Written by: Zachary Loudermilk Bhatia
Edited by: Ryan Lee
Edited by: Ryan Lee
Why do living things age? This question has stumped scientists, theologists, and philosophers for millennia. Recent advances in molecular biology have identified a factor of ageing: the epigenome. A recent discovery, the epigenome has been brought into the public eye for the effects that deoxyribose nucleic acid (DNA) modification of germline cells, or spermatocytes and oocytes, have on future generations (Escher 2019). While not fully understood, the epigenome of a cell is the entire set of post-translational modifications to DNA and the histone proteins that bind it.
DNA is a long, double-stranded molecule consisting of a pattern of four nucleotides - cytosine, guanine, adenine, and thymine - in a pattern that is unique to an organism. Cytosine, a circular pyrimidine nucleotide base, can be methylated - the mechanism of an additional carbon saturated with hydrogens added to position 5 of the cytosine ring (Bernstein 2007). The cytosine methylation affects which transcription proteins can bind to a particular section of DNA. The individual effects of epigenomic alterations are dependent on the DNA sequences involved and the effects on protein expression can vary from vast rate enhancements to complete silencing of a particular gene (Bernstein 2007). In addition to cytosine methylation, the epigenome also consists of histone modifications. Histones are specialised globular proteins that bind to DNA with a long tail-like structure. Histones collect into octamers of four pairs: H3, H4, H2A, and H2B; DNA winds around this octamer structure twice, being held in place as the histone tails bind to the DNA molecule (Peterson 2004). Histone tails, being more than 100 protein residues (units) long, can be the target of countless combinations of protein residue post-translational modifications (Peterson 2004). While the extent of post-translational histone modifications has not been fully explored, it is essential to know that the proteins holding DNA can be modified at any time following transcription and that these modifications affect how proteins such as transcription factors bind to DNA.
This brings us to how the epigenome affects ageing. While all somatic cells have the same genome, different types of cells will have unique epigenomes. The genome represents the organism, and the epigenome represents which DNA sequences are expressed in a given cell. For example, a person’s liver cells and cranial neurons will contain the same DNA sequence but will express unique segments of the overall DNA sequence; epigenetic markers control which DNA sequences are expressed in a pluripotent stem cell and can thus be used to control cell type differentiation into liver cells, cranial neurons, and any other type of somatic cells (Wu 2006). Cells that lose their epigenome will lose their differentiation and function; for example, a neuron that loses part of its epigenome will not produce the proteins needed to differentiate into a neuron and will thus express less neuron character. The epigenomic patterns of differentiated cells are very delicate; damage to DNA can result in the loss of this delicate and specialised epigenomic pattern (Yang 2023).
Damage to the DNA phosphate backbone induces the repair of DNA. Double-stranded breakage (DSB) of DNA triggers a cascade of reaction mechanisms to repair the damage (Pardo 2009); DNA damage is very common, occurring 10-50 times in every cell every 24 hours (Vilenchik 2003). However, the DSB repair mechanism does not always conserve post-translational modifications to DNA. Researchers developed a strain of mutant mice with a controllable mechanism for creating a high rate of DSBs. The mice with inducible changes to their epigenome (ICE mice) express the gene for the endonuclease I-Ppol, an enzyme capable of splitting DNA and creating DSBs without producing a high rate of mutation. I-Ppol was engineered to be controlled by the estrogen receptor-modulating drug tamoxifen. In the presence of tamoxifen, I-Ppol is activated and creates targeted DSBs within the mouse genome. In the absence of tamoxifen, I-Ppol is degraded. ICE mouse embryonic cells exposed to tamoxifen were estimated to include age-related CpG methylation profiles indicating the ICE embryos were 50% older than a control; ICE cells exposed to tamoxifen were 3-4x more likely to senesce, or stop replicating and deteriorate, than a control (Yang 2023).
To test the effects of induced double-stranded breakage, adolescent ICE mice aged 4-6 months were exposed to tamoxifen in their water for three consecutive weeks, during which I-Ppol was estimated to be expressed in 61-72% of muscle, liver, and neural cells (Yang 2023). Within one month of treatment, researchers noted “alopecia and a loss of pigment on the feet, tail, ears, and nose” of ICE mice exposed to tamoxifen (Yang 2023). Within 10 months, the 14-16 month-old ICE mice developed age-related symptoms identical to age-related symptoms normally found in 24-month-old mice including significantly reduced fat mass, muscle mass, and endurance, significantly weakened grip strength, vision and hearing, thinning and greying fur, impaired movement, and significantly weakened short-term and long-term memory recall compared to control mice (Yang 2023). In every sense of the word, these ICE mice were simply older despite having been alive for the same amount of time as their counterparts.
Double-stranded breakage of DNA is extremely damaging long-term, often imminently resulting in DNA sequence loss and cell death; as such, it is more important for the health of an individual for a DSB to be repaired quickly and efficiently than it is for a DSB to be repaired faithfully to the epigenomic pattern of a specific cell. The molecular mechanism for DSB repair known as nonhomologous end-joining (NHEJ) reconnects the broken strands of DNA, but does not always conserve the important Epigenetic information; the accumulation of incidental Epigenetic losses over long periods of time is correlated with aging.
References
Amorim, J. A., Coppotelli, G., Rolo, A. P., Palmeira, C. M., Ross, J. M., & Sinclair, D. A. (2022). Mitochondrial and metabolic dysfunction in ageing and age-related diseases. Nature Reviews. Endocrinology, 18(4), 243–258. https://doi.org/10.1038/s41574-021-00626-7
Chang, H. H. Y., Pannunzio, N. R., Adachi, N., & Lieber, M. R. (2017). Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nature Reviews Molecular Cell Biology, 18(8), Article 8. https://doi.org/10.1038/nrm.2017.48
Endogenous DNA double-strand breaks: Production, fidelity of repair, and induction of cancer. (n.d.-a). https://doi.org/10.1073/pnas.2135498100
Escher, J., & Robotti, S. (2019). Pregnancy drugs, fetal germline epigenome, and risks for next-generation pathology: A call to action. Environmental and Molecular Mutagenesis, 60(5), 445–454. https://doi.org/10.1002/em.22288
Friedberg, E. C. (2003). DNA damage and repair. Nature, 421(6921), Article 6921. https://doi.org/10.1038/nature01408
Lu, Y., Brommer, B., Tian, X., Krishnan, A., Meer, M., Wang, C., Vera, D. L., Zeng, Q., Yu, D., Bonkowski, M. S., Yang, J.-H., Zhou, S., Hoffmann, E. M., Karg, M. M., Schultz, M. B., Kane, A. E., Davidsohn, N., Korobkina, E., Chwalek, K., … Sinclair, D. A. (2020). Reprogramming to recover youthful epigenetic information and restore vision. Nature, 588(7836), 124–129. https://doi.org/10.1038/s41586-020-2975-4
Tian, X., Firsanov, D., Zhang, Z., Cheng, Y., Luo, L., Tombline, G., Tan, R., Simon, M., Henderson, S., Steffan, J., Goldfarb, A., Tam, J., Zheng, K., Cornwell, A., Johnson, A., Yang, J.-N., Mao, Z., Manta, B., Dang, W., … Gorbunova, V. (2019). SIRT6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species. Cell, 177(3), 622-638.e22. https://doi.org/10.1016/j.cell.2019.03.043
Wu, H., & Sun, Y. E. (2006). Epigenetic Regulation of Stem Cell Differentiation. Pediatric Research, 59(4), Article 4. https://doi.org/10.1203/01.pdr.0000203565.76028.2a
Yang, J.-H., Hayano, M., Griffin, P. T., Amorim, J. A., Bonkowski, M. S., Apostolides, J. K., Salfati, E. L., Blanchette, M., Munding, E. M., Bhakta, M., Chew, Y. C., Guo, W., Yang, X., Maybury-Lewis, S., Tian, X., Ross, J. M., Coppotelli, G., Meer, M. V., Rogers-Hammond, R., … Sinclair, D. A. (2023). Loss of epigenetic information as a cause of mammalian aging. Cell, 186(2), 305-326.e27. https://doi.org/10.1016/j.cell.2022.12.027
DNA is a long, double-stranded molecule consisting of a pattern of four nucleotides - cytosine, guanine, adenine, and thymine - in a pattern that is unique to an organism. Cytosine, a circular pyrimidine nucleotide base, can be methylated - the mechanism of an additional carbon saturated with hydrogens added to position 5 of the cytosine ring (Bernstein 2007). The cytosine methylation affects which transcription proteins can bind to a particular section of DNA. The individual effects of epigenomic alterations are dependent on the DNA sequences involved and the effects on protein expression can vary from vast rate enhancements to complete silencing of a particular gene (Bernstein 2007). In addition to cytosine methylation, the epigenome also consists of histone modifications. Histones are specialised globular proteins that bind to DNA with a long tail-like structure. Histones collect into octamers of four pairs: H3, H4, H2A, and H2B; DNA winds around this octamer structure twice, being held in place as the histone tails bind to the DNA molecule (Peterson 2004). Histone tails, being more than 100 protein residues (units) long, can be the target of countless combinations of protein residue post-translational modifications (Peterson 2004). While the extent of post-translational histone modifications has not been fully explored, it is essential to know that the proteins holding DNA can be modified at any time following transcription and that these modifications affect how proteins such as transcription factors bind to DNA.
This brings us to how the epigenome affects ageing. While all somatic cells have the same genome, different types of cells will have unique epigenomes. The genome represents the organism, and the epigenome represents which DNA sequences are expressed in a given cell. For example, a person’s liver cells and cranial neurons will contain the same DNA sequence but will express unique segments of the overall DNA sequence; epigenetic markers control which DNA sequences are expressed in a pluripotent stem cell and can thus be used to control cell type differentiation into liver cells, cranial neurons, and any other type of somatic cells (Wu 2006). Cells that lose their epigenome will lose their differentiation and function; for example, a neuron that loses part of its epigenome will not produce the proteins needed to differentiate into a neuron and will thus express less neuron character. The epigenomic patterns of differentiated cells are very delicate; damage to DNA can result in the loss of this delicate and specialised epigenomic pattern (Yang 2023).
Damage to the DNA phosphate backbone induces the repair of DNA. Double-stranded breakage (DSB) of DNA triggers a cascade of reaction mechanisms to repair the damage (Pardo 2009); DNA damage is very common, occurring 10-50 times in every cell every 24 hours (Vilenchik 2003). However, the DSB repair mechanism does not always conserve post-translational modifications to DNA. Researchers developed a strain of mutant mice with a controllable mechanism for creating a high rate of DSBs. The mice with inducible changes to their epigenome (ICE mice) express the gene for the endonuclease I-Ppol, an enzyme capable of splitting DNA and creating DSBs without producing a high rate of mutation. I-Ppol was engineered to be controlled by the estrogen receptor-modulating drug tamoxifen. In the presence of tamoxifen, I-Ppol is activated and creates targeted DSBs within the mouse genome. In the absence of tamoxifen, I-Ppol is degraded. ICE mouse embryonic cells exposed to tamoxifen were estimated to include age-related CpG methylation profiles indicating the ICE embryos were 50% older than a control; ICE cells exposed to tamoxifen were 3-4x more likely to senesce, or stop replicating and deteriorate, than a control (Yang 2023).
To test the effects of induced double-stranded breakage, adolescent ICE mice aged 4-6 months were exposed to tamoxifen in their water for three consecutive weeks, during which I-Ppol was estimated to be expressed in 61-72% of muscle, liver, and neural cells (Yang 2023). Within one month of treatment, researchers noted “alopecia and a loss of pigment on the feet, tail, ears, and nose” of ICE mice exposed to tamoxifen (Yang 2023). Within 10 months, the 14-16 month-old ICE mice developed age-related symptoms identical to age-related symptoms normally found in 24-month-old mice including significantly reduced fat mass, muscle mass, and endurance, significantly weakened grip strength, vision and hearing, thinning and greying fur, impaired movement, and significantly weakened short-term and long-term memory recall compared to control mice (Yang 2023). In every sense of the word, these ICE mice were simply older despite having been alive for the same amount of time as their counterparts.
Double-stranded breakage of DNA is extremely damaging long-term, often imminently resulting in DNA sequence loss and cell death; as such, it is more important for the health of an individual for a DSB to be repaired quickly and efficiently than it is for a DSB to be repaired faithfully to the epigenomic pattern of a specific cell. The molecular mechanism for DSB repair known as nonhomologous end-joining (NHEJ) reconnects the broken strands of DNA, but does not always conserve the important Epigenetic information; the accumulation of incidental Epigenetic losses over long periods of time is correlated with aging.
References
Amorim, J. A., Coppotelli, G., Rolo, A. P., Palmeira, C. M., Ross, J. M., & Sinclair, D. A. (2022). Mitochondrial and metabolic dysfunction in ageing and age-related diseases. Nature Reviews. Endocrinology, 18(4), 243–258. https://doi.org/10.1038/s41574-021-00626-7
Chang, H. H. Y., Pannunzio, N. R., Adachi, N., & Lieber, M. R. (2017). Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nature Reviews Molecular Cell Biology, 18(8), Article 8. https://doi.org/10.1038/nrm.2017.48
Endogenous DNA double-strand breaks: Production, fidelity of repair, and induction of cancer. (n.d.-a). https://doi.org/10.1073/pnas.2135498100
Escher, J., & Robotti, S. (2019). Pregnancy drugs, fetal germline epigenome, and risks for next-generation pathology: A call to action. Environmental and Molecular Mutagenesis, 60(5), 445–454. https://doi.org/10.1002/em.22288
Friedberg, E. C. (2003). DNA damage and repair. Nature, 421(6921), Article 6921. https://doi.org/10.1038/nature01408
Lu, Y., Brommer, B., Tian, X., Krishnan, A., Meer, M., Wang, C., Vera, D. L., Zeng, Q., Yu, D., Bonkowski, M. S., Yang, J.-H., Zhou, S., Hoffmann, E. M., Karg, M. M., Schultz, M. B., Kane, A. E., Davidsohn, N., Korobkina, E., Chwalek, K., … Sinclair, D. A. (2020). Reprogramming to recover youthful epigenetic information and restore vision. Nature, 588(7836), 124–129. https://doi.org/10.1038/s41586-020-2975-4
Tian, X., Firsanov, D., Zhang, Z., Cheng, Y., Luo, L., Tombline, G., Tan, R., Simon, M., Henderson, S., Steffan, J., Goldfarb, A., Tam, J., Zheng, K., Cornwell, A., Johnson, A., Yang, J.-N., Mao, Z., Manta, B., Dang, W., … Gorbunova, V. (2019). SIRT6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species. Cell, 177(3), 622-638.e22. https://doi.org/10.1016/j.cell.2019.03.043
Wu, H., & Sun, Y. E. (2006). Epigenetic Regulation of Stem Cell Differentiation. Pediatric Research, 59(4), Article 4. https://doi.org/10.1203/01.pdr.0000203565.76028.2a
Yang, J.-H., Hayano, M., Griffin, P. T., Amorim, J. A., Bonkowski, M. S., Apostolides, J. K., Salfati, E. L., Blanchette, M., Munding, E. M., Bhakta, M., Chew, Y. C., Guo, W., Yang, X., Maybury-Lewis, S., Tian, X., Ross, J. M., Coppotelli, G., Meer, M. V., Rogers-Hammond, R., … Sinclair, D. A. (2023). Loss of epigenetic information as a cause of mammalian aging. Cell, 186(2), 305-326.e27. https://doi.org/10.1016/j.cell.2022.12.027
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