Cited by 1,109Epigenetics and DNA MethylationGenomics and Chromatin DynamicsGenetic Syndromes and Imprinting

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Epigenetics and gene expression

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Gibney, E R, Nolan, C M·2010·Heredity

DOI 10.1038/hdy.2010.54

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Abstract

Transcription, translation and subsequent protein modification represent the transfer of genetic information from the archival copy of DNA to the short-lived messenger RNA, usually with subsequent production of protein. Although all cells in an organism contain essentially the same DNA, cell types and functions differ because of qualitative and quantitative differences in their gene expression. Thus, control of gene expression is at the heart of differentiation and development. Epigenetic processes, including DNA methylation, histone modification and various RNA-mediated processes, are thought to influence gene expression chiefly at the level of transcription; however, other steps in the process (for example, translation) may also be regulated epigenetically. The following paper will outline the role epigenetics is believed to have in influencing gene expression.

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Kim, T. W., Han, S. R., Kim, J., Yoo, S., Lee, M., Lee, S., Kang, Y. H., & Lee, H. Y. (2019) · Oncology Reports · doi:10.3892/or.2019.7099 · Cited by 12
“Given the epigenetic regulation mechanism via the relationship between DNA methylation and opposite gene expression (33), and the finding that the TESC promoter was highly methylated in gastric cancer cell lines with the exception of SNU-620 cells, cell viability following 5-aza-2c-deoxycytidine (5'-aza-dC) treatment…”
Background
Switch to Autophagy the Key Mechanism for Trabecular Meshwork Death in Severe Glaucoma
Rao, A., Sahay, P., Chakraborty, M., Prusty, B. K., Srinivasan, S., Jhingan, G. D., Mishra, P., Modak, R., & Suar, M. (2021) · Clinical ophthalmology · doi:10.2147/opth.s292218 · Cited by 12
How Epigenetics Can Enhance Pig Welfare?
da Silva, A. N., Araújo, M. S., Pértille, F., & Zanella, A. J. (2021) · Animals · doi:10.3390/ani12010032 · Cited by 19
“In addition, these specific patterns are maintained and inherited during the mitotic, and possibly meiotic, divisions of the cells [63].”
Background
Analysis method of epigenetic DNA methylation to dynamically investigate the functional activity of transcription factors in gene expression
Feng, W., Dong, Z., He, B., & Wang, K. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-532 · Cited by 12
“DNA methylation is known to repress transcription factor binding ability [15-23]; therefore, we designed a general model to describe such an effect, where a nonlinear S-function is adopted to normalize the effect between 0 and 1.”
Method
Epigenetic‐Imprinting Changes Caused by Neonatal Fasting Stress Protect From Future Fasting Stress
Jiang, Y., Denbow, C. J., Meiri, N., & Denbow, D. M. (2015) · Journal of Neuroendocrinology · doi:10.1111/jne.12333 · Cited by 12
DNA methylation biomarkers for the diagnosis and treatment management of breast cancer: where are we now?
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“It is well established that epigenetic mechanisms play a crucial role in the differentiation of cells and tissues in multicellular organisms [3].”
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“For example, the US National Institutes of Health (2009) described epige-netics as both heritable changes in gene activity and expression (in the progeny of cells or individuals) and stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable [14].”
Human papillomavirus-mediated cervical cancer: epigenetic interplay and clinical implications
Sisodiya, S., Singh, P., Joshi, T., Aftab, M., Firdausi, N., Khan, A., Mishra, N., Khan, N. J., Tanwar, P., Gupta, V., et al. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1633283 · Cited by 11
“Epigenetics involves the regulation of gene expression through heritable modifications that do not alter the underlying DNA sequence (Hamilton, 2011; Gibney and Nolan, 2010; Dasari et al., 2015; Hanahan, 2022).”
The maternal effects of dietary restriction on Dnmt expression and reproduction in two clones of Daphnia pulex
Agrelius, T. C., Altman, J. E., & Dudycha, J. L. (2022) · Heredity · doi:10.1038/s41437-022-00581-7 · Cited by 11
“DNA methylation and histone modification remodel chromatin, while the other is a small-RNA-mediated regulatory process (Berger 2007; Gibney and Nolan 2010).”
Background
Histone Demethylase Modulation: Epigenetic Strategy to Combat Cancer Progression
Srivastava, R., Singh, R., Jauhari, S., Lodhi, N., & Srivastava, R. (2023) · Epigenomes · doi:10.3390/epigenomes7020010 · Cited by 12
Interplay between epigenome and 3D chromatin structure
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Sex-specific epigenetics drive low GPER expression in gastrointestinal smooth muscles in type 2 diabetic mice
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Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans
Chang, W.-J., Baker, M. S., Laritsky, E., Gunasekara, C., Maduranga, U., Galliou, J. M., McFadden, J. W., Waltemyer, J. R., Berggren-Thomas, B., Tate, B. N., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03307-6 · Cited by 11
“Epi-genetic marks stably affect gene expression [5].”
Exploring the key role of DNA methylation as an epigenetic modulator in oxidative stress related islet cell injury in patients with type 2 diabetes mellitus: a review
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“[ 18].”
The Histomorphology to Molecular Transition: Exploring the Genomic Landscape of Poorly Differentiated Epithelial Endometrial Cancers
Molefi, T., Mabonga, L., Hull, R., Mwazha, A., Sebitloane, M., & Dlamini, Z. (2025) · Cells · doi:10.3390/cells14050382 · Cited by 12
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Histone Modifications, Internucleosome Dynamics, and DNA Stresses: How They Cooperate to “Functionalize” Nucleosomes
Krajewski, W. A. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.873398 · Cited by 13
“So, despite the nucleosomes being the key elements in gene regulation (Gibney and Nolan, 2010), it is still understudied how they relieve their intrinsically repressive effects on DNA expression.”
Background
Unlocking the Secret to Higher Crop Yield: The Potential for Histone Modifications
Fang, W., Fasano, C., & Perrella, G. (2023) · Plants · doi:10.3390/plants12081712 · Cited by 11
“Histone modifications specifically refer to the post-translational modifications on N-terminal tails, including but not limited to methylation, acetylation, phosphorylation, ubiquitination, glycosylation, and sumoylation [11], that ultimately may determine chromatin configuration (open or closed) and regulate gene tra…”
Background
DNA methylation associated with polycystic ovary syndrome: a systematic review
Miranda, A. G., Seneda, M. M., & Faustino, L. R. (2023) · Archives of Gynecology and Obstetrics · doi:10.1007/s00404-023-07025-5 · Cited by 11
“Epigenetic processes include DNA cytosine methylation, modifications of histone proteins present in the nucleosome, and mechanisms mediated by noncoding RNA [8].”
Impaired ATF3 signaling involves SNAP25 in SOD1 mutant ALS patients
Yazar, V., Kühlwein, J. K., Knehr, A., Grozdanov, V., Ekici, A. B., Ludolph, A. C., & Danzer, K. M. (2023) · Scientific Reports · doi:10.1038/s41598-023-38684-8 · Cited by 11
Quantification of modified nucleotides and nucleosides by isotope dilution mass spectrometry
Marchante-Gayón, J. M., Carcelén, J. N., Rodríguez, H. P., Pineda‐Cevallos, D., Sánchez, L. R., González‐Gago, A., Rodríguez‐González, P., & Alonso, J. I. G. (2023) · Mass Spectrometry Reviews · doi:10.1002/mas.21865 · Cited by 11
Polycomb recruitment at the Class II transactivator gene
Boyd, N., Morgan, J. E., & Greer, S. F. (2015) · Molecular Immunology · doi:10.1016/j.molimm.2015.08.003 · Cited by 11
“PTMs function to regulate chromatin dynamics by modifying histone-DNA interactions, altering higher order chromatin structure, and recruiting other chromatin factors [5].”
Background
Toward development of epigenetic drugs for central nervous system disorders: Modulating neuroplasticity via H3K4 methylation
Ricq, E. L., Hooker, J. M., & Haggarty, S. J. (2016) · Psychiatry and Clinical Neurosciences · doi:10.1111/pcn.12426 · Cited by 12
Skeletal Muscle Fiber Types in Neuromuscular Diseases
Glaser, J., & Suzuki, M. (2018) · InTech eBooks · doi:10.5772/intechopen.79474 · Cited by 11
“This carries heavy implications for training status and disease state in humans [3, 23, 24].”
Background
Genetic Engineering Applications to Improve Cellulase Production and Efficiency: Part I
Phillips, E. (2019) · Elsevier eBooks · doi:10.1016/b978-0-444-64223-3.00013-8 · Cited by 11
Natural Products Extracted from Fungal Species as New Potential Anti-Cancer Drugs: A Structure-Based Drug Repurposing Approach Targeting HDAC7
Maruca, A., Rocca, R., Catalano, R., Mesiti, F., Costa, G., Lanzillotta, D., Salatino, A., Ortuso, F., Trapasso, F., Alcaro, S., et al. (2020) · Molecules · doi:10.3390/molecules25235524 · Cited by 11
“Epigenetic alterations are reversible modifications on DNA or histones that affect gene expression without altering the DNA sequence, with an important role in gene regulation [1,2].”
Background
Does the Expression and Epigenetics of Genes Involved in Monogenic Forms of Parkinson’s Disease Influence Sporadic Forms?
Lanore, A., Lesage, S., Mariani, L., Menon, P. J., Ravassard, P., Cheval, H., Corti, O., Brice, A., & Corvol, J. (2022) · Genes · doi:10.3390/genes13030479 · Cited by 11
“The effect of histone modification is mediated either by directly affecting the structure of chromatin, by disrupting the binding of proteins that associate with chromatin or by attracting certain effector proteins to chromatin [5].”
Background
Epigenetics and reproductive isolation: a commentary on Westram et al., 2022
Planidin, N. P., de Carvalho, C. F., Feder, J. L., Gompert, Z., & Nosil, P. (2022) · Journal of Evolutionary Biology · doi:10.1111/jeb.14033 · Cited by 11
“These tags can alter processes such as DNA packaging and gene expression, by influencing the action of DNA interacting proteins such as histones and transcription factors (Gibney & Nolan, 2010).”
Background
The Future of Epigenetics: Emerging Technologies and Clinical Applications
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“4,6 Our analysis of epigenetic-related publications indicates that the early 2000s exhibited limited research output and represents the foundational era when epigenetics was being established as a field.”
Epigenetic Regulation of Key Enzymes CYP7a1 and HMGCR Affect Hepatic Cholesterol Metabolism in Different Breeds of Piglets
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“CpG island cytosine methylation located in promoter genes is associated with gene suppression (31, 32), while histone acetylation is related to the activation of transcription (20, 29, 30).”
Background
High-dimension to high-dimension screening for detecting genome-wide epigenetic and noncoding RNA regulators of gene expression
Ke, H., Ren, Z., Qi, J., Chen, S., Tseng, G. C., Ye, Z., & Ma, T. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac518 · Cited by 10
DNA methylation at the suppressor of cytokine signaling 3 (SOCS3) gene influences height in childhood
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“Environmental factors can in ﬂ uence a phenotype through their impact on epigenetic processes such as DNA methylation (DNAm) and histone modi ﬁ cations, both of which can in ﬂ uence gene expression 15 .”
Physical Exercise–Induced DNA Methylation in Disease-Related Genes in Healthy Adults—A Systematic Review With Bioinformatic Analysis
Vasileva, F., Hristovski, R., Font‐Lladó, R., Georgiev, G., Sacot, A., López‐Ros, V., Calleja-González, J., Barretina, J., López‐Bermejo, A., & Prats‐Puig, A. (2023) · The Journal of Strength and Conditioning Research · doi:10.1519/jsc.0000000000004686 · Cited by 11
“Methylation changes around the transcription start site (TSS) are highly influencing gene expression (7,29,31,63,74).”
BackgroundInfluential
Non‐canonical nitric oxide signalling and DNA methylation: Inflammation induced epigenetic alterations and potential drug targets
Switzer, C. (2023) · British Journal of Pharmacology · doi:10.1111/bph.16302 · Cited by 10
“While the regulation of a specific locus can be affected by many proximal and distal elements, the general effect of promoter CpG island methylation is gene silencing, while promoter CpG demethylation is associated with gene expression (Gibney & Nolan, 2010).”
Aerobic exercise alters DNA hydroxymethylation levels in an experimental rodent model of temporal lobe epilepsy
Jago, S. S., Bahabry, R., Schreiber, A. M., Homola, J., Ngyuen, T., Meijia, F., Allendorfer, J. B., & Lubin, F. D. (2023) · Epilepsy & Behavior Reports · doi:10.1016/j.ebr.2023.100642 · Cited by 10
Wonder symphony: epigenetics and the enchantment of the arts
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“Epigenetics is the study of heritable changes in gene expression that occur without altering the underlying DNA sequence [1].”
Background
Exploring the epigenome to identify biological links between the urban environment and neurodegenerative disease: an evidence review
Glover, S., Hill, C., McGuinness, B., McKnight, A. J., & Hunter, R. F. (2024) · Cities & Health · doi:10.1080/23748834.2024.2335707 · Cited by 14
“The epigenome helps regulate gene expression to enable required cellular functions and to help people respond to environmental stimuli (Gibney and Nolan 2010).”
Targeting the Wnt/β-catenin cascade in osteosarcoma: The potential of ncRNAs as biomarkers and therapeutics
Fuloria, S., Yadav, G., Menon, S. V., Ali, H., Pant, K., Kaur, M., Deorari, M., Sekar, M., Narain, K., Kumar, S., et al. (2024) · Pathology - Research and Practice · doi:10.1016/j.prp.2024.155346 · Cited by 11
Socioeconomic status as a potential mediator of arterial aging in marginalized ethnic and racial groups: current understandings and future directions
Darvish, S., Mahoney, S. A., Venkatasubramanian, R., Rossman, M. J., Clayton, Z. S., & Murray, K. O. (2024) · Journal of Applied Physiology · doi:10.1152/japplphysiol.00188.2024 · Cited by 11
Unraveling the molecular landscape of osteoarthritis: A comprehensive review focused on the role of non-coding RNAs
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Multi-omics profiling of DNA methylation and gene expression alterations in human cocaine use disorder
Zillich, E., Belschner, H., Avetyan, D., Andrade-Brito, D., Martínez‐Magaña, J. J., Frank, J., Mechawar, N., Turecki, G., Cabana‐Domínguez, J., Fernàndez‐Castillo, N., et al. (2024) · Translational Psychiatry · doi:10.1038/s41398-024-03139-9 · Cited by 12
The epigenetic impact of fatty acids as DNA methylation modulators
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Authors: Gibney, E. R., & Nolan, C. M.
Affiliations: University College Dublin (IE)
Corresponding author: Nolan, C M
ORCID: Gibney, E R
Nolan, C M
Venue: Heredity
Publisher: Springer Science and Business Media LLC
Published: 2010-05-12
Volume: 105
Issue: 1
Pages: 4-13
ISSN: 0018-067X (ISSN-L)
1365-2540
DOI: 10.1038/hdy.2010.54
OpenAlex: W1974450480
Cited by: 1,109
References: 119
Citations by year: 2026: 68 · 2025: 148 · 2024: 175 · 2023: 147 · 2022: 115 · 2021: 102 · 2020: 70 · 2019: 33 · 2018: 42 · 2017: 28 · 2016: 32 · 2015: 22 · 2014: 29 · 2013: 32 · 2012: 31
FWCI: 2.72
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Heredity (publishedVersion)
PubMed (publishedVersion)
Funders: Science Foundation Ireland (RFP06)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
Keywords: epigenetics, gene expression regulation, transcriptional regulation, DNA methylation, histone modifications, RNA-mediated gene regulation, cell differentiation, development (biology), translational regulation, protein modification
MeSH terms: Animals, Cell Differentiation, Humans, DNA Modification Methylases, Gene Expression, Cell Lineage, Heredity, Epigenesis, Genetic

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