Book contents
- Nutritional Psychiatry
- Nutritional Psychiatry
- Copyright page
- Contents
- Contributors
- Preface
- Chapter 1 Basic Principles of Nutrition
- Chapter 2 Diet and the Microbiome–Gut–Brain Axis
- Chapter 3 The Mediterranean Diet and Mental Health
- Chapter 4 Psychobiotics and Fermented Foods
- Chapter 5 Diet Interventions for Anxiety and Depression
- Chapter 6 Schizophrenia, Microbiota and Nutrition
- Chapter 7 Recognising the Importance of Nutrition for Child and Adolescent Mental Health
- Chapter 8 Old Age and Nutrition
- Chapter 9 Broad-Spectrum Micronutrients and Mental Health
- Chapter 10 Epigenetics
- Index
- References
Chapter 10 - Epigenetics
Published online by Cambridge University Press: 17 August 2023
By
Edited by
Book contents
- Nutritional Psychiatry
- Nutritional Psychiatry
- Copyright page
- Contents
- Contributors
- Preface
- Chapter 1 Basic Principles of Nutrition
- Chapter 2 Diet and the Microbiome–Gut–Brain Axis
- Chapter 3 The Mediterranean Diet and Mental Health
- Chapter 4 Psychobiotics and Fermented Foods
- Chapter 5 Diet Interventions for Anxiety and Depression
- Chapter 6 Schizophrenia, Microbiota and Nutrition
- Chapter 7 Recognising the Importance of Nutrition for Child and Adolescent Mental Health
- Chapter 8 Old Age and Nutrition
- Chapter 9 Broad-Spectrum Micronutrients and Mental Health
- Chapter 10 Epigenetics
- Index
- References
Summary
Like microorganisms, the human subspecies can be characterised by subtle differences at the genomic and epigenomic levels. The divergence is due to epigenetic adaptations to variations in environmental conditions and dietary staples. It is evident that environments or food choices which may be essential to sustain life in one population may be toxic to another. However, the recognition of evolutionary biodiversity has been largely ignored with universal nutritional standards and fortification of dietary staples with epigenetic modulators. Because of environmental concerns, global consumption of plants as a primary food is rising; epigenetic adaptation of biological pathways and microbiomes is required to adjust for the loss of bioactive molecules previously obtained from animal-based diets. The resulting epigenetic inflexibility may lead to over- or under-compensation of biological pathways and disease.
This chapter discusses the modern interpretation of epigenetics as the complex plasticity of the epigenome and its DNA sequence, demonstrating the potential for modulation of epigenetic pathways through nutritional, microbiome and environmental modifications.
- Type
- Chapter
- Information
- Nutritional PsychiatryA Primer for Clinicians, pp. 172 - 211Publisher: Cambridge University PressPrint publication year: 2023
References
Waddington, C. H., 1939. An introduction to modern genetics. Physiological Entomology, 14(4–6), p. 82.Google Scholar
Luger, K., A. W., Mä Der, R. K., Richmond, D. F., Sargent and Richmond, T. J., 1997. Crystal structure of the nucleosome core particle at 2.8 A° resolution. Nature, 389.Google Scholar
Segal, E. and Widom, J., 2009. PolydA:dT tracts: major determinants of nucleosome organization. Current Opinion in Structural Biology, 19(1), pp. 65–71.Google Scholar
Singh, V., B. I., Fedeles and Essigmann, J. M., 2015. Role of tautomerism in RNA biochemistry. RNA, 21(1), pp. 1–13.CrossRefGoogle ScholarPubMed
Karwowski, B. T., 2020. The electronic property differences between dA::dG and dA::d goxo: a theoretical approach. Molecules, 25(17).Google Scholar
J. C., Lindon, G. E., Tranter and Holmes, J. L., 1999. Chemical reactions studied by electronic spectroscopy. In Encyclopedia of spectroscopy and spectrometry 2 (pp. 246–52). Elsevier.Google Scholar
B. I., Fedeles, Li, D. and Singh, V., 2022. Structural insights to tautomeric dynamics in nucleic acids and in antiviral nucleoside analogs. Frontiers in Molecular Biosciences, 8.Google Scholar
Grifoni, E., Piccini, G. and Parrinello, M., 2020. Tautomeric equilibrium in condensed phases. Journal of Chemical Theory and Computation, 16(10), pp. 6027–31.Google Scholar
Tolosa, S., Hidalgo, A. and Sansón, J. A., 2012. Amino acid tautomerization reactions in aqueous solution via concerted and assisted mechanisms using free energy curves from MD simulation. The Journal of Physical Chemistry A, 116(43), pp. 13033–44.Google Scholar
Haynes, A. and Tekel, S., 2017. Molecular structures guide the engineering go chromatin. Nucleic Acids Research, 45 13), pp. 7555–70.Google Scholar
Cooper, G. M., 2000. The organization of cellular genomes. In The cell: a molecular approach. ASM Press.Google Scholar
Happel, N., and Doenecke, D., 2009. Histone H1 and its isoforms: contribution to chromatin structure and function. Gene, 431(1–2), pp. 1–12.Google Scholar
Churchill, A. and Suzuki, M., 1989. ‘SPKK’ motifs prefer to bind to DNA at A/T-rich sites. The EMBO Journal, 8(13).Google Scholar
McGinty, K. and Tan, S., 2015. Nucleosome structure and function. Chemical Reviews, 115(6), pp. 2255–73.Google Scholar
Vogler, C., Huber, C., Waldmann, T., et al., 2010. Histone H2A C-terminus regulates chromatin dynamics, remodelling, and histone H1 binding. PLOS Genetics, 6(12), pp. 1–12.Google Scholar
Freitas, A., Sklenar, R. and Parthun, R., 2004. Application of mass spectrometry to the identification and quantification of histone post-translational modifications. Journal of Cellular Biochemistry, 924, pp. 691–700.Google Scholar
J. E., Krebs, E. S., Goldstein and Kilpatrick, S. T., 2018. Lewin’s genes XII. Jones Bartlett Learning.Google Scholar
Bednar, J., Garcia-Saez, I., Boopathi, R., et al., 2017. Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1. Molecular Cell, 663(8), pp. 384–97.Google Scholar
C. L., Woodcock, A. I., Skoultchi and Fan, Y., 2006. Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length. Chromosome Research, 14(1), pp. 17–25.Google Scholar
Bates, L. and Thomas, O., 1981. Histones Hl and H5: one or two molecules per nucleosome? Nucleic Acids Research, 9(221981).Google Scholar
Widlund, R., Cao, H., Simonsson, S., et al., 1997. Identification and characterization of genomic nucleosome-positioning sequences. Journal of Molecular Biology, 2674, pp. 807–17.Google Scholar
P. T., Lowary and Widom, J., 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. Journal of Molecular Biology, 2761, pp. 19–42.Google Scholar
Menon, V. and Ghaffari, S., 2021. Erythroid enucleation: a gateway into a ‘bloody’ world. Experimental Hematology, 95, pp. 13–22.Google Scholar
B. D., Strahl and Allis, D. C., 2000. The language of covalent histone modifications. Nature, 403.Google Scholar
Sedley, L., 2020. Advances in nutritional epigenetics: a fresh perspective for an old idea – lessons learned, limitations, and future directions. Epigenetics Insights, 13.Google Scholar
D. J., Clark and Kimurai, T., 1990. Electrostatic mechanism of chromatin folding. Journal of Molecular Biology, 211.Google Scholar
Ramazi, S. and Zahiri, J., 2021. Post-translational modifications in proteins: resources, tools and prediction methods. Database (Oxford), 2021, baab012.Google Scholar
Portela, A. and Esteller, M., 2010. Epigenetic modifications and human disease. Nature Biotechnology, 2810, pp. 1057–68.Google Scholar
Sadakierska-Chudy, A., R. M., Kostrzewa and Filip, M. A., 2015. Comprehensive view of the epigenetic landscape part I: DNA methylation, passive and active DNA demethylation, pathways and histone variants. Neurotoxicity Research, 27(1), pp. 84–97.Google Scholar
Biswas, S. and Rao, C. M., 2018. Epigenetic tools: the writers, the readers and the erasers and their implications in cancer therapy. European Journal of Pharmacology, 837, pp. 8–24.Google Scholar
S. J., Mentch and Locasale, J. W., 2016. One-carbon metabolism and epigenetics: understanding the specificity. Annals of the New York Academy of Sciences, 13631, pp. 91–8.Google Scholar
Farra, A. H., 2010. Methionine synthase polymorphisms MTR 2756 Agt;G and MTR 2758 Cgt;G frequencies and distribution in the Jordanian population and their correlation with neural tube defects in the population of the northern part of Jordan. Indian Journal of Human Genetics, 16(3), pp. 138–43.Google Scholar
Murray, B., Antonyuk, S. V., Marina, A., et al., 2014. Structure and function study of the complex that synthesizes S -adenosylmethionine. IUCr Journal, 1(4), pp. 240–9.Google Scholar
Bing, Y., Zhu, S., Yu, G., et al., 2014. Glucocorticoid-induced S-adenosylmethionine enhances the interferon signaling pathway by restoring STAT1 protein methylation in hepatitis B virus-infected cells. Journal of Biological Chemistry, 28947, pp. 32639–55.Google Scholar
Pé Rez-Mato, I., Castro, C., Ruiz, A., F. J., Corrales and Mato, J. M., 1999. Methionine adenosyltransferase S-nitrosylation is regulated by the basic and acidic amino acids surrounding the target thiol.Journal of Biological Chemistry, 274(24).Google Scholar
Soderberg, T., 2022. Steric effects on nucleophilicity. In Organic chemistry with a biological emphasis. LibreTexts.Google Scholar
S. S., Dhareshwar and Stella, V. J., 2008. Your prodrug releases formaldehyde: should you be concerned? No!Journal of Pharmaceutical Sciences, 9710, pp. 4184–93.Google Scholar
A. R., Dahl and Hadley, W. M., 1983. Formaldehyde production promoted by rat nasal cytochrome P-450-dependent monooxygenases with nasal decongestants, essences, solvents, air pollutants, nicotine, and cocaine as substrates. Toxicology and Applied Pharmacology, 672, pp. 200–5.Google Scholar
Burgos-Barragan, G., Wit, N., Meiser, J., et al., 2017. Mammals divert endogenous genotoxic formaldehyde into one-carbon metabolism. Nature, 5487(669), pp. 549–54.Google Scholar
Rossi, M., Amaretti, A. and Raimondi, S., 2011. Folate production by probiotic bacteria. Nutrients, 31, pp. 118–34.Google Scholar
P. P., Chaudhary, P. L., Conway and Schlundt, J., 2018. Methanogens in humans: potentially beneficial or harmful for health. Applied Microbiology and Biotechnology, 10(27), pp. 3095–104.Google Scholar
H. J., Sofia, Chen, G., B. G., Hetzler, J. F., Reyes-Spindola and N. E, Miller., 2001. Radical SAM. a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods.Nucleic Acids Research, 29(5).Google Scholar
B. J., Landgraf, E. L., McCarthy and Booker, S. J., 2016. Radical adenosylmethionine enzymes in human health and disease. Annual Review of Biochemistry, 85(1), pp. 485–514.Google Scholar
N. D., Lanz and Booker, S. J., 2015. Auxiliary iron-sulfur cofactors in radical SAM enzymes. Biochimica et Biophysica Acta, 1853(6), pp. 1316–34.Google Scholar
Fujimori, D. G., 2013. Radical SAM-mediated methylation reactions. Current Opinion in Chemical Biology, 17(4), pp. 597–604.Google Scholar
S. C., Wang and Frey, P. A., 2007. S-adenosylmethionine as an oxidant: the radical SAM superfamily. Trends in Biochemical Sciences, 32(3), pp. 101–10.Google Scholar
A. C., Brown and Suess, D. L. M., 2020. Reversible formation of alkyl radicals at [Fe4S4] clusters and its implications for selectivity in radical SAM enzymes. Journal of the American Chemical Society, 142(33), pp. 14240–8.Google Scholar
Shi, R., Hou, W., Z. Q., Wang and Xu, X., 2021. Biogenesis of iron–sulfur clusters and their role in DNA metabolism. Frontiers in Cell and Developmental Biology, 9.Google Scholar
G. D., Shimberg, J. D., Pritts and Michel, S. L. J., 2018. Iron–sulfur clusters in zinc finger proteins. Methods in Enzymology, 599, 101–37.Google Scholar
Sadakierska-Chudy, A. and Filip, M. A., 2015. Comprehensive view of the epigenetic landscape. Part II: histone post-translational modification. Nucleosome level and chromatin regulation by ncRNAs. Neurotoxicity Research, 27(2), pp. 172–97.Google Scholar
D. F., Rolfe and Brown, G. C., 1997. Cellular energy utilization and molecular origin of standard metabolic rate in mammals. Physiological Reviews, 77(3), pp. 731–58.Google Scholar
J. C., Black and Whetstine, J. R., 2012. LOX out. Histones: a new enzyme is nipping at your tails. Molecular Cell, 46(3), pp. 243–4.Google Scholar
M. A., Adams-Cioaba, J. C., Krupa, Xu, C., J. S., Mort and Min, J., 2011. Structural basis for the recognition and cleavage of histone H3 by cathepsin L. Nature Communications, 2(1).Google Scholar
Sancar, A., 2000. Cryptochrome: the second photoactive pigment in the eye and its role in circadian photoreception. Annual Review of Biochemistry, 69, pp. 31–67.Google Scholar
Khalyfa, A., Gaddameedhi, S., Crooks, E., et al., 2020. Circulating exosomal miRNAs signal circadian misalignment to peripheral metabolic tissues. International Journal of Molecular Sciences, 21(17), pp. 1–25.Google Scholar
Okamoto-Uchida, Y., Izawa, J. and Hirayama, J. A., 2018. Molecular link between the circadian clock: DNA damage responses and oncogene activation. IntechOpen. https://doi.org/10.5772/intechopen.81063.Google Scholar
Lavebratt, C., L. K., Sjöholm, Soronen, P., et al., 2010. Cry2 is associated with depression. PLoS ONEx, 5(2).Google Scholar
Hirano, A., Shi, G., C. R., Jones, et al., 2016. Cryptochrome 2 mutation yields advanced sleep phase in humans. eLife, 5, p. 16695.Google Scholar
Terai, Y., Sato, R., Matsumura, R., Iwai, S. and Yamamoto, J., 2020. Enhanced DNA repair by DNA photolyase bearing an artificial light-harvesting chromophore. Nucleic Acids Research, 48(18), pp. 10076–86.Google Scholar
Su, Y., Cailotto, C., Foppen, E., et al., 2016. The role of feeding rhythm, adrenal hormones and neuronal inputs in synchronizing daily clock gene rhythms in the liver. Molecular and Cellular Endocrinology, 422, pp. 125–31.Google Scholar
Johnson, C. H., 2013. Circadian clocks and cell division: what’s the pacemaker? Cell Cycle, 9(19), pp. 3864–73.Google Scholar
Potten, C. S., 1998. Stem cells in gastrointestinal epithelium: numbers, characteristics and death. Philosophical Transactions of the Royal Society B, 353(1370), pp. 821–30.Google Scholar
Ozer, G., Luque, A. and Schlick, T., 2015. The chromatin fiber: multiscale problems and approaches. Current Opinion in Structural Biology, 31, pp. 124–39.Google Scholar
Routh, A., Sandin, S. and Rhodes, D., 2008. Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proceedings of the National Academy of Sciences of the United States of America, 105(26), pp. 8872–7.Google Scholar
M. D., Adams, S. E., Celniker, R. A., Holt, et al., 2000. The genome sequence of drosophila melanogaster. Science, 287(5461), pp. 2185–95.Google Scholar
Rajewska, M., Wegrzyn, K. and Konieczny, I., 2012. AT-rich region and repeated sequences: the essential elements of replication origins of bacterial replicons. FEMS Microbiology Reviews, 36(2), pp. 408–34.Google Scholar
Shi, W. and Zhou, W., 2006. Frequency distribution of TATA Box and extension sequences on human promoters. BMC Bioinformatics, 7S4, s2.Google Scholar
Phillips, D., 1963. The presence of acetyl groups in histones. Biochemical Journal, 87(2), pp. 258–63.Google Scholar
Shukla, S., Levine, C., R. P., Sripathi, et al., 2018. The kat in the HAT: the histone acetyl transferase KAT6b (MYST4) is downregulated in murine macrophages in response to LPS. Mediators of Inflammation, 2018, pp. 1–11.Google Scholar
Shogren-Knaak, M., Ishii, H., J. M., Sun, et al., 2006. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science, 311(5762), pp. 844–7.Google Scholar
Nitsch, S., Zorro Shahidian, L. and Schneider, R., 2021. Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism. EMBO Reports, 22(7).Google Scholar
C. L., Linster, Van Schaftingen, E. and Hanson, A. D., 2013. Metabolite damage and its repair or pre-emption. Nature Chemical Biology, 9(2), pp. 72–80.Google Scholar
Fan, F., H. J., Williams, J. G., Boyer, et al., 2012. On the catalytic mechanism of human ATP citrate lyase. Biochemistry, 51(25), pp. 5198–211.Google Scholar
Xu, Y., Shi, Z. and Bao, L., 2022. An expanding repertoire of protein acylations. Molecular and Cellular Proteomics, 21(3).Google Scholar
Seto, E. and Yoshida, M., 2014. Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harbor Perspectives in Biology, 64.Google Scholar
H., Biava, 2022. The chemistry of NAD+ and FAD. In Biochemistry, ed. H. Jakubowski. LibreTexts.Google Scholar
Kim, J., S. H., Lee, Tieves, F., et al., 2019. Nicotinamide adenine dinucleotide as a photocatalyst. Science Advances, 5(7).Google Scholar
J. L., Feldman, K. E., Dittenhafer-Reed, Thelen, J. N., et al., 2015. Kinetic and structural basis for acyl-group selectivity and NAD+ dependence in sirtuin-catalyzed deacylation. Biochemistry, 54(19), pp. 3037–50.Google Scholar
Fellows, R., Denizot, J., Stellato, C., et al., 2018. Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases. Nature Communications, 9(1), p. 105.Google Scholar
Yang, Z., He, M., Austin, J., Pfleger, J. and Abdellatif, M., 2021. Histone H3K9 butyrylation is regulated by dietary fat and stress via an Acyl-CoA dehydrogenase short chain-dependent mechanism. Molecular Metabolism, 53, p. 101249.Google Scholar
M. G., Kearse and Wilusz, J. E., 2017. Non-AUG translation: a new start for protein synthesis in eukaryotes. Genes & Development, 31, pp. 1717–31Google Scholar
Peabody, D. S., 1989. Translation initiation at non-AUG triplets in mammalian cells. Journal of Biological Chemistry, 26(49), pp. 5031–5.Google Scholar
Echingoya, K., Koyama, M., Negishi, L., et al., 2020. Nucleosome binding by the pioneer transcription factor OCT4.Scientific Reports, 10(1), p. 11832.Google Scholar
Kujirai, T. and Kurumizaka, H., 2020. Transcription through the nucleosome. Current Opinion in Structural Biology, 61, pp. 42–9.Google Scholar
O. I., Kulaeva, F. K., Hsieh, H. W., Chang, D. S., Luse and Studitsky, V. M., 2013. Mechanism of transcription through a nucleosome by RNA polymerase II. Biochimica et Biophysica Acta, 1829(1), pp. 76–83.Google Scholar
B. J. E., Martin, Brind’Amour, J., Kuzmin, A., et al., 2021. Transcription shapes genome-wide histone acetylation patterns. Nature Communications, 12(1).Google Scholar
Banine, F., Bartlett, C., Gunawardena, R., et al., 2005. SWI/SNF Chromatin-remodeling factors induce changes in DNA methylation to promote transcriptional activation. Cancer Research, 65(9).Google Scholar
Mathur, R. and Roberts, C. W. M., 2018. Swi/snf baf complexes: guardians of the epigenome. Annual Review of Cancer Biology, 2, pp. 413–27.Google Scholar
G. A., Josling, S. A., Selvarajah, Petter, M. and Duffy, M. F., 2012. The role of bromodomain proteins in regulating gene expression. Genes, 3(2), pp. 320–43.Google Scholar
Farnung, L. and S. M, Vos., 2022. Assembly of RNA polymerase II transcription initiation complexes. Current Opinion in Structural Biology, 73, p. 102335.Google Scholar
S. A., Lambert, Jolma, A., L. F., Campitelli, et al., 2018. The human transcription factors. Cell, 8(4), pp. 650–65.Google Scholar
B. M., Dancy and Cole, P. A., 2015. Protein lysine acetylation by p300/CBP. Chemical Reviews, 115(6), pp. 2419–52.Google Scholar
J. C., Hansen, Maeshima, K. and Hendzel, M. J., 2021. The solid and liquid states of chromatin. Epigenetics & Chromatin, 14(1).Google Scholar
B. A., Gibson, L. K., Doolittle, M. W. G., Schneider, et al., 2019. Organization of chromatin by intrinsic and regulated phase separation. Cell, 179(2), pp. 470–84.Google Scholar
Thoma, F., T. H., Koller and Klug, A., 1979. Involvement of histone H1 in the organisation of the nucleosome and of the salt-dependent superstructures of chromatin. Journal of Cell Biology, 83, pp. 403–27.Google Scholar
Worcel, A., Strogatz, S. and Riley, D., 1981. Structure of chromatin and the linking number of DNA. Proceedings of the National Academy of Sciences of the United States of America, 78(3), pp. 1461–5.Google Scholar
C. L., Woodcock, L. L., Frado and Rattner, J. B., 1984. The higher-order structure of chromatin: evidence for a helical ribbon arrangement. Journal of Cell Biology, 99(1), pp. 42–52.Google Scholar
S. P., Williams, B. D., Athey, L. J., Muglia, et al., 1986. Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length. Biophysical Journal, 49(1), pp. 233–48.Google Scholar
Song, F., Chen, P., Sun, D., et al., 2014. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science, 344(6182), pp. 376–80.Google Scholar
S. E., Farr, E. J., Woods, J. A., Joseph, Garaizar, A. and Collepardo-Guevara, R., 2021. Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions. Nature Communications, 12(1).Google Scholar
P. H., Von Hippel, N. P., Johnson and Marcus, A. H., 2013. 50 years of DNA ‘breathing’: reflections on old and new approaches [For special issue of biopolymers on 50 years of nucleic acids research]. Biopolymers, 99(12), pp. 923–54.Google Scholar
Hospital, A., J. R., Goñi, Orozco, M. and Gelpí, J. L., 2015. Molecular dynamics simulations: advances and applications. Advances and Applications in Bioinformatics and Chemistry, 8(1), pp. 37–47.Google Scholar
Ł., Szyc, Yang, M., E. T. J., Nibbering and Elsaesser, T., 2010. Ultrafast vibrational dynamics and local interactions of hydrated DNA. Angewandte Chemie, 49(21), pp. 3598–610.Google Scholar
S. K., Pal, Zhao, L. and Zewail, A. H., 2003. Water at DNA surfaces: ultrafast dynamics in minor groove recognition. Proceedings of the National Academy of Sciences of the United States of America, 8(14).Google Scholar
Lieberman-Aiden, E., Van Berkum, N., Williams, L., et al., 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326(5950), pp. 289–93.Google Scholar
D. L., Spector and Lamond, A. I., 2011. Nuclear speckles. Cold Spring Harbor Perspectives in Biology, 32.Google Scholar
S. S. P., Rao, M. H., Huntley, N. C., Durand, et al., 2014. 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159(7), pp. 1665–80.Google Scholar
McArthur, E. and Capra, J. A., 2021. Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. American Journal of Medical Genetics, 108(2), pp. 269–83.Google Scholar
R. P., Martin and Krawetz, S. A., 2000. Characterizing a human lysyl oxidase chromosomal domain. Molecular Biotechnology, 15(3), pp. 225–36.Google Scholar
J. R., Dixon, Selvaraj, S., Yue, F., et al., 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485(7398), pp. 376380.Google Scholar
Ejlassi-Lassallette, A. and Thiriet, C., 2012. Replication-coupled chromatin assembly of newly synthesized histones: distinct functions for the histone tail domains. Biochemistry and Cell Biology, 90(1), pp. 14–21.Google Scholar
Harris, E., Bohni, R., Schneiderman, H., et al., 1991. Regulation of histone mRNA in the unperturbed cell cycle: evidence suggesting control at two posttranscriptional step. Molecular and Cellular Biology, 11(5).Google Scholar
M. A., Christophorou, Castelo-Branco, G., R. P., Halley-Stott, et al., 2014. Citrullination regulates pluripotency and histone H1 binding to chromatin. Nature, 507(7490), pp. 104–8.Google Scholar
Lio, C. W, J., Yue, X., I. F., López-Moyado, et al., 2020. TET methylcytosine oxidases: new insights from a decade of research. Journal of Biosciences, 45(1), p. 21.Google Scholar
D. M., Woodcock, P. J., Crowther and Diver, W. P., 1987. The majority of methylated deoxycytidines in human DNA are not in the CpG dinucleotide. Biochemical and Biophysical Research Communications, 145(2), pp. 888–94.Google Scholar
Hayatsu, H., Wataya, Y. and Kai, K., 1970. Addition of sodium bisulfite to uracil and cytosine. Journal of the American Chemical Society, 92(3), pp. 724–6.Google Scholar
Laurent, L., Wong, E., Li, G., et al., 2010. Dynamic changes in the human methylome during differentiation. Genome Research, 20(3), pp. 320–31.Google Scholar
Lister, R., Pelizzola, M., R. H., Dowen, et al., 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462(7271), pp. 315–22.Google Scholar
Patil, V., R. L., Ward and Hesson, L. B., 2014. The evidence for functional non-CpG methylation in mammalian cells. Epigenetics, 9(6), pp. 823–8.Google Scholar
Straussman, R., Nejman, D., Roberts, D., et al., 2009. Developmental programming of CpG island methylation profiles in the human genome. Nature Structural & Molecular Biology, 16(5), pp. 564–71.Google Scholar
J. L., Miller and Grant, P. A., 2013. The role of DNA methylation and histone modifications in transcriptional regulation in humans. Subcellular Biochemistry, 61, pp. 289–317.Google Scholar
Doi, A., I. H., Park, Wen, B., et al., 2009. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells. embryonic stem cells and fibroblasts. Nature Genetics, 4112, pp. 1350–3.Google Scholar
Hellman, A. and Chess, A., 2007. Gene body-specific methylation on the active X chromosome. Science, 315(5815), pp. 1141–3.Google Scholar
Hervouet, E., Peixoto, P., Delage-Mourroux, R., Boyer-Guittaut, M. and Cartron, P. F., 2018. Specific or not specific recruitment of DNMTs for DNA methylation, an epigenetic dilemma. Clinical Epigenetics, 10(1).Google Scholar
Adam, S., Anteneh, H., Hornisch, M., et al., 2020. DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation. Nature Communications, 11(1), p. 3723.Google Scholar
Okano, M., D. W., Bell, D. A., Haber and Li, E., 1999. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell, 99(3), pp. 247–57.Google Scholar
Dong, C., Zhang, H., Xu, C., C. H., Arrowsmith and Min, J., 2014. Structure, and function of dioxygenases in histone demethylation and DNA/RNA demethylation. IUCrJ, 1, pp. 540–9.Google Scholar
Xu, C., Liu, K., Lei, M., et al., 2018. DNA sequence recognition of human CXXC domains and their structural determinants. Structure, 26(1), pp. 85–95.Google Scholar
Hashimoto, H., Zhang, X., P. M., Vertino and Cheng, X., 2015. The mechanisms of generation, recognition, and erasure of DNA 5-methylcytosine and thymine oxidation. Journal of Biological Chemistry, 290(34), pp. 20723–33.Google Scholar
Song, J., Rechkoblit, O., T. H., Bestor and Patel, D. J., 2011. Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science, 331(6020), pp. 1036–40.Google Scholar
Pradhan, M., P. O., Estève, G. C., Hang, et al., 2008. CXXC domain of human DNMT1 is essential for enzymatic activity. Biochemistry, 47(38), pp. 10000–9.Google Scholar
Li, D., Guo, B., Wu, H., Tan, L. and Lu, Q., 2015. TET family of dioxygenases: crucial roles and underlying mechanisms. Cytogenet and Genome Research, 146(3), pp. 171–80.Google Scholar
H. K., Long, N. P., Blackledge and Klose, R. J., 2013.ZF-CxxC domain-containing proteins: CpG islands and the chromatin connection. Biochemical Society Transactions, 41(3), pp. 727–40.Google Scholar
Olinski, R., Starczak, M. and Gackowski, D., 2016. Enigmatic 5-hydroxymethyluracil: oxidatively modified base, epigenetic mark or both? Reviews in Mutation Research, 767, pp. 59–66.CrossRefGoogle ScholarPubMed
Xu, Y., Wu, F., Tan, L., et al., 2011. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Molecular Cell, 42(4), pp. 451–64.Google Scholar
Lurlaro, M., Ficz, G., Oxley, D., et al., 2013. A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation. Genome Biology, 14(10).Google Scholar
E. A., Raiber, Murat, P., D. Y., Chirgadze, Beraldi, D. and B. F, Luisi., 2015. Balasubramanian S: 5-formylcytosine alters the structure of the DNA double helix. Nature Structural & Molecular Biology, 22(1), pp. 44–9.Google Scholar
Bachman, M., Uribe-Lewis, S., Yang, X., et al., 2015. Balasubramanian S: 5-Formylcytosine can be a stable DNA modification in mammals. Nature Chemical Biology, 118, pp. 555–7.Google Scholar
Carson, S., Wilson, J., Aksimentiev, A., P. R., Weigele and Wanunu, M., 2015. Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA. Nucleic Acids Research, 44(5), pp. 2085–92.Google Scholar
Chrysanthou, S., C. E., Senner, Woods, L., et al., 2018. Critical role of TET1/2 proteins in cell-cycle progression of trophoblast stem cells. Stem Cell Reports, 10(4), pp. 1355–68.Google Scholar
Sepulveda, H., Villagra, A. and Montecino, M., 2017. Tet-mediated DNA demethylation is required for SWI/SNF-dependent chromatin remodeling and histone-modifying activities that trigger expression of the Sp7 osteoblast master gene during mesenchymal lineage commitment. Molecular and Cellular Biology, 37(20).Google Scholar
R. C., Allshire and Madhani, H. D., 2018. Ten principles of heterochromatin formation and function. Nature Reviews Molecular Cell Biology, 19(4), pp. 229–44.Google Scholar
M. A., Dawson, A. J., Bannister, Göttgens, B., et al., 2009. JAK2 phosphorylates histone H3Y41 and excludes HP1α from chromatin. Nature, 461(7265), pp. 819–22.Google Scholar
A. G., Larson, Elnatan, D., M. M., Keenen, et al., 2017. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature, 547(7662), pp. 236–40.Google Scholar
Kumar, S., Kiso, A. and Abenthung Kithan, N., 2009. Chromosome banding and mechanism of chromosome aberrations. In Cytogenetics: classical and molecular strategies for analysing heredity material. IntechOpen.Google Scholar
Holmquist, G. P., 1989. Evolution of chromosome bands: molecular ecology of noncoding DNA. Journal of Molecular Evolution, 286, pp. 469–86.Google Scholar
Lu, Z., A. C., Carter and Chang, H. Y., 2017. Mechanistic insights in X-chromosome inactivation. Philosophical Transactions of the Royal Society B, 372(1733), p. 20160356.Google Scholar
Lee, H., Zhang, Z. and Krause, H. M., 2019. Long noncoding RNAs and repetitive elements: junk or intimate evolutionary partners? Trends in Genetics, 35(12), pp. 892–902.Google Scholar
D. L., Mager and Stoye, J. P., 2015. Mammalian endogenous retroviruses. Microbiology Spectrum, 3(1).Google Scholar
E. S., Lander, L. M., Linton, Birren, B., et al., 2001. Initial sequencing and analysis of the human genome. Nature, 409(6822), pp. 860–921.Google Scholar
Zhang, X., Zhang, R. and Yu, J., 2020. New understanding of the relevant role of LINE-1 retrotransposition in human disease and immune modulation. Frontiers in Cell and Developmental Biology, 8.Google Scholar
Dewannieux, M., Esnault, C. and Heidmann, T., 2003. LINE-mediated retrotransposition of marked Alu sequences. Nature Genetics, 35(1), pp. 41–8.Google Scholar
Esnault, C., Maestre, J. and Heidmann, T., 2000. Human LINE retrotransposons generate processed pseudogenes. Nature Genetics, 24(4), pp. 363–7.Google Scholar
F. J., Sanchez-Luque, M. J. H. C., Kempen, Gerdes, P., et al., 2019. LINE-1 evasion of epigenetic repression in humans. Molecular Cell, 75(3), pp. 590–604.Google Scholar
J. L., Garcia-Perez, M. C. N., Marchetto, A. R., Muotri, et al., 2007. LINE-1 retrotransposition in human embryonic stem cells. Human Molecular Genetics, 16(13), pp. 1569–77.Google Scholar
Zhang, X., Zhang, R. and Yu, J., 2020. New understanding of the relevant role of LINE-1 retrotransposition in human disease and immune modulation. Frontiers in Cell and Developmental Biology, 8.Google Scholar
D. M., Terry and Devine, S. E., 2020. Aberrantly high levels of somatic LINE-1 expression and retrotransposition in human neurological disorders. Frontiers in Genetics, 10.Google Scholar
Troskie, R., G. J., Faulkner and Cheetham, S. W., 2021. Processed pseudogenes: a substrate for evolutionary innovation. BioEssays, 43(11), p. 2100186.Google Scholar
J. S., Mattick and Makunin, I. V., 2005. Small regulatory RNAs in mammals. Human Molecular Genetics, 14(1).Google Scholar
Alles, J., Fehlmann, T., Fischer, U., et al., 2019. An estimate of the total number of true human miRNAs. Nucleic Acids Research, 47(7), pp. 3353–64.Google Scholar
R. C., Friedman, K. K. H., Farh, C. B., Burge and Bartel, D. P., 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Research, 19(1), pp. 92–105.Google Scholar
M. V., Lorio, Piovan, C. and Croce, C. M., 2010. Interplay between microRNAs and the epigenetic machinery: an intricate network. Biochimica et Biophysica Acta, 1799(10–12), pp. 694–701.Google Scholar
Kawaji, H. and Hayashizaki, Y., 2008. Exploration of small RNAs. PLOS Genetics, 4(1), p. 22.Google Scholar
Watanabe, T., Takeda, A., Tsukiyama, T., et al., 2006. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes & Development, 20(13), pp. 1732–43.Google Scholar
Lipardi, C., Wei, Q. and Paterson, B. M., 2001. RNAi as random degradative PCR. Cell, 107(3), pp. 297–307.Google Scholar
Czech, B. and Hannon, G. J., 2016. One loop to rule them all: the ping-pong cycle and piRNA-guided silencing. Trends in Biochemical Sciences, 41(4), pp. 324–37.Google Scholar
Lipovich, L., Johnson, R. and Lin, C. Y., 2010. MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. Biochimica et Biophysica Acta, 1799(9), pp. 597–615.Google Scholar
Milligan, M. J. and Lipovich, L., 2015. Pseudogene-derived lncRNAs: emerging regulators of gene expression. Frontiers in Genetics, 6.Google Scholar
J. J., Żylicz, Bousard, A., Žumer, K., et al., 2019. The implication of early chromatin changes in X chromosome activation. Cell, 176(1–2), pp. 182–97.e23.Google Scholar
Soldà, G., Boi, S., Duga, S., et al., 2005. In vivo RNA–RNA duplexes from human α3 and α5 nicotinic receptor subunit mRNAs. Gene, 345(2), pp. 155–64.Google Scholar
Mohammad, F., Mondal, T. and Kanduri, C., 2009. Epigenetics of imprinted long non-coding RNAs. Epigenetics, 4(5), pp. 277–86.Google Scholar
Yelin, R., Dahary, D., Sorek, R., et al., 2003. Widespread occurrence of antisense transcription in the human genome. Nature Biotechnology, 21(4), pp. 379–86.Google Scholar
Newall, A. E. T., 2001. Primary non-random X inactivation associated with disruption of Xist promoter regulation. Human Molecular Genetics, 10(6), pp. 581–9.Google Scholar
Furlan, G. and Galupa, R., 2022. Mechanisms of choice in X-chromosome activation. Cells, 11(3).Google Scholar
Tu, Y., Chen, C., Pan, J., et al., 2012. The ubiquitin proteasome pathway UPP in the regulation of cell cycle control and DNA damage repair and its implication in tumorigenesis. International Journal of Clinical and Experimental Pathology, 5(8).Google Scholar
J. M., LaSalle, L. T., Reiter and Chamberlain, S. J., 2015. Epigenetic regulation of UBE3A and roles in human neurodevelopmental disorders. Epigenomics, 7(7), pp. 1213–28.Google Scholar
Weber, M. J., 2006. Mammalian small nucleolar RNAs are mobile genetic elements. PLOS Genetics, 2(12), p. 205.Google Scholar
Bergeron, D., Laforest, C., Carpentier, S., et al., 2021. SnoRNA copy regulation affects family size, genomic location and family abundance levels. BMC Genomics, 22(1), p. 414.Google Scholar
Kiss-László, Z., Henry, Y., J. P., Bachellerie, Caizergues-Ferrer, M. and Kiss, T., 1996. Site-specific ribose methylation of pre-ribosomal RNA: a novel function for small nucleolar RNAs. Cell, 85(7), pp. 1077–88.Google Scholar
Kishore, S. and Stamm, S., 2006. Regulation of alternative splicing by snoRNAs. Cold Spring Harbor Symposia on Quantitative Biology, 71, pp. 329–34.Google Scholar
M. F., Lanfranco, N. C., Anastasio, P. K., Seitz and Cunningham, K. A., 2010. Quantification of RNA editing of the serotonin 2 C receptor 5HT2CR ex vivo: constitutive activity in receptors and other proteins part B. In Methods in enzymology, ed. Conn, P. M. (pp. 311–28). Elsevier Academic.Google Scholar
L. A., Farrelly, R. E., Thompson, Zhao, S., et al., 2019. Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3. Nature, 567(7749), pp. 535–9.Google Scholar
S. M., Rueter, T. R., Dawson and Emeson, R. B., 1999. Regulation of alternative splicing by RNA editing. Nature, 399(6731), pp. 75–80.Google Scholar
Vitali, P., Basyuk, E., Le Meur, E., et al., 2005. ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs. Journal of Cell Biology, 169(5), pp. 745–53.Google Scholar
Stamm, S., S. B., Gruber, A. G., Rabchevsky and Emeson, R. B., 2017. The activity of the serotonin receptor 2 C is regulated by alternative splicing. Human Genetics, 136(9), pp. 1079–91.Google Scholar
Flomen, R., Knight, J., Sham, P., Kerwin, R. and Makoff, A., 2004. Evidence that RNA editing modulates splice site selection in the 5-HT2 C receptor gene. Nucleic Acids Research, 32(7), pp. 2113–122.Google Scholar
Kishore, S. and Stamm, S., 2006. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2 C. Science, 311(5758), pp. 230–2.Google Scholar
M. G., Butler, M. F., Theodoro, D. C., Bittel, et al., 2007. X-chromosome inactivation patterns in females with Prader–Willi syndrome. American Journal of Medical Genetics A, 143A(5), pp. 469–75.Google Scholar
Wang, Q., P. J., O’Brien, C. X., Chen, et al., 2000. Altered G protein-coupling functions of RNA editing isoform and splicing variant serotonin 2 C receptors. Journal of Neurochemistry, 74.Google Scholar
Van De Wouw, M., R. M., Stilling, V. L., Peterson, et al., 2019. Host microbiota regulates central nervous system serotonin receptor 2 C editing in rodents. ACS Chemical Neuroscience, 10(9), pp. 3953–60.Google Scholar
Belair, C., Sim, S., K. Y., Kim, et al., 2019. The RNA exosome nuclease complex regulates human embryonic stem cell differentiation. Journal of Cell Biology, 218(8) pp. 2564–82.Google Scholar
Kawamura, Y., Sanchez Calle, A., Yamamoto, Y., T. A., Sato and Ochiya, T., 2019. Extracellular vesicles mediate the horizontal transfer of an active LINE-1 retrotransposon. Journal of Extracellular Vesicles, 8(1).Google Scholar
Ratajczak, J., Miekus, K., Kucia, M., et al., 2006. Embryonic stem cell-derived microvesicles reprogram hematopoietic progenitors: evidence for horizontal transfer of mRNA and protein delivery. Leukemia, 20(5), pp. 847–56.Google Scholar
Guo, J., Cheng, P., Yuan, H. and Liu, Y., 2009. The exosome regulates circadian gene expression in a posttranscriptional negative feedback loop. Cell, 138(6), pp. 1236–46.Google Scholar
Khalyfa, A., V. A., Poroyko, Qiao, Z., et al., 2017. Exosomes and metabolic function in mice exposed to alternating dark-light cycles mimicking night shift work schedules. Frontiers in Physiology, 8.Google Scholar
Forterre, A., Jalabert, A., Chikh, K., et al., 2014. Myotube-derived exosomal miRNAs downregulate Sirtuin1 in myoblasts during muscle cell differentiation. Cell Cycle, 13(1), pp. 78–89.Google Scholar
K. W., Adolph, L. R., Kreisman and Kuehn, R. L., 1986. Assembly of chromatin fibers into metaphase chromosomes analyzed by transmission electron microscopy and scanning electron microscopy. Biophysical Journal, 49(1), pp. 221–31.Google Scholar
Bonner, J., 1965. The template activity of chromatin. Journal of Cellular and Comparative Physiology, 66(s1), pp. 77–90.Google Scholar
Sinden, R. R., 1994. Introduction to the structure, properties, and reactions of DNA. In DNA structure and function (pp. 1–57). Elsevier.Google Scholar
Tashiro, R. and Sugiyama, H., 2022. Photoreaction of DNA containing 5‐halouracil and its products. Photochemistry and Photobiology, 98(3), pp. 532–45.Google Scholar
Hori, M., Yonei, S., Sugiyama, H., et al., 2003. Identification of high excision capacity for 5-hydroxymethyluracil mispaired with guanine in DNA of Escherichia coli MutM, Nei and Nth DNA glycosylases. Nucleic Acids Research, 31(4), pp. 1191–6.Google Scholar
Cremer, C. and Gray, J. W., 1982. Application of the BrdU/thymidine method to flow cytogenetics: differential quenching/enhancement of hoechst 33258 fluorescence of late-replicating chromosomes 1.Somatic Cell Genetics, 8(3).Google Scholar
O. O., Brovarets’ and Hovorun, D. M., 2015. Tautomeric transition between wobble A·C DNA base mispair and Watson-Crick-like A·C* mismatch: Microstructural mechanism and biological significance. Physical Chemistry Chemical Physics, 17(23), pp. 15103–10.Google Scholar
N. K., Kochetkov and Budowsky, E. I., 1969. The chemical modification of nucleic acids. In Progress in nucleic acid research and molecular biology (pp. 403–38). Elsevier.Google Scholar
Tung, F., K. H., Tsai and Marfey, P., 1972. Bromination of calf thymus chromatin. Biochimica et Biophysica Acta, 277(1), pp. 117–28.Google Scholar
S. M., Valenzuela, Mazzanti, M., Tonini, R., et al., 2000. The nuclear chloride ion channel NCC27 is involved in regulation of the cell cycle. The Journal of Physiology, 529(3), pp. 541–52.Google Scholar
Maier, J. A., 2013. Magnesium and cell cycle. In Encyclopedia of metalloproteins, ed. Kretsinger, R. H., Uversky, V. N. and Permyakov, E. A. (pp. 1227–32). Springer.Google Scholar
Maeshima, K., Matsuda, T., Shindo, Y., et al., 2018. Transient rise in free Mg2+ ions released from ATP-mg hydrolysis contributes to mitotic chromosome condensation. Current Biology, 28(3), pp. 444–51.Google Scholar
A. B., Robertson, Klungland, A., Rognes, T. and Leiros, I., 2009. Base excision repair: the long and short of it. Cellular and Molecular Life Sciences, 66(6), pp. 981–93.Google Scholar
Li, H., Li, Q., Ma, Z., et al., 2019. AID modulates carcinogenesis network via DNA demethylation in bladder urothelial cell carcinoma. Cell Death & Disease, 10(4), p. 251.Google Scholar
A. N., Lane and Fan, T. W. M., 2015. Regulation of mammalian nucleotide metabolism and biosynthesis. Nucleic Acids Research, 43(4), pp. 2466–85.Google Scholar
N. M., Luscombe, R. A., Laskowski and Thornton, J. M., 2001. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Research, 29(13).Google Scholar
Pospisil, P., Ballmer, P., Scapozza, L. and Folkers, G., 2003. Tautomerism in computer-aided drug design. Journal of Receptors and Signal Transduction, 23(4), pp. 361–71.Google Scholar
Suckling, C., Gibson, C. and Huggan, J., 2008. Bicyclic 6–6 systems: pteridines. In Comprehensive heterocyclic chemistry III, ed. Katrizky, A. R., Ramsten, C. A., Scriven, E. F. V. and Taylor, R. J. K. (pp. 915–75). Elsevier.Google Scholar
Sato, K., Kanno, J., Tominaga, T., Matsubara, Y. and Kure, S., 2006. De novo and salvage pathways of DNA synthesis in primary cultured neural stem cells. Brain Research, 1071(1), pp. 24–33.Google Scholar
A. M., Gazzali, Lobry, M., Colombeau, L., et al., 2016. Stability of folic acid under several parameters. European Journal of Pharmaceutical Sciences, 93, pp. 419–30.Google Scholar
Di Liberto, V., Mudò, G., Garozzo, R., et al., 2016. The guanine-based purinergic system: the tale of an orphan neuromodulation. Frontiers in Pharmacology, 7.Google Scholar
Prabhu, Y. and Eichinger, L., 2006. The Dictyostelium repertoire of seven transmembrane domain receptors. European Journal of Cell Biology, 85(9–10), pp. 937–46.Google Scholar
N. M., Duc, H. R., Kim and Chung, K. Y., 2015. Structural mechanism of G protein activation by G protein-coupled receptor. European Journal of Pharmacology, 76(3), pp. 214–22.Google Scholar
L. A., Catapano and Manji, H. K., 2006. G protein-coupled receptors in major psychiatric disorders. Biochimica et Biophysica Acta, 1768(4), pp. 976–93.Google Scholar
D. R., Brandts and Ross, E. M., 1985. GTPase activity of the stimulatory GTP-binding regulatory protein of adenylate cyclase: accumulation and turnover of enzyme nucleotide intermediates.Journal of Biological Chemistry, 260(1), p. 266472.Google Scholar
J. M., López, E. L., Outtrim, Fu, R., et al., 2020. Physiological levels of folic acid reveal purine alterations in Lesch-Nyhan disease. Proceedings of the National Academy of Sciences of the United States of America, 117(22), pp. 12071–9.Google Scholar
G. S., Ducker and Rabinowitz, J. D., 2015. ZMP: a master regulator of one-carbon metabolism. Molecular Cell, 57(2), pp. 203–4.Google Scholar
Hartley, D. M. and Snodgrass, S. R., 1990. Folate interactions with cerebral G proteins. Neurochemical Research, 15(7), pp. 681–6.Google Scholar
R. J. W., De Wit and Bulgakov, R., 2021. Guanine nucleotides modulate the ligand binding properties of cell surface folate receptors in Dictyostelium discoideum. FEBS Letters, 179(2).Google Scholar
D. S., Rosenblatt and Erbe, R. W., 1977. Methylenetetrahy drofolate reductase in cultured human cells. I. Growth and metabolic studies. Pediatric Research, 11(11), pp. 1137–41.Google Scholar
M. A., Sheraz, S. H., Kazi, Ahmed, S., Anwar, Z. and Ahmad, I., 2014. Photo, thermal and chemical degradation of riboflavin. Beilstein Journal of Organic Chemistry, 10, pp. 1999–2012.Google Scholar
Mack, M. and Grill, S., 2006. Riboflavin analogs and inhibitors of riboflavin biosynthesis. Applied Microbiology and Biotechnology, 71(3), pp. 265–75.Google Scholar
Fanet, H., Capuron, L., Castanon, N., Calon, F. and Vancassel, S., 2020. Tetrahydrobiopterin BH4 pathway: from metabolism to neuropsychiatry. Current Neuropharmacology, 19(5), pp. 591–609.Google Scholar
Nalini, A., Pandraud, A., Mok, K. and Houlden, H., 2013. Madras motor neuron disease MMND is distinct from the riboflavin transporter genetic defects that cause Brown–Vialetto–Van Laere syndrome. Journal of the Neurological Sciences, 334(1–2), pp. 119–22.Google Scholar
J. A., Bashford, F. A., Chowdhury and Shaw, C. E., 2017. Remarkable motor recovery after riboflavin therapy in adult-onset Brown–Vialetto–Van Laere syndrome. Practical Neurology, 17(1), pp. 53–6.Google Scholar
Carreau, C., Lenglet, T., Mosnier, I., et al., 2020. Juvenile ALS-like phenotype dramatically improved after high-dose riboflavin treatment. Annals of Clinical and Translational Neurology, 7(2), pp. 250–3.Google Scholar
Timmerman, V. and De Jonghe, P., 2014. Promising riboflavin treatment for motor neuron disorder. Brain, 137(1), pp. 2–3.Google Scholar
J. O., Johnson, J. R., Gibbs, Megarbane, A., et al., 2012. Exome sequencing reveals riboflavin transporter mutations as a cause of motor neuron disease. Brain, 135(9), pp. 2875–82.Google Scholar
G. E., Treadwell, D. J. E., Metzler, Treadwell, E. and Present, J., 1972. Photoconversion of Riboflavin to Lumichrome in Plant Tissues.Plant Physiology, 49.Google Scholar
Darguzyte, M., Drude, N., Lammers, T. and Kiessling, F., 2020. Riboflavin-targeted drug delivery. Cancers (Basel), 12(2).Google Scholar
H. M., Said and Ma, T. Y. 1994. Mechanism of riboflavine uptake by Caco-2 human intestinal epithelial cells. American Journal of Physiology, 266(1), pp. 15–21.Google Scholar
Kalucka, J., Missiaen, R., Georgiadou, M., et al., 2015. Metabolic control of the cell cycle. Cell Cycle, 14(21), pp. 3379–88.Google Scholar
J. T., Brosnan, E. P., Wijekoon, Warford-Woolgar, L., et al., 2009. Creatine synthesis is a major metabolic process in neonatal piglets and has important implications for amino acid metabolism and methyl balance. Journal of Nutrition, 139(7), pp. 1292–7.Google Scholar
Kurtz, P. and Rocha, E. E. M., 2020. Nutrition therapy, glucose control, and brain metabolism in traumatic brain jury: a multimodal monitoring approach. Frontiers in Neuroscience, 14.Google Scholar
Liu, Y., Chen, C., Wang, X., et al., 2022. An epigenetic role of mitochondria in cancer. Cells, 11(16), p. 2518.Google Scholar
N. G., Norwitz, S. S., Dalai and Palmer, C. M., 2020. Ketogenic diet as a metabolic treatment for mental illness. Current Opinion in Endocrinology, Diabetes and Obesity, 27(5), pp. 269–74.Google Scholar
Dickerson, R. N., 2016. Nitrogen balance and protein requirements for critically Ill older patients. Nutrients, 8(4).Google Scholar
F. J., Steyn, Z. A., Ioannides, R. P. A., Van Eijk, et al., 2018. Hypermetabolism in ALS is associated with greater functional decline and shorter survival. Journal of Neurology, Neurosurgery, and Psychiatry, 89(10), pp. 1016–23.Google Scholar
Soyka, M., Koch, W., H. J., Möller, Rüther, T. and Tatsch, K., 2005. Hypermetabolic pattern in frontal cortex and other brain regions in unmedicated schizophrenia patients: results from a FDG-PET study. European Archives of Psychiatry and Clinical Neuroscience, 255(5), pp. 308–12.Google Scholar
Xie, X., Yang, H., J. J., An, et al., 2019. Activation of anxiogenic circuits instigates resistance to diet-induced obesity via increased energy expenditure. Cell Metabolism, 29(4), pp. 917–31.Google Scholar
D. F., Rolfe and Brown, G. C., 1997. Cellular energy utilization and molecular origin of standard metabolic rate in mammals. Physiological Reviews, 773, pp. 731–58.Google Scholar
J. S., Baker, M. C., McCormick and Robergs, R. A., 2010. Interaction among skeletal muscle metabolic energy systems during intense exercise. Journal of Nutrition and Metabolism, 2010, pp. 1–13.Google Scholar
A. L., Green, Wang, S., Purvis, S., et al., 2007. Identifying cardiorespiratory neurocircuitry involved in central command during exercise in humans. The Journal of Physiology, 578(2), pp. 605–12.Google Scholar
Asahara, R., Matsukawa, K., Ishii, K., Liang, N. and Endo, K., 2016. The prefrontal oxygenation and ventilatory responses at start of one-legged cycling exercise have relation to central command. Journal of Applied Physiology, 121(5), pp. 1115–26.Google Scholar
Marina, N., Kasymov, V., G. L., Ackland, Kasparov, S. and Gourine, A. V., 2016. Astrocytes and brain hypoxia. Advances in Experimental Medicine and Biology, 903, pp. 201–7.Google Scholar
Crawford, J. H., 2006. Hypoxia, red blood cells, and nitrite regulate NO-dependent hypoxic vasodilation. Blood, 107(2), pp. 566–74.Google Scholar
A. C. L., Nobrega, O’Leary, D., B. M., Silva, et al., 2014. Neural regulation of cardiovascular response to exercise: role of central command and peripheral afferents. BioMed Research International, 2014, pp. 1–20.Google Scholar
A. K., Mustafa, M. M., Gadalla and Snyder, S. H., 2009. Signaling by gasotransmitters. Science Signaling, 2(68).Google Scholar
Ishikawa, M., Kajimura, M., Adachi, T., et al., 2005. Carbon monoxide from heme oxygenase-2 is a tonic regulator against NO-dependent vasodilatation in the adult rat cerebral microcirculation. Circulation Research, 97(12).Google Scholar
G. K., Kolluru, Shen, X., Yuan, S. and Kevil, C. G., 2017. Gasotransmitter heterocellular signalling. Antioxidants & Redox Signaling, 26(16), pp. 936–60.Google Scholar
Wang, R. 2002. Two’s company, three’s a crowd: can H2S be the third endogenous gaseous transmitter? The FASEB Journal, 13, pp. 1792–8.Google Scholar
E. B., Randi, Zuhra, K., Pecze, L., Panagaki, T. and Szabo, C., 2021. Physiological concentrations of cyanide stimulate mitochondrial Complex IV and enhance cellular bioenergetics. Proceedings of the National Academy of Sciences of the United States of America, 118(20).Google Scholar
Aryal, P., M. S. P., Sansom and Tucker, S. J., 2015. Hydrophobic gating in ion channels. Journal of Molecular Biology, 427(1), pp. 121–30.Google Scholar
Pé Rez-Mato, I., Castro, C., Ruiz, A., F. J., Corrales and Mato, J. M., 1999. Methionine adenosyltransferase S-nitrosylation is regulated by the basic and acidic amino acids surrounding the target thiol. Journal of Biological Chemistry, 274(24).Google Scholar
Kabe, Y., Yamamoto, T., Kajimura, M., et al., 2016. Cystathionine β-synthase and PGRMC1 as CO sensors. Free Radical Biology and Medicine, 99, pp. 333–44.Google Scholar
Kabil, O., Yadav, V. and Banerjee, R., 2016. Heme-dependent metabolite switching regulates H2S synthesis in response to endoplasmic reticulum ER stress. Journal of Biological Chemistry, 291(32), pp. 16418–23.Google Scholar
Allen, P. J., 2012. Creatine metabolism and psychiatric disorders: does creatine supplementation have therapeutic value? Neuroscience & Biobehavioral Reviews, 36(5), pp. 1442–62.Google Scholar
R. B., Kreider and Stout, J. R., 2021. Creatine in health and disease. Nutrients, 13(2), pp. 1–28.Google Scholar
Halbrich, M., Barnes, J., Bunge, M. and Joshi, C., 2008. A V139 M mutation also causes the reversible CNS phenotype in CMTX. Canadian Journal of the Neurological Sciences, 35(3), pp. 372–4.Google Scholar
Bauer, J., Biolo, G., Cederholm, T., et al., 2013. Evidence-based recommendations for optimal dietary protein intake in older people: a position paper from the pro-tage study group. Journal of the American Medical Directors Association, 14(8), pp. 542–59.Google Scholar
Sriperm, N., G. M., Pesti and Tillman, P. B., 2011. Evaluation of the fixed nitrogen-to-protein N:P conversion factor 6.25 versus ingredient specific N:P conversion factors in feedstuffs. Journal of the Science of Food and Agriculture, 91(7), pp. 1182–6.Google Scholar
Maxwell, J., Gwardschaladse, C., Lombardo, G., et al., 2017. The impact of measurement of respiratory quotient by indirect calorimetry on the achievement of nitrogen balance in patients with severe traumatic brain injury. European Journal of Trauma and Emergency Surgery, 43(6), pp. 775–82.Google Scholar
Tsukada, Y., Fang, J., Erdjument-Bromage, H., et al., 2006. Histone demethylation by a family of JmjC domain-containing proteins. Nature, 439(7078), pp. 811–16.Google Scholar
Kamen, M. D., 1963. Early history of carbon-14 discovery of this supremely important tracer was expected in the physical sense but not in the chemical sense. Science, 140(3567), pp. 584–90.Google Scholar
Wilkinson, D. J., 2018. Historical and contemporary stable isotope tracer approaches to studying mammalian protein metabolism. Mass Spectrometry Reviews, 37(1), pp. 57–80.Google Scholar
Dingwall, S., C. E., Mills, Phan, N., Taylor, K. and Boreham, D. R., 2011. Human health and the biological effects of tritium in drinking water: prudent policy through science – addressing the ODWAC new recommendation. Dose-Response, 9(1), pp. 6–31.Google Scholar
Ball, D. W., 2004. How radioactive is your banana? Journal of Chemical Education, 81(10), p. 1440Google Scholar
Liang, M., 2018. Epigenetic mechanisms and hypertension. AHA Hypertension, 72(6), pp. 1244–54.Google Scholar
Hancock, A. M., Alkorta-Aranburu, G., Witonsky, D. B. and Di Rienzo, A., 2010. Adaptations to new environments in humans: the role of subtle allele frequency shifts. Philosophical Transactions of the Royal Society B, 365(1552), pp. 2459–68.Google Scholar
White, T. D., Asfaw, B., DeGusta, D., et al., 2003. Pleistocene Homo sapiens from Middle Awash. Ethiopia. Nature, 423(6941), pp. 742–7.Google Scholar
Luca, F., Perry, G. H. and Di Rienzo, A., 2010. Evolutionary adaptations to dietary changes. Annual Review of Nutrition, 30, pp. 291–314.Google Scholar
Hancock, A. M., Witonsky, D. B., Ehler, E., et al., 2010. Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency. Proceedings of the National Academy of Sciences of the United States of America, 107(suppl. 2), pp. 8924–30.Google Scholar
Heyn, H., Moran, S., Hernando-Herraez, I., et al., 2013. DNA methylation contributes to natural human variation. Genome Research, 23(9), pp. 1363–72.Google Scholar
Yafei, W., Lijun, P., Jinfeng, W. and Xiaoying, Z., 2012. Is the prevalence of MTHFR C677 T polymorphism associated with ultraviolet radiation in Eurasia? Journal of Human Genetics, 57(12), pp. 780–6.Google Scholar
Cordain, L. and Hickey, M. S., 2006. Ultraviolet radiation represents an evolutionary selective pressure for the south-to-north gradient of the MTHFR 677TT genotype. The American Journal of Clinical Nutrition, 84(5), p. 1243.Google Scholar
Kious, B. M., Bakian, A., Zhao, J., et al., 2019. Altitude and risk of depression and anxiety: findings from the intern health study. International Review of Psychiatry, 31(7–8), pp. 637–45.Google Scholar
Smith, B., 1995. The emergence of agriculture. Bulletin of Science, Technology & Society, 15(1).Google Scholar
Valeggia, C. R. and Snodgrass, J. J., 2015. Health of Indigenous peoples. Annual Review of Anthropology, 44(1), pp. 117–35.Google Scholar
Evans, L., 1996. Domestication of crop plants. In Crop evolution, adaptation and yield (pp. 106–7). Cambridge University Press.Google Scholar
Moreira, X., Abdala-Roberts, L., Gols, R. and Francisco, M., 2018. Plant domestication decreases both constitutive and induced chemical defences by direct selection against defensive traits. Scientific Reports, 8(1).Google Scholar
Zohary, D., Hopf, M. and Weiss, E., 2012. Domestication of plants in the old world, 4th ed. Oxford University Press.Google Scholar
Fahrbach, S. E., Smagghe, G. and Velarde, R. A., 2012. Nuclear receptors. Annual Review of Entomology, 57(1), pp. 83–106.Google Scholar
Dolan, L. C., Matulka, R. A. and Burdock, G. A., 2010. Naturally occurring food toxins. Toxins, 29, pp. 2289–332.Google Scholar
Altamura, M. R., Long, L. and Hasselstrom, T., 1959. Giotrin from fresh cabbage. Journal of Biological Chemistry, 234(7), pp. 1847–9.Google Scholar
Negi, V. S., Pal, A. and Borthakur, D., 2021. Biochemistry of plants N–heterocyclic non-protein amino acids. Amino Acids, 53(6), pp. 801–12.Google Scholar
Martinez, M., Ahmed, A. H., Loh, A. P. and Oswald, R. E., 2014. Thermodynamics and mechanism of the interaction of willardiine partial agonists with a glutamate receptor: Implications for drug development. Biochemistry, 53(23), pp. 3790–5.Google Scholar
Kenten, R. H., 1957. The partial purification and properties of a thiaminase from bracken [Pteridium aquilinum L. Kuhn]. Biochemical Journal, 67.Google Scholar
Zallot, R., Yazdani, M., Goyer, A., et al., 2014. Salvage of the thiamine pyrimidine moiety by plant TenA proteins lacking an active-site cysteine. Biochemical Journal, 463(1), pp. 145–55.Google Scholar
Candau, M. and Massengo, J., 1982. Evidence of a thiamine deficiency in sheep fed maize silage. Annales de recherches veterinaires, 13(4), pp. 329–40.Google Scholar
Chandrakumar, A., Bhardwaj, A. and T’Jong, G. W., 2019. Review of thiamine deficiency disorders: Wernicke encephalopathy and Korsakoff psychosis. Journal of Basic and Clinical Physiology and Pharmacology, 30(2), pp. 153–62.Google Scholar
Martinez-Zamudio, R. and Ha, H. C., 2011. Environmental epigenetics in metal exposure. Epigenetics, 6(7), pp. 820–7.Google Scholar
Wolf, T., Baier, S. R. and Zempleni, J., 2015. The intestinal transport of bovine milk exosomes Is mediated by endocytosis in human colon carcinoma CACO-2 cells and rat small intestinal IEC-6 cells1-3. Journal of Nutrition, 145(10), pp. 2201–6.Google Scholar
Onwezen, M. C., Bouwman, E. P., Reinders, M. J. and Dagevos, H., 2021. A systematic review on consumer acceptance of alternative proteins: pulses, algae, Insects, plant-based meat alternatives. and cultured meat. Appetite, 159.Google Scholar
Fowler, S., Roush, R. and Wise, J., 2013. The cell cycle. In Concepts of biology. OpenStax.Google Scholar
Segal, D. J. and LaSalle, J. M., 2018. UBE3A: an e3 ubiquitin ligase with genome-wide impact in neurodevelopment disease. Frontiers in Molecular Neuroscience, 11, p. 476.Google Scholar