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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Background
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Background
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Background
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“The transcriptional regulation of genes can be affected by many factors, such as DNA methylation, histone modifications, and availability of transcription factors (Gibney and Nolan 2010; van Breda et al. 2015).”
Background
The role of maternal DNA methylation in pregnancies complicated by gestational diabetes
Dias, S. C., Willmer, T., Adam, S., & Pheiffer, C. (2022) · Frontiers in Clinical Diabetes and Healthcare · doi:10.3389/fcdhc.2022.982665 · Cited by 17
Epigenetic modifications in radiation-induced non-targeted effects and their clinical significance
He, X., Cai, L., Tang, H., Chen, W., & Hu, W. (2023) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2023.130386 · Cited by 20
Neural crest cells and fetal alcohol spectrum disorders: Mechanisms and potential targets for prevention
Chen, S., & Maharajan, K. (2023) · Pharmacological Research · doi:10.1016/j.phrs.2023.106855 · Cited by 19
“cell development by acting as an epigenetic modulator— DNA methyltransferase (DNMT) and histone deacetylases (HDACs) are the essential enzymes involved in DNA methylation and histone deacetylation, respectively [102,56,84].”
Living in a noisy world—origins of gene expression noise and its impact on cellular decision‐making
Pal, S., & Dhar, R. (2024) · FEBS Letters · doi:10.1002/1873-3468.14898 · Cited by 18
“Another example of a major difference between prokaryotic and eukaryotic gene regulation is the existence of nucleosome binding and elaborate histone modiﬁcation patterns in eukaryotes [15].”
The Omics Revolution in Understanding Chicken Reproduction: A Comprehensive Review
Wadood, A. A., & Zhang, X. (2024) · Current Issues in Molecular Biology · doi:10.3390/cimb46060373 · Cited by 17
“Epigenomics is the field of study that specifically examines the modifications in gene expression that are not a result of changes in the DNA sequence [126].”
Background
Increased Age Is Associated With Epigenetic and Structural Changes in Chromatin From Neuronal Nuclei
Rodrigues, H. F., de Souza, T. A., Ghiraldini, F. G., Mello, M. L. S., & Moraes, A. D. S. (2013) · Journal of Cellular Biochemistry · doi:10.1002/jcb.24705 · Cited by 17
Microsatellite instability and promoter hypermethylation of MLH1 and MSH2 in patients with sporadic colorectal cancer.
Vlaykova, T. I., Mitkova, A. V., Stancheva, G. S., Kadiyska, T., Gulubova, M. V., Yovchev, Y., Cirovski, G., Chilingirov, P., Damyanov, D., Kremensky, I. M., et al. (2011) · PubMed · Cited by 17
Long Noncoding RNA H19 Participates in the Regulation of Adipose-Derived Stem Cells Cartilage Differentiation
Pang, H., Zhao, Q., Ma, Y., Song, Y., Min, J., Lu, J., Li, H., & Zhao, D.-Q. (2019) · Stem Cells International · doi:10.1155/2019/2139814 · Cited by 17
“transcriptional, and posttranslational [50, 51].”
Daurinol Attenuates Autoimmune Arthritis via Stabilization of Nrp1–PTEN–Foxp3 Signaling in Regulatory T Cells
Park, M.-J., Moon, S., Lee, E., Kim, E., Baek, J.-A., Kim, S. Y., Jung, K. A., Lee, S., Choi, J. W., Kim, D.-S., et al. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01526 · Cited by 17
“Epigenetic changes including DNA methylation affect cell differentiation and lineage stabilization at the level of transcription (49, 50).”
Background
Transcriptomics- and metabolomics-based integration analyses revealed the potential pharmacological effects and functional pattern of in vivo Radix Paeoniae Alba administration
Wang, S., Chen, H., Zheng, Y., Li, Z., Cui, B., Zhao, P., Zheng, J., Lü, R., & Sun, N. (2020) · Chinese Medicine · doi:10.1186/s13020-020-00330-0 · Cited by 17
“Although the mapping relationship between the metabolome and transcriptome is not direct in the information transmission sequence of the central principle [9], with increasing examples of their combined application, the analytical methods have become increasingly mature and reasonable.”
Background
Environmental enrichment during early rearing provokes epigenetic changes in the brain of a salmonid fish
Reiser, S., Pohlmann, D. M., Blancke, T., Koops, U., & Trautner, J. (2021) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2021.100838 · Cited by 17
Animal Foetal Models of Obesity and Diabetes – From Laboratory to Clinical Settings
Grzęda, E., Matuszewska, J., Ziarniak, K., Gertig-Kolasa, A., Krzyśko-Pieczka, I., Skowrońska, B., & Sliwowska, J. H. (2022) · Frontiers in Endocrinology · doi:10.3389/fendo.2022.785674 · Cited by 19
Saffron, Its Active Components, and Their Association with DNA and Histone Modification: A Narrative Review of Current Knowledge
Rashid, M., Brim, H., & Ashktorab, H. (2022) · Nutrients · doi:10.3390/nu14163317 · Cited by 20
Evaluation of DNA methylation profiles of the CpG island of the ABCB1 gene in dogs with lymphoma
Tomiyasu, H., Fujiwara‐Igarashi, A., Goto‐Koshino, Y., Fujino, Y., Ohno, K., & Tsujimoto, H. (2014) · American Journal of Veterinary Research · doi:10.2460/ajvr.75.9.835 · Cited by 17
“10 Among these mechanisms, DNA methylation in the CpG island is associated with silencing gene expression.”
Background
Hepatitis B virus basal core promoter mutations show lower replication fitness associated with cccDNA acetylation status
Koumbi, L., Pollicino, T., Raimondo, G., Stampoulis, D., Khakoo, S. I., & Karayiannis, P. (2016) · Virus Research · doi:10.1016/j.virusres.2016.04.022 · Cited by 17
Mice lacking uterine enhancer of zeste homolog 2 have transcriptomic changes associated with uterine epithelial proliferation
Mesa, A. M., Mao, J., Nanjappa, M. K., Medrano, T. I., Tevosian, S. G., Yu, F., Kinkade, J. A., Lyu, Z., Liu, Y., Joshi, T., et al. (2019) · Physiological Genomics · doi:10.1152/physiolgenomics.00098.2019 · Cited by 17
“This phosphorylation occurs during mitosis by cyclindependent kinases, which facilitate PRC2 interaction with noncoding RNAs, enabling recruitment to target genes (27).”
Background
Biomarkers of post-traumatic stress disorder from emotional trauma: A systematic review
Paganin, W., & Signorini, S. (2023) · European Journal of Trauma & Dissociation · doi:10.1016/j.ejtd.2023.100328 · Cited by 16
Endothelial-to-Mesenchymal Transition in Health and Disease: Molecular Insights and Therapeutic Implications
Kim, R., & Chang, W. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms262311724 · Cited by 21
“Epigenetics refers to the heritable changes in gene expression without alterations in the DNA sequence, primarily via DNA methylation, histone modifications, and noncoding RNA-mediated regulation [71].”
Early life adversity across different cell- types in the brain
Warhaftig, G., Almeida, D. M., & Turecki, G. (2023) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2023.105113 · Cited by 20
DNA methylation abnormalities induced by advanced maternal age in villi prime a high-risk state for spontaneous abortion
Qin, M. H., Chen, W., Hua, L., Meng, Y., Wang, J., Li, H., Yang, R., Yan, L., & Qiao, J. (2023) · Clinical Epigenetics · doi:10.1186/s13148-023-01432-w · Cited by 19
“Epigenomes play important roles in regulating gene expression [16].”
Background
Unraveling the Epigenetic Tapestry: Decoding the Impact of Epigenetic Modifications in Hidradenitis Suppurativa Pathogenesis
Nardacchione, E. M., Tricarico, P. M., de Moura, R. R., D’Adamo, P., Thasneem, A., Suleman, M., Marzano, A. V., Crovella, S., & Moltrasio, C. (2023) · Genes · doi:10.3390/genes15010038 · Cited by 16
Identification of crosstalk genes and immune characteristics between Alzheimer’s disease and atherosclerosis
An, W., Zhou, J., Qiu, Z., Wang, P., Han, X., Cheng, Y., He, Z., An, Y., & Li, S. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1443464 · Cited by 18
“By studying gene expression, we can discern which genes are activated or suppressed under certain conditions, thus unveiling the biochemical reactions and signal transduction processes within cells (24).”
Background
Multiplexed In Situ Imaging of Site-Specific m6A Methylation with Proximity Hybridization Followed by Primer Exchange Amplification (m6A-PHPEA)
Song, M., Wang, J., Hou, J., Fu, T., Feng, Y., Lv, W., Ge, F., Peng, R., Han, D., & Tan, W. (2024) · ACS Nano · doi:10.1021/acsnano.4c08407 · Cited by 16
Plasmodium blood stage development requires the chromatin remodeller Snf2L
Watzlowik, M. T., Silberhorn, E., Das, S., Singhal, R., Venugopal, K., Holzinger, S., Stokes, B. H., Schadt, E. E., Sollelis, L., Bonnell, V. A., et al. (2025) · Nature · doi:10.1038/s41586-025-08595-x · Cited by 15
Activity Comparison of Epigenetic Modulators against the Hemoprotozoan Parasites Babesia divergens and Plasmodium falciparum
Vanheer, L. N., & Kafsack, B. F. C. (2021) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.0c00853 · Cited by 16
Potential Serum Biomarkers for Postoperative Neurocognitive Disorders Based on Proteomic Analysis of Cognitive-Related Brain Regions
Li, Y., Chen, L., Li, Z., Song, Y., Yuan, Y., Liu, T., Hong, J., Wang, Q., Chang, H., Kuang, Z., et al. (2021) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2021.741263 · Cited by 16
“From this process, genetic information from the archival copy of DNA to the short-lived mRNA, and ultimately to specific proteins (Gibney and Nolan, 2010).”
Background
Molecular and Phenotypic Effects of Early Exposure to an Environmentally Relevant Pesticide Mixture in the Pacific Oyster, Crassostrea Gigas
Dourdin, T. S., Rivière, G., Cormier, A., Poi, C. D., Guyomard, K., Rabiller, M., Akcha, F., Sadialiou, T. B., Monier, P. L., & Sussarellu, R. (2023) · Environmental Pollution · doi:10.1016/j.envpol.2023.121472 · Cited by 16
“It is essential for the regulation of gene expression [34] and is implicated in phenotypic plasticity, adaptation and non-genetic inheritance [35].”
UHRF2 mRNA Expression is Low in Malignant Glioma but Silencing Inhibits the Growth of U251 Glioma Cells in vitro
Wu, T., Zhang, W., Su, Z., Chen, S., Chen, G., Wei, Y., Sun, T., Xie, X., Li, B., Zhou, Y.-X., et al. (2012) · Asian Pacific Journal of Cancer Prevention · doi:10.7314/apjcp.2012.13.10.5137 · Cited by 16
A G-Quadruplex Structure in the Promoter Region of CLIC4 Functions as a Regulatory Element for Gene Expression
Huang, M.-C., Chu, I.-T., Wang, Z., Lin, S., Chang, T., & Chen, C. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19092678 · Cited by 16
“The regulation of gene expression includes multiple mechanisms such as transcription factor binding [8] and epigenetic modification, which involves DNA methylation, histone modification, and microRNA interaction [9].”
Background
The epigenetic landscape of rheumatoid arthritis: Pathogenesis and drug therapeutic potentials
Huang, C., Liang, Y., Li, Y., Quan, W., Ouyang, L., & Zhang, J. (2025) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2025.08.022 · Cited by 20
“The corresponding epigenetic proteins have been identified as ‘writers’ or ‘erasers’ that modify DNA and histones by adding or removing specific functional groups, thereby modulating gene expression 51,52 .”
Gene regulatory networks: from correlative models to causal explanations
Maizels, R. J., & Briscoe, J. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00939-1 · Cited by 21
“The role of other forms of regulation, such as histone modifications, DNA methylation and non-coding RNAs, also seems to display context-dependent function 141 .”
Influence of antidepressant treatment on SLC6A4 methylation in Korean patients with major depression
Moon, Y. K., Kim, H. S., Kim, S., Lim, S., & Kim, D. K. (2022) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32921 · Cited by 17
“These results suggest the possible involvement of other epigenetic mechanisms, such as histone modification and RNA-based mechanisms, in gene expression (Gibney & Nolan, 2010).”
Background
Genome-wide analysis of bromodomain gene family in Arabidopsis and rice
Abiraami, T. V., Sanyal, R. P., Misra, H. S., & Saini, A. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1120012 · Cited by 15
“The transcription status of genes is influenced by both genetic and epigenetic components (Singh, 1998), and unlike the geneticelements (core promoter, cis-elements, enhancers, silencers), the epigenetic controls involve nonsequence-based modifications to alter the expression of genes (Gibney and Nolan, 2010; Lämke an…”
Cardiomyocyte Ploidy, Metabolic Reprogramming and Heart Repair
Elia, A., Mohsin, S., & Khan, M. (2023) · Cells · doi:10.3390/cells12121571 · Cited by 15
“Notably, epigenetic modifications significantly impact gene expression and DNA binding proteins [95].”
Background
N6-Methyladenosine mRNA Modification: From Modification Site Selectivity to Neurological Functions
Zhang, Z., & Wang, X. (2023) · Accounts of Chemical Research · doi:10.1021/acs.accounts.3c00440 · Cited by 15
Mdivi-1: Effective but complex mitochondrial fission inhibitor
Ahn, S. I., Choi, S. K., Kim, M. J., Wie, J., & You, J. S. (2024) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2024.149886 · Cited by 16
Neuronal-specific methylome and hydroxymethylome analysis reveal significant loci associated with alcohol use disorder
Andrade-Brito, D., Núñez-Ríos, D. L., Martínez‐Magaña, J. J., Nagamatsu, S. T., Rompala, G. R., Zillich, L., Witt, S. H., Clark, S. L., Lattig, M. C., PGC SUD Epigenetics Working Group, et al. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1345410 · Cited by 15
“The 5mC mechanism involves the addition of a methyl group to the carbon 5 position of the nucleotide, which is catalyzed by DNA methyltransferases (DNMTs) (Gibney and Nolan, 2010).”
Background
Histone modifications affecting plant dormancy and dormancy release: common regulatory effects on hormone metabolism
Sato, H., & Yamane, H. (2024) · Journal of Experimental Botany · doi:10.1093/jxb/erae205 · Cited by 15
Epigenetics in Glaucoma
D’Esposito, F., Gagliano, C., Bloom, P., Cordeiro, M. F., Avitabile, A., Gagliano, G., Costagliola, C., Avitabile, T., Musa, M., & Zeppieri, M. (2024) · Medicina · doi:10.3390/medicina60060905 · Cited by 15

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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