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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Guo, Z., Lü, J., Li, J., Wang, P., Li, Z., Yao, Z., Guo, K., Wang, J., Ye, J., & Liu, P. (2018) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2018.05.009 · Cited by 44
DNA methylation in promoter regions of genes involved in the reproductive and metabolic function of children born to women with PCOS
Echiburú, B., Milagro, F. I., Crisosto, N., Pérez‐Bravo, F., Flores, C., Arpón, A., Salas‐Pérez, F., Recabarren, S. E., Sir‐Petermann, T., & Maliqueo, M. A. (2020) · Epigenetics · doi:10.1080/15592294.2020.1754674 · Cited by 43
A Comparison of Immune Responses Exerted Following Syngeneic, Allogeneic, and Xenogeneic Transplantation of Mesenchymal Stem Cells into the Mouse Brain
Hwang, J. W., Lee, N. K., Yang, J. H., Son, H. J., Bang, S. I., Chang, J. W., & Na, D. L. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21093052 · Cited by 43
“Epigenetics involves the modification of gene expression without altering the DNA sequence [53,54].”
Background
Non-alcoholic Steatohepatitis Pathogenesis, Diagnosis, and Treatment
Zhu, B., Chan, S., Li, J., Li, K. S., Wu, H., Cui, K., & Chen, H. (2021) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2021.742382 · Cited by 47
Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders
Loh, D., & Reiter, R. J. (2021) · Antioxidants · doi:10.3390/antiox10091483 · Cited by 45
Learning the Regulatory Code of Gene Expression
Zrimec, J., Buric, F., Kokina, M., García, V., & Zelezniak, A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.673363 · Cited by 45
“…positioning, other epigenetic mechanisms (where functionally relevant changes to the genome do not involve a change in the nucleotide sequence), such as histone modi ﬁ cation and DNA methylation, also play a vital part in transcriptional regulation (Gibney and Nolan, 2010; Miller and Grant, 2013).”
Background
Variation of global DNA methylation levels with age and in autistic children
Tsang, S., Ahmad, T., Mat, F. W. K., Zhao, C., Xiao, S., Xia, K., & Xue, H. (2016) · Human Genomics · doi:10.1186/s40246-016-0086-y · Cited by 41
“DNA methylation is the most common epigenetic modification that plays an essential role in the regulation of tissue-specific gene expression, cellular differentiation, chromosome stabilization, genomic imprinting, and suppression of transposable element mobility [1, 2].”
Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies
Khunsriraksakul, C., McGuire, D., Sauteraud, R., Chen, F., Yang, L., Wang, L., Hughey, J. M., Eckert, S., Weissenkampen, J. D., Shenoy, G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30956-7 · Cited by 40
Sex-specific DNA methylation: impact on human health and development
Govender, P., Ghai, M., & Okpeku, M. (2022) · Molecular Genetics and Genomics · doi:10.1007/s00438-022-01935-w · Cited by 45
“He argued that initial differences between males and females, which are not specific to any particular taxa are determined by differential methylation in nuclear DNA between sexes (Gorelick 2003), prompting Muller’s rachet (Piferrer 2021).”
Background
Endothelial-to-mesenchymal transition: An underappreciated mediator of diabetic complications
Wang, E., Wang, H., & Chakrabarti, S. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1050540 · Cited by 44
Specific Association of Teratogen and Toxicant Metals in Hair of Newborns with Congenital Birth Defects or Developmentally Premature Birth in a Cohort of Couples with Documented Parental Exposure to Military Attacks: Observational Study at Al Shifa Hospital, Gaza, Palestine
Manduca, P., Naim, A., & Signoriello, S. (2014) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph110505208 · Cited by 41
“Epigenetic changes [3–9] are a landmark during embryonic development and germ cells determination.”
Background
The Multifaceted Neurotoxicity of Astrocytes in Ageing and Age-Related Neurodegenerative Diseases: A Translational Perspective
Bouvier, D. S., Fixemer, S., Heurtaux, T., Jeannelle, F., Frauenknecht, K. B. M., & Mittelbronn, M. G. A. (2022) · Frontiers in Physiology · doi:10.3389/fphys.2022.814889 · Cited by 43
“It encompasses several distinct modifications of the DNA that impact transcriptional activity while leaving the nucleotide sequence unchanged (Gibney and Nolan, 2010).”
Background
Comparative Analysis of Multi-Omics Integration Using Graph Neural Networks for Cancer Classification
Alharbi, F., Vakanski, A., Zhang, B., Elbashir, M. K., & Mohammed, M. (2025) · IEEE Access · doi:10.1109/access.2025.3540769 · Cited by 40
“…is a fundamental cellular process that governs the translation of genetic information encoded in DNA into functional proteins, which in turn define a The associate editor coordinating the review of this manuscript and approving it for publication was Wei Ni. cell’s functionality and phenotype [1].”
Environmental Xenobiotics and Epigenetic Modifications: Implications for Human Health and Disease
Sobral, A. F., Cunha, A., Costa, I. D., Silva‐Carvalho, M., Silva, R. V. D. S., & Barbosa, D. J. (2025) · Journal of Xenobiotics · doi:10.3390/jox15040118 · Cited by 48
“Epigenetics is the study of heritable but reversible modifications in gene activity that do not involve changes in the deoxyribonucleic acid (DNA) sequence, but are essential for proper cellular function [11].”
DNA Methylation in the Neuropeptide S Receptor 1 (NPSR1) Promoter in Relation to Asthma and Environmental Factors
Reinius, L. E., Gref, A., Sääf, A. M., Acevedo, N., Joerink, M., Kupczyk, M., D’Amato, M., Bergström, A., Melén, E., Scheynius, A., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053877 · Cited by 42
“Methylation of DNA has previously been shown to regulate gene expression [2] and it is believed that the occurrence of these marks/modifications can be affected by the environment and that this could partly explain the increase in the prevalence of asthma and allergy [3].”
Background
Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics
Krajewski, W. A., Li, J., & Dou, Y. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky526 · Cited by 40
The molecular mechanisms and therapeutic potential of EZH2 in breast cancer
Adibfar, S., Elveny, M., Kashikova, H. S., Mikhailova, M. V., Farhangnia, P., Vakili‐Samiani, S., Tarokhian, H., & Jadidi‐Niaragh, F. (2021) · Life Sciences · doi:10.1016/j.lfs.2021.120047 · Cited by 41
Overexpression of Cancer-Associated Genes via Epigenetic Derepression Mechanisms in Gynecologic Cancer
Jeong, H. M., Kwon, M. J., & Shin, Y. K. (2014) · Frontiers in Oncology · doi:10.3389/fonc.2014.00012 · Cited by 40
Epigenetic enzymes influenced by oxidative stress and hypoxia mimetic in osteoblasts are differentially expressed in patients with osteoporosis and osteoarthritis
Vrtačnik, P., Zupan, J., Mlakar, V., Kranjc, T., Marc, J., Kern, B., & Ostanek, B. (2018) · Scientific Reports · doi:10.1038/s41598-018-34255-4 · Cited by 39
Connecting the dots: investigating the link between environmental, genetic, and epigenetic influences in metabolomic alterations in oral squamous cell carcinoma
Gupta, I., Badrzadeh, F., Tsentalovich, Y. P., & Gaykalova, D. A. (2024) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-024-03141-5 · Cited by 41
“Oncogene-induced metabolic reprogramming influences the epigenetic landscape by modulating the activity of enzymes involved in DNA and histone modifications [236].”
Influential
Epigenetic landscape and miRNA involvement during neural crest development
Strobl‐Mazzulla, P. H., Marini, M., & Buzzi, A. L. (2012) · Developmental Dynamics · doi:10.1002/dvdy.23868 · Cited by 39
An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver
Xie, L., Weichel, B., Ohm, J. E., & Zhang, K. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-s3-s4 · Cited by 38
“DNA methylation of cytosine at position C5 in CpG dinucleotides is reported to influence specific gene expression, especially to suppress gene expression [1].”
Background
DNA methylation and histone modifications induced by abiotic stressors in plants
Czajka, K. M., Mehes-Smith, M., & Nkongolo, K. K. C. (2021) · Genes & Genomics · doi:10.1007/s13258-021-01191-z · Cited by 40
“Overall, DNA methylation is essential for maintaining stable and unique gene expression patterns in differentiated cell types (Gibney and Nolan 2010; Moore et al. 2013).”
BackgroundInfluential
A glucose–target of rapamycin signaling axis integrates environmental history of heat stress through maintenance of transcription-associated epigenetic memory in Arabidopsis
Sharma, M., Sharma, M., Muhammed Jamsheer, K., & Laxmi, A. (2022) · Journal of Experimental Botany · doi:10.1093/jxb/erac338 · Cited by 39
DNA methylation drives a new path in gastric cancer early detection: Current impact and prospects
Wang, X., Dong, Y., Zhang, H., Zhao, Y., Miao, T., Mohseni, G., Du, L., & Wang, C. (2023) · Genes & Diseases · doi:10.1016/j.gendis.2023.02.038 · Cited by 39
“DNA methylation can alter gene expression without changing the gene sequence, leading to changes in DNA conformation, chromatin structure, and DNA stability, which control gene expression.(8,9) Typically, most CGI-containing gene promoter regions are unmethylated.”
Background
Histone Deacetylase Inhibitor Trichostatin a Promotes the Apoptosis of Osteosarcoma Cells through p53 Signaling Pathway Activation
Deng, Z., Liu, X., Jin, J., Xu, H., Gao, Q., Wang, Y., & Zhao, J. (2016) · International Journal of Biological Sciences · doi:10.7150/ijbs.16569 · Cited by 40
“Mammalian HDACs are classified into four classes, including class I HDACs (HDACs 1, 2, 3 and 8), class II HDACs (HDACs 4 to 7,9 and 10), class III HDACs (Sirtuin 1-7) and class IV HDAC (HDAC11) [14].”
Background
A universal framework for single-cell multi-omics data integration with graph convolutional networks
Gao, H., Zhang, B., Liu, L., Li, S., Gao, X., & Yu, B. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad081 · Cited by 38
“CITE-seq enables the detection of surface proteins and transcriptome profiling simultaneously in each single cell, which provide association between RNA expression pattern and different surface proteins [57, 58].”
Background
Particulate matter-induced epigenetic modifications and lung complications
Afthab, M., Hambo, S., Kim, H. J., Alhamad, A., & Harb, H. (2024) · European Respiratory Review · doi:10.1183/16000617.0129-2024 · Cited by 41
Epigenetic regulation of hypoxia inducible factor in diseases and therapeutics
Nguyen, M. P., Lee, S., & Lee, Y. M. (2013) · Archives of Pharmacal Research · doi:10.1007/s12272-013-0058-x · Cited by 37
Epigenetic Mechanisms in Hirschsprung Disease
Torroglosa, A., Villalba‐Benito, L., Luzón‐Toro, B., Fernández, R. M., Antiñolo, G., & Borrego, S. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20133123 · Cited by 41
“Each nucleosome consists of four duplicated units of histones (H2A, H2B, H3 and H4), resulting in a structure formed by the combination of eight histones (nucleosome core) around which DNA rolls up with unstructured tails [38].”
Background
Anesthesia and cancer recurrence: an overview
Brogi, E., & Forfori, F. (2022) · Journal of Anesthesia Analgesia and Critical Care · doi:10.1186/s44158-022-00060-9 · Cited by 37
“Finally, another important aspect is represented by the possible correlation between stress response and expression of specific genes or molecular pathways with the consequent changes in the cell signaling [26, 55, 56].”
Background
Epigenetics as a Therapeutic Target in Osteoarthritis
Núñez-Carro, C., Blanco-Blanco, M., Villagrán-Andrade, K. M., Blanco, F., & de Andrés, M. D. (2023) · Pharmaceuticals · doi:10.3390/ph16020156 · Cited by 38
Unlocking plant resilience: Advanced epigenetic strategies against heavy metal and metalloid stress
Iqbal, B., Ahmad, N., Li, G., Jalal, A., Khan, A. R., Zheng, X., Naeem, M. S., & Du, D. (2024) · Plant Science · doi:10.1016/j.plantsci.2024.112265 · Cited by 37
IL‐10 expression in macrophages from neonates born from obese mothers is suppressed by IL‐4 and LPS/INFγ
Cifuentes‐Zúñiga, F., Arroyo‐Jousse, V., Soto‐Carrasco, G., Casanello, P. C., Uauy, R. D., Krause, B. J., & Castro-Rodríguez, J. A. (2017) · Journal of Cellular Physiology · doi:10.1002/jcp.25845 · Cited by 36
Differential methylation and expression of genes in the hypoxia-inducible factor 1 signaling pathway are associated with paclitaxel-induced peripheral neuropathy in breast cancer survivors and with preclinical models of chemotherapy-induced neuropathic pain
Kober, K. M., Lee, M.-C., Olshen, A. B., Conley, Y. P., Sirota, M., Keiser, M. J., Hammer, M. J., Abrams, G., Schumacher, M. A., Levine, J. D., et al. (2020) · Molecular Pain · doi:10.1177/1744806920936502 · Cited by 35
“One potential epigenetic mechanism is DNA methylation, which regulates gene expression by adding or removing methyl groups at the 50-position of DNA cytosine residues.(39) Methylation of DNA can impact transcription by recruiting or blocking TFs, which results in changes in gene expression.”
Background
Translating Lung Function Genome-Wide Association Study (GWAS) Findings
Kheirallah, A. K., Miller, S., Hall, I. P., & Sayers, I. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2015.12.002 · Cited by 36
“For example, H3K4me3 tends to highlight actively transcribed loci while H3K27me3 associates with the silenced X-chromosome in females (Gibney & Nolan, 2010).”
Background
Epigenetics and Helicobacter pylori
Capparelli, R., & Iannelli, D. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23031759 · Cited by 35
“The review focuses on CpG methylation, which persists after DNA replication and is often associated with the inheritance of repressed genes [2] (Figure 1).”
Background
Gene regulation technologies for gene and cell therapy
Butterfield, G. L., Reisman, S. J., Iglesias, N., & Gersbach, C. A. (2025) · Molecular Therapy · doi:10.1016/j.ymthe.2025.04.004 · Cited by 43
DNA Methylation Profiling Reveals Correlation of Differential Methylation Patterns with Gene Expression in Human Epilepsy
Wang, L., Fu, X., Peng, X., Xiao, Z., Li, Z., Chen, G., & Wang, X. (2016) · Journal of Molecular Neuroscience · doi:10.1007/s12031-016-0735-6 · Cited by 35
The metabolic-epigenetic nexus in type 2 diabetes mellitus
Davison, G. W., Irwin, R. E., & Walsh, C. P. (2021) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2020.12.025 · Cited by 35
DNA Methylation Analysis Identifies Patterns in Progressive Glioma Grades to Predict Patient Survival
Weng, J., & Salazar, N. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22031020 · Cited by 35
“These PTMs affect gene expression by controlling accessibility of the chromatin structure to expose DNA-binding sites or by closing DNA-binding sites to facilitate transcription [11].”
Background
Multiple layers of complexity in cis‐regulatory regions of developmental genes
Frankel, N. (2012) · Developmental Dynamics · doi:10.1002/dvdy.23871 · Cited by 34

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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