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Epigenetics and gene expression
Open accessAbstract
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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“There are three main types of epigenetic modifications: DNA methylation, histone modifications, and various RNA-mediated processes (39, 40).”
From Epigenetic Modifications in Stress Response Genes Associated With Childhood Trauma (2019) · cites this paper as [40]
In the citing paper
“As these modifications accumulate and interact with one-another to produce tightly regulated changes in gene expression, it is not sufficient to only study differences in single DNA methylation loci.9”
From The role of epigenetics in psychological resilience (2021) · cites this paper as [9]
In the citing paper
“As these modifications accumulate and interact with one-another to produce tightly regulated changes in gene expression, it is not sufficient to only study differences in single DNA methylation loci.9”
From The role of epigenetics in psychological resilience (2021) · cites this paper as [9]
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Research works printed but not linked: 2
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“In addition to the direct modification of DNA and DNA bound histones, gene expression is also regulated epigenetically at the transcript level (Gibney and Nolan, 2010).”
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“Epigenetic modi fi cations generally include DNA methylation and histone modi fi cations (methylation, acetylation, lactylation, etc.) (Figure 2), which regulate gene expression at the transcriptional level [15,16].”
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“DNMTI maintains methylation patterns during DNA replication [50,51], while DNMT3TA and DNMT3B establish de novo methylation patterns [52].”
The Plant Circadian Clock and Chromatin Modifications
Yang, P., Wang, J., Hung, F., Yang, S., & Wu, K. (2018) · Genes · doi:10.3390/genes9110561 · Cited by 10
“Multiple chemical and reversible modifications of DNA and histones, such as DNA methylation, histone acetylation, and histone methylation regulate chromatin activity and function [54,55].”
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“DNA methylation is one of the major epigenetic mechanisms that protect the stability of the genome in the cell [12], including regulation of gene expression [13] and chromatin structure [14].”
BackgroundPlasma MicroRNA Signature of Alcohol Consumption: The Rotterdam Study
Karabegović, I., Abozaid, Y. J., Maas, S. C. E., Labrecque, J. A., Bos, D., de Knegt, R. J., Ikram, M. A., Voortman, T., & Ghanbari, M. (2022) · Journal of Nutrition · doi:10.1093/jn/nxac216 · Cited by 10
“modifications, and RNA-mediated regulation by noncoding RNAs (20, 24).”
BackgroundAsh2l, an obligatory component of H3K4 methylation complexes, regulates neural crest development
Mohammadparast, S., & Chang, C. (2022) · Developmental Biology · doi:10.1016/j.ydbio.2022.09.008 · Cited by 9
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“The major epigenetic mechanisms include DNA methylation, histone protein posttranslational modifications, noncoding RNA regulation, and RNA editing [10].”
BackgroundGene expression and epigenetic markers of prion diseases
Viré, E. A., & Mead, S. (2022) · Cell and Tissue Research · doi:10.1007/s00441-022-03603-2 · Cited by 10
“Many definitions of epigenetics have been proposed since the term was first coined by Waddington in 1942 (Bird 2007) and not all necessarily encompass the requirement for maintenance through generations (Gibney and Nolan 2010).”
Alahmari, B., Cooper, M. L., Ziga, E. D., Ritchey, J., DiPersio, J. F., & Choi, J. (2018) · PLoS ONE · doi:10.1371/journal.pone.0207609 · Cited by 10
DNA methylation in the placenta and in cancerwith special reference to folate transporting genes
Farkas, S. A. (2014) · KTH Publication Database DiVA (KTH Royal Institute of Technology) · Cited by 10
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“20,21 29 These epigenetic alterations are typically classified into three categories, namely DNA methylation, histone modifications, and RNA-based epigenetic regulation, 21 which will be briefly introduced below.”
BackgroundLinowiecka, K., Guz, J., Dziaman, T., Urbanowska–Domańska, O., Zarakowska, E., Szpila, A., Szpotan, J., Skalska-Bugała, A., Mijewski, P., Siomek, A., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-56326-5 · Cited by 9
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Glucocorticoid receptor epigenetic activity in the heart
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Cell type-specific multi-omics analysis of cocaine use disorder in the human caudate nucleus
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InfluentialPhthalates and epigenetics: An emerging public health concern
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“Epigenetic changes such as DNA methylation, noncoding RNAs, and histone modifications are critical for controlling gene expression in prokaryotes and eukaryotic organisms (Adiga et al., 2023; Adiga et al., 2024; Gibney and Nolan, 2010).”
Phytic acid (InsP6) activates HDAC3 epigenetic axis to maintain intestinal barrier function
Chatterjee, S., Sin, Z., Tran, N., Preval, L. V., Shukla, A., Tran, T., Koshkaryan, G., Ritter, K., Su, X. B., Ragsac, S. J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-68994-0 · Cited by 8
A transcription-centric model of SNP-age interaction
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Vogt, G. (2022) · Current Zoology · doi:10.1093/cz/zoac094 · Cited by 15
“If genetic diversity is not sufficient to explain the phenotypic diversity and environmental acclimatization in marbled crayfish, what else could be the underlying mechanism? A promising candidate is epigenetic diversity, because epigenetic mechanism like DNA methylation, histone modifications, and noncoding RNAs can…”
BackgroundThe epigenetic regulator BRD4 is required for myofibroblast differentiation of knee fibroblasts
Dudakovic, A., Bayram, B., Bettencourt, J. W., Limberg, A. K., Galvan, M. L., Carrasco, M. E., Stans, B., Thaler, R., Morrey, M. E., Sánchez‐Sotelo, J., et al. (2023) · Journal of Cellular Biochemistry · doi:10.1002/jcb.30368 · Cited by 9
DNA methylation dynamics in a coastal foundation seagrass species under abiotic stressors
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Epigenetic Regulation of MAP3K8 in EBV-Associated Gastric Carcinoma
Roy, G., Yang, T., Liu, S., Luo, Y., Liu, Y.-T., & Zhong, Q. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24031964 · Cited by 9
“Epigenetic processes, such as DNA methylation, histone modification, and various RNA-mediated processes have been reported to influence gene expression predominantly at the transcription levels; however, other steps in the process may also be regulated epigenetically [54].”
BackgroundThe epigenetic legacy of ICU feeding and its consequences
Vanhorebeek, I., & den Berghe, G. V. (2023) · Current Opinion in Critical Care · doi:10.1097/mcc.0000000000001021 · Cited by 10
“Epigenetic mechanisms lead to functionally relevant changes in gene-expression without altering the genetic code [57].”
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“Gene expression is the phenotypic, or outward, manifestation resulting from the sequential processes of transcription and translation and is regulated by epigenetic modifications (5,30).”
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“The PTMs are regulated by a group of enzymes including but not limited to histone acetyltransferases (HATs), histone deacetyltransferases (HDACs), histone methyltransferases (HMTs) and histone kinases (Gibney and Nolan 2010).”
BackgroundEpigenetic Studies in the Male APP/BIN1/COPS5 Triple-Transgenic Mouse Model of Alzheimer’s Disease
Martínez-Iglesias, O. A., Naidoo, V., Carrera, I., & Cacabelos, R. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23052446 · Cited by 10
“Classic epigenetic mechanisms include DNA methylation, chromatin remodeling/histone modifications, and micro RNA (miRNA) regulation [19–21], and affect gene expression patterns [22].”
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Epigenetics and Phenotypic Plasticity in Animals
Vogt, G. (2022) · Springer eBooks · doi:10.1007/978-3-031-13771-6_3 · Cited by 9
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“Additionally, further studies are needed to define ethnic and racial differences [2, 21, 32].”
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Molekulare Mechanismen der Anpassungsfähigkeit der Skelettmuskulatur
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Epigenetics Connects the Genome to Its Environment
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Halblander, F. N., Meng, F. W., & Murphy, P. J. (2023) · Developmental Biology · doi:10.1016/j.ydbio.2023.12.010 · Cited by 10
Manav, N., Jit, B. P., Kataria, B., & Sharma, A. K. (2024) · Epigenomics · doi:10.1080/17501911.2024.2351788 · Cited by 9
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“Firstly, unlike genomic data, the epigenome is inherently specific to cell type and will vary significantly across tissues sampled from the same organism (Gibney and Nolan 2010).”
Pagano, L., Lagrotteria, D., Facconi, A., Saraceno, C., Longobardi, A., Bellini, S., Ingannato, A., Bagnoli, S., Ducci, T., Mingrino, A., et al. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26094198 · Cited by 9
“These modifications can influence how genes are turned on or off and are crucial for various biological processes, including development, differentiation, and diseases [1–3].”
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“Epigenetic modifications were a plausible mediator of critical period closure because they are relatively stable, regulated by experience, and coordinate transcription of sets of genes (Allis and Jenuwein, 2016; Gibney and Nolan, 2010).”
BackgroundMinor DNA methylation changes are observed in spermatozoa prepared using different protocols
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“DNA methylation is one of the main epigenetic mechanisms governing gene regulation (Gibney & Nolan, 2010).”
Backgroundrafiey, M., Nosrati, R., & Babaei, P. (2022) · Neuroscience Letters · doi:10.1016/j.neulet.2022.136881 · Cited by 8
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“Considerable evidence suggests that epigenetic modifications exert a central role in the cellular programming of gene expression [12].”
BackgroundYu, H., Song, W., Chen, X., Zhao, Q., & Du, X. (2023) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2023.114578 · Cited by 8
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“On the other hand, HDACs deacetylate histones and generally inhibit gene transcription (Gibney and Nolan 2010).”
BackgroundSposito, F., Pennington, S. H., David, C. A. W., Duggan, J., Northey, S. J., Biagini, G. A., Liptrott, N. J., Charras, A., McNamara, P. S., & Hedrich, C. M. (2023) · Mucosal Immunology · doi:10.1016/j.mucimm.2023.08.002 · Cited by 8
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“Years of genetic and genomic studies of susceptibility to ALI/ARDS led to the conclusion that gene expression is controlled not only by modification(s) of the gene but also by the interaction of the gene with the environment(213) and by epigenetic mechanisms.(214) Both ALI and ARDS are the result of a complex interpla…”
BackgroundThe Role of Epigenetic Changes in Benzene- Induced Acute Myeloid Leukaemia
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DNA methylation patterns of the S100A14, POU2F3 and SFN genes in equine sarcoid tissues
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“They may or may not be inherited and cause stable cellular alterations without changing the DNA sequence, thereby influencing the transcriptional potential of cells [1,2].”
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“If a transcription factor regulates its target gene differently across distinct cells, it could be because of differences in the epigenetic modi fi cations in the promoter region of the target gene (Gibney and Nolan, 2010).”
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“46 In particular, while low promoter methylation is usually associated with decreased gene expression, the relationship can also be inverted, especially in the gene body, where the effects of DNA methylation are less understood.”
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“Generally, DNA methylation represses gene transcription, while histone acetylation promotes gene transcription [6].”
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Molecular and clinical aspects of histone-related disorders
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“Epigenetic gene expression regulation is controlled by an intricate system that revolves around the interaction between DNA and histone proteins within the chromatin structure [1].”
Metadata
- Authors
- Gibney, E. R., & Nolan, C. M.
- Affiliations
- University College Dublin (IE)
- Corresponding author
- Nolan, C M
- Venue
- Heredity
- Published
- 2010-05-12
- Volume
- 105
- Issue
- 1
- Pages
- 4-13
- ISSN
- 0018-067X (ISSN-L)
- 1365-2540
- 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
- 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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