J., & Marraffini, L. A. (2019). Molecular mechanisms of CRISPR–Cas spacer acquisition. Nature Reviews Microbiology, 17(1), 7-12.

Shivram, H., Cress, B. F., Knott, G. J., & Doudna, J. A. (2021). Controlling and enhancing CRISPR systems. Nature chemical biology, 17(1), 10-19.

Ansari, I., Chaturvedi, A., Chitkara, D., & Singh, S. (2022, August). CRISPR/Cas mediated epigenome editing for cancer therapy. In Seminars in Cancer Biology (Vol. 83, pp. 570-583). Academic Press.

Mahmoud, A. M., & Ali, M. M. (2019). Methyl donor micronutrients that modify DNA methylation and cancer outcome. Nutrients, 11(3), 608.

Luo, C., Hajkova, P., & Ecker, J. R. (2018). Dynamic DNA methylation: In the right place at the right time. Science, 361(6409), 1336-1340.

Sankar, A., Mohammad, F., Sundaramurthy, A. K., Wang, H., Lerdrup, M., Tatar, T., & Helin, K. (2022). Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals. Nature genetics, 54(6), 754-760.

Zhang, Y., Sun, Z., Jia, J., Du, T., Zhang, N., Tang, Y., ... & Fang, D. (2021). Overview of histone modification. Histone Mutations and Cancer, 1-16.

Liu, G., Yin, K., Zhang, Q., Gao, C., & Qiu, J. L. (2019). Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo. Genome biology, 20, 1-11.

Verkuijl, S. A., & Rots, M. G. (2019). The influence of eukaryotic chromatin state on CRISPR–Cas9 editing efficiencies. Current opinion in biotechnology, 55, 68-73.

Li, Xiaoyi, Wei Chen, Beth K. Martin, Diego Calderon, Choli Lee, Junhong Choi, Florence M. Chardon et al. "Chromatin context-dependent regulation and epigenetic manipulation of prime editing." Cell (2023).

Feliciello, I., Pezer, Ž., Sermek, A., Bruvo Mađarić, B., Ljubić, S., & Ugarković, Đ. (2021). Satellite DNA-mediated gene expression regulation: Physiological and evolutionary implication. Satellite DNAs in Physiology and Evolution, 145-167.

Li, H., Li, K., Zhang, K., Li, Y., Gu, H., Liu, H., ... & Cai, D. (2021). The Circadian physiology: implications in livestock health. International journal of molecular sciences, 22(4), 2111.

Witzigmann, D., Kulkarni, J. A., Leung, J., Chen, S., Cullis, P. R., & van der Meel, R. (2020). Lipid nanoparticle technology for therapeutic gene regulation in the liver. Advanced drug delivery reviews, 159, 344-363.

Lu, H., Sun, J., Liang, W., Zhang, J., Rom, O., Garcia-Barrio, M. T., ... & Fan, Y. (2019). Novel gene regulatory networks identified in response to nitro-conjugated linoleic acid in human endothelial cells. Physiological genomics, 51(6), 224-233.

Unnikrishnan, A., Freeman, W. M., Jackson, J., Wren, J. D., Porter, H., & Richardson, A. (2019). The role of DNA methylation in epigenetics of aging. Pharmacology & therapeutics, 195, 172-185.

Topper, M. J., Vaz, M., Marrone, K. A., Brahmer, J. R., & Baylin, S. B. (2020). The emerging role of epigenetic therapeutics in immuno-oncology. Nature Reviews Clinical Oncology, 17(2), 75-90.

Lee, D. Y., & Chiu, J. J. (2019). Atherosclerosis and flow: roles of epigenetic modulation in vascular endothelium. Journal of Biomedical Science, 26, 1-17.

Nemec, S., & Kilian, K. A. (2021). Materials control of the epigenetics underlying cell plasticity. Nature Reviews Materials, 6(1), 69-83.

Poças-Fonseca, M. J., Cabral, C. G., & Manfrão-Netto, J. H. C. (2020). Epigenetic manipulation of filamentous fungi for biotechnological applications: a systematic review. Biotechnology letters, 42(6), 885-904.

da Silva, R. A., Fernandes, C. J. D. C., Feltran, G. D. S., Gomes, A. M., de Camargo Andrade, A. F., Andia, D. C., ... & Zambuzzi, W. F. (2019). Laminar shear stress‐provoked cytoskeletal changes are mediated by epigenetic reprogramming of TIMP1 in human primary smooth muscle cells. Journal of Cellular Physiology, 234(5), 6382-6396.

Chen, D., & Kerr, C. (2019). The epigenetics of stem cell aging comes of age. Trends in cell biology, 29(7), 563-568.

Hamilton, P. J., Burek, D. J., Lombroso, S. I., Neve, R. L., Robison, A. J., Nestler, E. J., & Heller, E. A. (2018). Cell-type-specific epigenetic editing at the Fosb gene controls susceptibility to social defeat stress. Neuropsychopharmacology, 43(2), 272-284.

Zhang, Z., Zhai, Y., Ma, X., Zhang, S., An, X., Yu, H., & Li, Z. (2018). Down-regulation of H3K4me3 by MM-102 facilitates epigenetic reprogramming of porcine somatic cell nuclear transfer embryos. Cellular Physiology and Biochemistry, 45(4), 1529-1540.

Ferrari, A., Longo, R., Silva, R., Mitro, N., Caruso, D., De Fabiani, E., & Crestani, M. (2019). Epigenome modifiers and metabolic rewiring: New frontiers in therapeutics. Pharmacology & Therapeutics, 193, 178-193.

Ji, S., Xiong, M., Chen, H., Liu, Y., Zhou, L., Hong, Y., ... & Sun, X. (2023). Cellular rejuvenation: molecular mechanisms and potential therapeutic interventions for diseases. Signal Transduction and Targeted Therapy, 8(1), 116.

Choupani, J., Mansoori Derakhshan, S., Bayat, S., Alivand, M. R., & Shekari Khaniani, M. (2018). Narrower insight to SIRT1 role in cancer: A potential therapeutic target to control epithelial–mesenchymal transition in cancer cells. Journal of cellular physiology, 233(6), 4443-4457.

Iranifar, E., Seresht, B. M., Momeni, F., Fadaei, E., Mehr, M. H., Ebrahimi, Z., ... & Mirzaei, H. (2019). Exosomes and microRNAs: new potential therapeutic candidates in Alzheimer disease therapy. Journal of cellular physiology, 234(3), 2296-2305.

Fathollahi, A., Aslani, S., Jamshidi, A., & Mahmoudi, M. (2019). Epigenetics in osteoarthritis: novel spotlight. Journal of cellular physiology, 234(8), 12309-12324.

Kular, L., & Kular, S. (2018). Epigenetics applied to psychiatry: clinical opportunities and future challenges. Psychiatry and clinical neurosciences, 72(4), 195-211.

Han, L. K., Verhoeven, J. E., Tyrka, A. R., Penninx, B. W., Wolkowitz, O. M., Månsson, K. N., ... & Picard, M. (2019). Accelerating research on biological aging and mental health: Current challenges and future directions. Psychoneuroendocrinology, 106, 293-311.

Dittami, S. M., Arboleda, E., Auguet, J. C., Bigalke, A., Briand, E., Cárdenas, P., ... & Not, F. (2021). A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ, 9, e10911.

Rong, L., Li, N., & Zhang, Z. (2022). Emerging therapies for glioblastoma: current state and future directions. Journal of Experimental & Clinical Cancer Research, 41(1), 142.

Bishop, D. J., Botella, J., Genders, A. J., Lee, M. J., Saner, N. J., Kuang, J., ... & Granata, C. (2019). High-intensity exercise and mitochondrial biogenesis: current controversies and future research directions. Physiology, 34(1), 56-70.